fmt: reapplied formatting for the sse_transport module

# Conflicts:
#	docs/PHASE-1-IMPLEMENTATION-PLAN.md
#	src/cli/completer.rs
#	src/client/common.rs
#	src/config/agent.rs
#	src/config/input.rs
#	src/config/macros.rs
#	src/config/mod.rs
#	src/config/session.rs
#	src/function/mod.rs
#	src/function/supervisor.rs
#	src/function/todo.rs
#	src/function/user_interaction.rs
#	src/main.rs
#	src/mcp/mod.rs
#	src/rag/mod.rs
#	src/repl/mod.rs

Cargo.toml

@@ -10,7 +10,7 @@ repository = "https://github.com/Dark-Alex-17/loki"
 categories = ["command-line-utilities"]
 readme = "README.md"
 license = "MIT"
-rust-version = "1.95.0"
+rust-version = "1.89.0"
 exclude = [".github", "CONTRIBUTING.md"]
 
 [dependencies]
@@ -22,7 +22,7 @@ dunce = "1.0.5"
 futures-util = "0.3.29"
 inquire = "0.9.4"
 is-terminal = "0.4.9"
-reedline = "0.47.0"
+reedline = "0.46.0"
 serde = { version = "1.0.152", features = ["derive"] }
 serde_json = { version = "1.0.93", features = ["preserve_order"] }
 serde_yaml = "0.9.17"
@@ -34,6 +34,10 @@ tokio = { version = "1.34.0", features = [
   "rt-multi-thread",
   "full",
 ] }
+tokio-graceful = "0.2.2"
+tokio-stream = { version = "0.1.15", default-features = false, features = [
+  "sync",
+] }
 crossterm = "0.29.0"
 chrono = "0.4.23"
 bincode = { version = "2.0.0", features = [
@@ -47,7 +51,7 @@ nu-ansi-term = "0.50.0"
 async-trait = "0.1.74"
 textwrap = "0.16.0"
 ansi_colours = "1.2.2"
-eventsource-stream = "0.2.3"
+reqwest-eventsource = "0.6.0"
 log = "0.4.28"
 log4rs = { version = "1.4.0", features = ["file_appender"] }
 shell-words = "1.1.0"
@@ -55,14 +59,20 @@ sha2 = "0.10.8"
 unicode-width = "0.2.0"
 async-recursion = "1.1.1"
 http = "1.1.0"
+http-body-util = "0.1"
+hyper = { version = "1.0", features = ["full"] }
+hyper-util = { version = "0.1", features = ["server-auto", "client-legacy"] }
+time = { version = "0.3.36", features = ["macros"] }
 indexmap = { version = "2.2.6", features = ["serde"] }
 hmac = "0.12.1"
 aws-smithy-eventstream = "0.60.4"
 urlencoding = "2.1.3"
+unicode-segmentation = "1.11.0"
 json-patch = { version = "4.0.0", default-features = false }
 bitflags = "2.5.0"
 path-absolutize = "3.1.1"
 hnsw_rs = "0.3.0"
+rayon = "1.10.0"
 uuid = { version = "1.9.1", features = ["v4"] }
 scraper = { version = "0.23.1", default-features = false, features = [
   "deterministic",
@@ -87,6 +97,7 @@ rmcp = { version = "1.5.0", features = [
 ] }
 num_cpus = "1.17.0"
 tree-sitter = "0.26.8"
+tree-sitter-language = "0.1"
 tree-sitter-python = "0.25.0"
 tree-sitter-typescript = "0.23"
 colored = "3.0.0"
@@ -96,24 +107,15 @@ clap_complete_nushell = "4.5.9"
 open = "5"
 rand = { version = "0.10.0", features = ["default"] }
 url = "2.5.8"
-self_update = { version = "0.44", default-features = false, features = [
-  "reqwest",
-  "rustls",
-  "archive-tar",
-  "compression-flate2",
-  "archive-zip",
-  "compression-zip-deflate",
-] }
 
 [dependencies.reqwest]
-version = "0.13.3"
+version = "0.12.0"
 features = [
   "json",
   "multipart",
-  "stream",
-  "form",
   "socks",
-  "rustls",
+  "rustls-tls",
+  "rustls-tls-native-roots",
 ]
 default-features = false
 

README.md

@@ -10,8 +10,7 @@ Loki is an all-in-one, batteries-included, LLM CLI tool featuring Shell Assistan
 Agents, and More.
 
 It is designed to include a number of useful agents, roles, macros, and more so users can get up and running with Loki 
-in as little time as possible. You can also install entire bundles of agents, roles, macros, tools, and MCP servers from 
-any git repository — see [Sharing Configurations](#sharing-configurations).
+in as little time as possible.
 
 ![Agent example](https://raw.githubusercontent.com/wiki/Dark-Alex-17/loki/images/agents/sql.gif)
 
@@ -21,7 +20,6 @@ Coming from [AIChat](https://github.com/sigoden/aichat)? Follow the [migration g
 * [AIChat Migration Guide](https://github.com/Dark-Alex-17/loki/wiki/AIChat-Migration): Coming from AIChat? Follow the migration guide to get started.
 * [Installation](#install): Install Loki
 * [Getting Started](#getting-started): Get started with Loki by doing first-run setup steps.
-* [Sharing Configurations](https://github.com/Dark-Alex-17/loki/wiki/Sharing-Configurations): Install bundles of agents, roles, macros, tools, and MCP servers from any git repo, and share your own.
 * [REPL](https://github.com/Dark-Alex-17/loki/wiki/REPL): Interactive Read-Eval-Print Loop for conversational interactions with LLMs and Loki.
   * [Custom REPL Prompt](https://github.com/Dark-Alex-17/loki/wiki/REPL-Prompt): Customize the REPL prompt to provide useful contextual information.
 * [Vault](https://github.com/Dark-Alex-17/loki/wiki/Vault): Securely store and manage sensitive information such as API keys and credentials.
@@ -38,8 +36,7 @@ Coming from [AIChat](https://github.com/sigoden/aichat)? Follow the [migration g
 * [Sessions](https://github.com/Dark-Alex-17/loki/wiki/Sessions): Manage and persist conversational contexts and settings across multiple interactions.
 * [Roles](https://github.com/Dark-Alex-17/loki/wiki/Roles): Customize model behavior for specific tasks or domains.
 * [Agents](https://github.com/Dark-Alex-17/loki/wiki/Agents): Leverage AI agents to perform complex tasks and workflows, including sub-agent spawning, teammate messaging, and user interaction tools.
-    * [Graph Agents](https://github.com/Dark-Alex-17/loki/wiki/Graph-Agents): Define an agent as a declarative, YAML-driven workflow. A directed graph of typed nodes (LLM calls, scripts, approvals, user input, RAG retrieval, sub-agent spawns).
-* [Todo System](https://github.com/Dark-Alex-17/loki/wiki/TODO-System): Built-in task tracking for improved LLM reliability with smaller models.
+    * [Todo System](https://github.com/Dark-Alex-17/loki/wiki/TODO-System): Built-in task tracking for improved agent reliability with smaller models.
 * [Environment Variables](https://github.com/Dark-Alex-17/loki/wiki/Environment-Variables): Override and customize your Loki configuration at runtime with environment variables.
 * [Client Configurations](https://github.com/Dark-Alex-17/loki/wiki/Clients): Configuration instructions for various LLM providers.
     * [Authentication (API Key & OAuth)](https://github.com/Dark-Alex-17/loki/wiki/Clients#authentication): Authenticate with API keys or OAuth for subscription-based access.
@@ -51,6 +48,16 @@ Coming from [AIChat](https://github.com/sigoden/aichat)? Follow the [migration g
 Loki requires the following tools to be installed on your system:
 * [jq](https://github.com/jqlang/jq)
     * `brew install jq`
+* [jira (optional)](https://github.com/ankitpokhrel/jira-cli/wiki/Installation) (For the `query_jira_issues` tool)
+    * `brew tap ankitpokhrel/jira-cli && brew install jira-cli`
+    * You'll need to [create a JIRA API token](https://id.atlassian.com/manage-profile/security/api-tokens) for authentication
+    * Then, save it as an environment variable to your shell profile:
+      ```sh
+      # ~/.bashrc or ~/.zshrc
+      export JIRA_API_TOKEN="your_jira_api_token_here"
+      ```
+    * Then run `jira init`, select installation type as `cloud`, and provide the required details to generate a config
+      file for the Jira CLI.
 * [usql](https://github.com/xo/usql) (For the `sql` agent)
     * `brew install xo/xo/usql`
 * [docker](https://docs.docker.com/engine/install/)
@@ -58,7 +65,7 @@ Loki requires the following tools to be installed on your system:
     * `curl -LsSf https://astral.sh/uv/install.sh | sh`
 
 These tools are used to provide various functionalities within Loki, such as document processing, JSON manipulation,
-etc., and they are used within agents and tools.
+interaction with Jira, and they are used within agents and tools.
 
 ## Install
 
@@ -130,29 +137,6 @@ To use a binary from the releases page on Linux/MacOS, do the following:
 3. Extract the binary with `tar -C /usr/local/bin -xzf loki-<arch>.tar.gz` (Note: This may require `sudo`)
 4. Now you can run `loki`!
 
-## Updating
-Loki can update itself in place to the latest GitHub release. Run `loki --update`
-for the newest release, or `loki --update v0.4.0` for a specific version:
-
-```shell
-loki --update
-loki --update v0.4.0
-```
-
-The same is available from within the REPL via `.update` and `.update v0.4.0`.
-
-If Loki was installed with a package manager, prefer that package manager so its
-records stay in sync with the binary on disk; i.e. `brew upgrade loki` for Homebrew,
-or `cargo install --locked loki-ai` for Cargo.
-
-When Loki detects a package-manager install it prints a warning and asks for
-confirmation. In a non-interactive shell (no TTY), pass `--force` to update
-anyway:
-
-```shell
-loki --update --force
-```
-
 ## Getting Started
 After installation, you can generate the configuration files and directories by simply running:
 
@@ -176,11 +160,12 @@ subscribers, Google Gemini), you can authenticate with your existing subscriptio
 # In your config.yaml
 clients:
   - type: claude
+    name: my-claude-oauth
     auth: oauth # Indicate you want to authenticate with OAuth instead of an API key
 ```
 
 ```sh
-loki --authenticate claude
+loki --authenticate my-claude-oauth
 # Or via the REPL: .authenticate
 ```
 

assets/agents/coder/README.md

@@ -1,82 +1,40 @@
 # Coder
 
-A graph-based implementation agent. Plans, implements, and runs build +
-tests in a bounded fix-loop until verified. Designed to be delegated to by
-the **[Sisyphus](../sisyphus/README.md)** agent.
+An AI agent that assists you with your coding tasks.
 
-Coder is a [graph agent](https://github.com/Dark-Alex-17/loki/wiki/Graph-Agents): its workflow is
-defined declaratively in `graph.yaml`, with verification and the
-implement-fix loop enforced as graph edges rather than prose.
+This agent is designed to be delegated to by the **[Sisyphus](../sisyphus/README.md)** agent to implement code specifications. Sisyphus
+acts as the coordinator/architect, while Coder handles the implementation details.
 
-## Workflow
+## Features
 
-```
-analyze_request (llm + output_schema)   plan + complexity extraction
-        ↓
-route_complexity (script)               opt-out approval gate (complexity ≥ 7)
-        ↓
-gate_approval (approval, optional)
-        ↓
-implement (llm + fs tools)              actual file edits
-        ↓
-verify_build (script)
-        ↓
-verify_tests (script)
-        ↓
-fix_loop_gate (script)                  back-edge to implement (bounded)
-        ↓
-end_success / end_rejected / end_failure
-```
+- 🏗️ Intelligent project structure creation and management
+- 🖼️ Convert screenshots into clean, functional code
+- 📁 Comprehensive file system operations (create folders, files, read/write files)
+- 🧐 Advanced code analysis and improvement suggestions
+- 📊 Precise diff-based file editing for controlled code modifications
 
-End nodes emit one of three sentinel outcomes for the caller:
+It can also be used as a standalone tool for direct coding assistance.
 
-- `CODER_COMPLETE` — build and tests passed.
-- `CODER_REJECTED` — user rejected the plan at the approval gate.
-- `CODER_FAILED` — fix-loop exhausted; build/tests still failing.
-
-## Tuning
-
-The agent's `project_dir` is exposed via the standard `variables:` block,
-so it accepts the runtime override flag:
-
-```sh
-# Invoke from inside the project (project_dir defaults to ".")
-cd /path/to/your/project
-loki -a coder "Add a foo() function..."
-
-# Or invoke from anywhere with an explicit override
-loki -a coder --agent-variable project_dir /path/to/your/project "Add..."
-```
-
-`graph.yaml` `initial_state` exposes:
-
-- `max_fix_attempts` (default `3`) — fix-loop budget before `end_failure`.
-
-Environment overrides honored by the script nodes:
-
-- `BUILD_CMD` — skip project-type detection for the build/check command.
-- `TEST_CMD` — skip detection for tests.
-- `CODER_AUTOAPPROVE=1` — bypass the approval gate (for non-interactive runs
-  where complexity might trip the gate).
-
-## Pro-Tip: IDE MCP Server
-
-Modern IDEs (JetBrains, VS Code, Cursor, Zed, etc.) expose MCP servers
-that let LLMs use IDE tools directly. To wire one in, edit `graph.yaml`:
+## Pro-Tip: Use an IDE MCP Server for Improved Performance
+Many modern IDEs now include MCP servers that let LLMs perform operations within the IDE itself and use IDE tools. Using
+an IDE's MCP server dramatically improves the performance of coding agents. So if you have an IDE, try adding that MCP
+server to your config (see the [MCP Server docs](../../../docs/function-calling/MCP-SERVERS.md) to see how to configure
+them), and modify the agent definition to look like this:
 
 ```yaml
+# ...
+
 mcp_servers:
-  - your-ide-mcp-server
+  - jetbrains # The name of your configured IDE MCP server
 
 global_tools:
-  # Keep read-only fs tools for files outside the IDE project
+  # Keep useful read-only tools for reading files in other non-project directories
   - fs_read.sh
   - fs_grep.sh
   - fs_glob.sh
 #  - fs_write.sh
 #  - fs_patch.sh
   - execute_command.sh
-```
 
-Then add the MCP server's write/patch tools to the `implement` node's
-`tools:` whitelist.
+# ...
+```

assets/agents/coder/config.yaml

@@ -0,0 +1,129 @@
+name: coder
+description: Implementation agent - writes code, follows patterns, verifies with builds
+version: 1.0.0
+temperature: 0.1
+
+auto_continue: true
+max_auto_continues: 15
+inject_todo_instructions: true
+
+variables:
+  - name: project_dir
+    description: Project directory to work in
+    default: '.'
+  - name: auto_confirm
+    description: Auto-confirm command execution
+    default: '1'
+
+global_tools:
+  - fs_read.sh
+  - fs_grep.sh
+  - fs_glob.sh
+  - fs_write.sh
+  - fs_patch.sh
+  - execute_command.sh
+
+instructions: |
+  You are a senior engineer. You write code that works on the first try.
+
+  ## Your Mission
+
+  Given an implementation task:
+  1. Check for orchestrator context first (see below)
+  2. Fill gaps only. Read files NOT already covered in context
+  3. Write the code (using tools, NOT chat output)
+  4. Verify it compiles/builds
+  5. Signal completion with a summary
+
+  ## Using Orchestrator Context (IMPORTANT)
+
+  When spawned by sisyphus, your prompt will often contain a `<context>` block
+  with prior findings: file paths, code patterns, and conventions discovered by
+  explore agents.
+
+  **If context is provided:**
+  1. Use it as your primary reference. Don't re-read files already summarized
+  2. Follow the code patterns shown. Snippets in context ARE the style guide
+  3. Read the referenced files ONLY IF you need more detail (e.g. full function
+     signature, import list, or adjacent code not included in the snippet)
+  4. If context includes a "Conventions" section, follow it exactly
+
+  **If context is NOT provided or is too vague to act on:**
+  Fall back to self-exploration: grep for similar files, read 1-2 examples,
+  match their style.
+
+  **Never ignore provided context.** It represents work already done upstream.
+
+  ## Todo System
+
+  For multi-file changes:
+  1. `todo__init` with the implementation goal
+  2. `todo__add` for each file to create/modify
+  3. Implement each, calling `todo__done` immediately after
+
+  ## Writing Code
+
+  **CRITICAL**: Write code using `write_file` tool, NEVER paste code in chat.
+
+  Correct:
+  ```
+  write_file --path "src/user.rs" --content "pub struct User { ... }"
+  ```
+
+  Wrong:
+  ```
+  Here's the implementation:
+  \`\`\`rust
+  pub struct User { ... }
+  \`\`\`
+  ```
+
+  ## File Reading Strategy (IMPORTANT - minimize token usage)
+
+  1. **Use grep to find relevant code** - `fs_grep --pattern "fn handle_request" --include "*.rs"` finds where things are
+  2. **Read only what you need** - `fs_read --path "src/main.rs" --offset 50 --limit 30` reads lines 50-79
+  3. **Never cat entire large files** - If 500+ lines, read the relevant section after grepping for it
+  4. **Use glob to find files** - `fs_glob --pattern "*.rs" --path src/` discovers files by name
+
+  ## Pattern Matching
+
+  Before writing ANY file:
+  1. Find a similar existing file (use `fs_grep` to locate, then `fs_read` to examine)
+  2. Match its style: imports, naming, structure
+  3. Follow the same patterns exactly
+
+  ## Verification
+
+  After writing files:
+  1. Run `verify_build` to check compilation
+  2. If it fails, fix the error (minimal change)
+  3. Don't move on until build passes
+
+  ## Completion Signal
+
+  When done, end your response with a summary so the parent agent knows what happened:
+
+  ```
+  CODER_COMPLETE: [summary of what was implemented, which files were created/modified, and build status]
+  ```
+
+  Or if something went wrong:
+  ```
+  CODER_FAILED: [what went wrong]
+  ```
+
+  ## Rules
+
+  1. **Write code via tools** - Never output code to chat
+  2. **Follow patterns** - Read existing files first
+  3. **Verify builds** - Don't finish without checking
+  4. **Minimal fixes** - If build fails, fix precisely
+  5. **No refactoring** - Only implement what's asked
+
+  ## Context
+  - Project: {{project_dir}}
+  - CWD: {{__cwd__}}
+  - Shell: {{__shell__}}
+  
+  ## Available tools:
+  {{__tools__}}

assets/agents/coder/graph.yaml

@@ -1,278 +0,0 @@
-name: coder
-description: |
-  Implementation agent. Plans, implements, and runs build + tests in a
-  bounded fix-loop until verified. Designed to be delegated to by sisyphus.
-version: "1.0"
-
-temperature: 0.1
-
-global_tools:
-  - fs_cat.sh
-  - fs_ls.sh
-  - fs_write.sh
-  - fs_patch.sh
-  - execute_command.sh
-
-variables:
-  - name: project_dir
-    description: |
-      Absolute path to the project directory. Defaults to "." which is the
-      directory you invoked `loki` from. Override at runtime with
-      `loki -a coder --agent-variable project_dir /abs/path "..."`.
-    default: "."
-
-settings:
-  max_loop_iterations: 20
-  log_state_snapshots: true
-  validate_before_run: true
-  timeout: 1800
-
-initial_state:
-  project_dir: ""
-  fix_attempts: 0
-  max_fix_attempts: 3
-  fix_instructions: ""
-  build_output: ""
-  tests_output: ""
-  last_node_output: ""
-  plan_summary: ""
-  files_to_modify: []
-  files_to_create: []
-  risks: []
-  complexity_score: 0
-
-start: resolve_paths
-
-nodes:
-  resolve_paths:
-    id: resolve_paths
-    type: script
-    description: Resolve project_dir to an absolute path from the agent variable
-    script: scripts/resolve_paths.sh
-    timeout: 5
-    fallback: end_failure
-
-  analyze_request:
-    id: analyze_request
-    type: llm
-    description: Extract a structured plan and complexity score from the orchestrator's prompt
-    instructions: |
-      You are a senior engineer's planning assistant. Read the orchestrator's
-      request and emit a structured plan. You only plan. You never edit files.
-
-      Score complexity from 1 to 10:
-        1-3: trivial - single file, <=20 lines changed, obvious approach
-        4-6: moderate - 2-5 files, clear approach, some pattern matching
-        7-10: complex - multi-component, ambiguous tradeoffs, refactoring,
-              or wide blast radius
-
-      Be specific in `files_to_modify` and `files_to_create`. All paths
-      MUST be absolute. The project root is {{project_dir}}. Prefer paths
-      like "{{project_dir}}/src/foo.rs" over "src/foo.rs". The implementer
-      uses these paths directly with fs_write and fs_patch tools, which
-      resolve relative paths against the loki invocation directory (NOT
-      the project dir). Empty arrays are fine if no files in that category.
-
-      `risks` is a list of short strings. Anything that could derail the
-      implementation: unknown dependencies, brittle tests, blast radius,
-      etc. Empty list is fine.
-
-      Project directory: {{project_dir}}
-    prompt: "{{initial_prompt}}"
-    tools: []
-    output_schema:
-      type: object
-      properties:
-        plan_summary:
-          type: string
-          description: 1-3 sentences summarizing what will be done
-        files_to_modify:
-          type: array
-          items: {type: string}
-        files_to_create:
-          type: array
-          items: {type: string}
-        complexity_score:
-          type: integer
-          minimum: 1
-          maximum: 10
-        risks:
-          type: array
-          items: {type: string}
-      required: [plan_summary, files_to_modify, files_to_create, complexity_score, risks]
-    state_updates:
-      last_node_output: "{{output}}"
-    fallback: end_failure
-    next: route_complexity
-
-  route_complexity:
-    id: route_complexity
-    type: script
-    description: Route to approval gate for complex plans; skip otherwise
-    script: scripts/route_complexity.sh
-    timeout: 5
-    fallback: implement
-
-  gate_approval:
-    id: gate_approval
-    type: approval
-    description: Optional human checkpoint for high-complexity plans
-    question: |
-      ## Plan
-      {{plan_summary}}
-
-      ## Files to modify
-      {{files_to_modify}}
-
-      ## Files to create
-      {{files_to_create}}
-
-      ## Risks
-      {{risks}}
-
-      Complexity: {{complexity_score}}/10
-
-      Approve this plan?
-    options:
-      - "yes"
-      - "no"
-    routes:
-      "yes": implement
-      "no": end_rejected
-    on_other: end_rejected
-
-  implement:
-    id: implement
-    type: llm
-    description: Write code via fs tools. Bounded tool-call loop.
-    instructions: |
-      You are a senior engineer. Implement the plan by writing code via
-      tools. Follow existing patterns in the codebase.
-
-      ## Writing code
-
-      1. Use `fs_patch` for surgical edits to existing files.
-      2. Use `fs_write` for new files or full rewrites.
-      3. NEVER output code to chat. Always use tools.
-      4. ALWAYS pass ABSOLUTE paths to fs_write and fs_patch. Relative
-         paths resolve against the loki invocation directory (not the
-         project dir), which is rarely what you want. The project root
-         is {{project_dir}}.
-
-      ## File reading
-
-      1. Use `execute_command` to grep/find:
-         `execute_command --command "grep -rn 'fn handle_request' --include='*.rs' ."`
-         `execute_command --command "find . -name '*.rs' -not -path '*/target/*'"`
-      2. Read only what you need:
-         `fs_cat --path "src/main.rs" --offset 50 --limit 30`
-      3. Never read entire large files. Use offset/limit.
-      4. Use `fs_ls` to list directory contents.
-
-      ## Pattern matching
-
-      Before writing ANY file:
-      1. Find a similar existing file (grep, then read).
-      2. Match its style: imports, naming, structure, error handling.
-      3. Follow the same patterns exactly. Do not invent new ones.
-
-      ## Fix loop
-
-      If the "Fix loop status" section in your user prompt is non-empty,
-      the previous attempt failed verification. Read the error, identify
-      the minimal fix, apply it. Do not refactor while fixing.
-
-      ## Rules
-
-      1. Match existing patterns - read examples first.
-      2. Minimal changes - implement only what's asked.
-      3. Never suppress errors (`as any`, `@ts-ignore`, `#[allow(...)]`
-         on unfamiliar lints, etc.).
-      4. No dead code, no commented-out blocks, no premature abstractions.
-      5. End your turn when editing is done. The graph runs verification next.
-
-      Project directory: {{project_dir}}
-    prompt: |
-      ## Plan summary
-      {{plan_summary}}
-
-      ## Files involved
-      - Modify: {{files_to_modify}}
-      - Create: {{files_to_create}}
-
-      ## Original request from the orchestrator
-      {{initial_prompt}}
-
-      ## Fix loop status
-      {{fix_instructions}}
-    tools:
-      - fs_cat
-      - fs_ls
-      - fs_write
-      - fs_patch
-      - execute_command
-    max_iterations: 30
-    state_updates:
-      last_node_output: "{{output}}"
-    fallback: end_failure
-    next: verify_build
-
-  verify_build:
-    id: verify_build
-    type: script
-    description: Run the project's check/build command. Routes to verify_tests on success, fix_loop_gate on failure.
-    script: scripts/verify_build.sh
-    timeout: 300
-    fallback: fix_loop_gate
-
-  verify_tests:
-    id: verify_tests
-    type: script
-    description: Run the project's test command. Routes to end_success on pass, fix_loop_gate on failure.
-    script: scripts/verify_tests.sh
-    timeout: 600
-    fallback: fix_loop_gate
-
-  fix_loop_gate:
-    id: fix_loop_gate
-    type: script
-    description: Budget gate. Loops back to implement with fix_instructions populated, or terminates as end_failure.
-    script: scripts/fix_loop_gate.sh
-    timeout: 5
-    fallback: end_failure
-
-  end_success:
-    id: end_success
-    type: end
-    output: |
-      CODER_COMPLETE
-      Plan: {{plan_summary}}
-      Files modified: {{files_to_modify}}
-      Files created: {{files_to_create}}
-      Build: passed
-      Tests: passed
-
-  end_rejected:
-    id: end_rejected
-    type: end
-    output: |
-      CODER_REJECTED
-      Plan was rejected at the approval gate.
-      Plan: {{plan_summary}}
-
-  end_failure:
-    id: end_failure
-    type: end
-    output: |
-      CODER_FAILED
-      Plan: {{plan_summary}}
-      Attempts: {{fix_attempts}}/{{max_fix_attempts}}
-
-      Last node output:
-      {{last_node_output}}
-
-      Last build output:
-      {{build_output}}
-
-      Last tests output:
-      {{tests_output}}

assets/agents/coder/scripts/fix_loop_gate.sh

@@ -1,49 +0,0 @@
-#!/usr/bin/env bash
-set -euo pipefail
-
-if [[ -n "${GRAPH_STATE_FILE:-}" ]]; then
-  state=$(cat "$GRAPH_STATE_FILE")
-elif [[ -n "${GRAPH_STATE:-}" ]]; then
-  state="$GRAPH_STATE"
-else
-  state='{}'
-fi
-
-fix_attempts=$(echo "$state" | jq -r '.fix_attempts // 0')
-max_fix_attempts=$(echo "$state" | jq -r '.max_fix_attempts // 3')
-build_ok=$(echo "$state" | jq -r '.build_ok | if . == null then "true" else (. | tostring) end')
-tests_ok=$(echo "$state" | jq -r '.tests_ok | if . == null then "true" else (. | tostring) end')
-build_output=$(echo "$state" | jq -r '.build_output // ""')
-tests_output=$(echo "$state" | jq -r '.tests_output // ""')
-
-if (( fix_attempts >= max_fix_attempts )); then
-  jq -nc \
-    --argjson n "$fix_attempts" \
-    '{
-      "fix_attempts": $n,
-      "_next": "end_failure"
-    }'
-  exit 0
-fi
-
-next_attempts=$((fix_attempts + 1))
-
-if [[ "$build_ok" != "true" ]]; then
-  fix_instructions=$(printf '## Fix loop status (attempt %d of %d)\n\nThe previous attempt failed the build.\n\nBuild output:\n```\n%s\n```\n\nIdentify the minimal fix and apply it. Do not refactor.' \
-    "$next_attempts" "$max_fix_attempts" "$build_output")
-elif [[ "$tests_ok" != "true" ]]; then
-  fix_instructions=$(printf '## Fix loop status (attempt %d of %d)\n\nBuild passed but tests failed.\n\nTest output:\n```\n%s\n```\n\nIdentify the minimal fix and apply it. Do not refactor.' \
-    "$next_attempts" "$max_fix_attempts" "$tests_output")
-else
-  fix_instructions=$(printf '## Fix loop status (attempt %d of %d)\n\nfix_loop_gate was reached but no failure was detected in state. Re-run the verification step.' \
-    "$next_attempts" "$max_fix_attempts")
-fi
-
-jq -nc \
-  --argjson n "$next_attempts" \
-  --arg fi "$fix_instructions" \
-  '{
-    "fix_attempts": $n,
-    "fix_instructions": $fi,
-    "_next": "implement"
-  }'

assets/agents/coder/scripts/resolve_paths.sh

@@ -1,12 +0,0 @@
-#!/usr/bin/env bash
-set -euo pipefail
-
-project_dir="${LLM_AGENT_VAR_PROJECT_DIR:-.}"
-resolved=$(cd "$project_dir" 2>/dev/null && pwd) || resolved="$project_dir"
-
-jq -nc \
-  --arg pd "$resolved" \
-  '{
-    "project_dir": $pd,
-    "_next": "analyze_request"
-  }'

assets/agents/coder/scripts/route_complexity.sh

@@ -1,23 +0,0 @@
-#!/usr/bin/env bash
-set -euo pipefail
-
-if [[ -n "${GRAPH_STATE_FILE:-}" ]]; then
-  state=$(cat "$GRAPH_STATE_FILE")
-elif [[ -n "${GRAPH_STATE:-}" ]]; then
-  state="$GRAPH_STATE"
-else
-  state='{}'
-fi
-
-complexity=$(echo "$state" | jq -r '.complexity_score // 0')
-
-if [[ "${CODER_AUTOAPPROVE:-0}" == "1" ]]; then
-  jq -nc '{"_next": "implement"}'
-  exit 0
-fi
-
-if (( complexity >= 7 )); then
-  jq -nc '{"_next": "gate_approval"}'
-else
-  jq -nc '{"_next": "implement"}'
-fi

assets/agents/coder/scripts/verify_build.sh

@@ -1,55 +0,0 @@
-#!/usr/bin/env bash
-set -uo pipefail
-
-# shellcheck disable=SC1091
-source "$(dirname "$0")/../../.shared/utils.sh"
-
-if [[ -n "${GRAPH_STATE_FILE:-}" ]]; then
-  state=$(cat "$GRAPH_STATE_FILE")
-elif [[ -n "${GRAPH_STATE:-}" ]]; then
-  state="$GRAPH_STATE"
-else
-  state='{}'
-fi
-
-project_dir=$(echo "$state" | jq -r '.project_dir // "."')
-
-if [[ -n "${BUILD_CMD:-}" ]]; then
-  cmd="$BUILD_CMD"
-else
-  project_info=$(detect_project "$project_dir")
-  cmd=$(echo "$project_info" | jq -r '.check // .build // ""')
-fi
-
-if [[ -z "$cmd" || "$cmd" == "null" ]]; then
-  jq -nc '{
-    "build_ok": true,
-    "build_output": "(no build/check command available for this project type)",
-    "_next": "verify_tests"
-  }'
-  exit 0
-fi
-
-exit_code=0
-output=$(cd "$project_dir" && eval "$cmd" 2>&1) || exit_code=$?
-
-if (( exit_code == 0 )); then
-  jq -nc \
-    --arg out "$output" \
-    --arg cmd "$cmd" \
-    '{
-      "build_ok": true,
-      "build_output": ("Ran: " + $cmd + "\n\n" + $out),
-      "_next": "verify_tests"
-    }'
-else
-  jq -nc \
-    --arg out "$output" \
-    --arg cmd "$cmd" \
-    --argjson rc "$exit_code" \
-    '{
-      "build_ok": false,
-      "build_output": ("Ran: " + $cmd + "\nExit code: " + ($rc | tostring) + "\n\n" + $out),
-      "_next": "fix_loop_gate"
-    }'
-fi

assets/agents/coder/scripts/verify_tests.sh

@@ -1,55 +0,0 @@
-#!/usr/bin/env bash
-set -uo pipefail
-
-# shellcheck disable=SC1091
-source "$(dirname "$0")/../../.shared/utils.sh"
-
-if [[ -n "${GRAPH_STATE_FILE:-}" ]]; then
-  state=$(cat "$GRAPH_STATE_FILE")
-elif [[ -n "${GRAPH_STATE:-}" ]]; then
-  state="$GRAPH_STATE"
-else
-  state='{}'
-fi
-
-project_dir=$(echo "$state" | jq -r '.project_dir // "."')
-
-if [[ -n "${TEST_CMD:-}" ]]; then
-  cmd="$TEST_CMD"
-else
-  project_info=$(detect_project "$project_dir")
-  cmd=$(echo "$project_info" | jq -r '.test // ""')
-fi
-
-if [[ -z "$cmd" || "$cmd" == "null" ]]; then
-  jq -nc '{
-    "tests_ok": true,
-    "tests_output": "(no test command available for this project type)",
-    "_next": "end_success"
-  }'
-  exit 0
-fi
-
-exit_code=0
-output=$(cd "$project_dir" && eval "$cmd" 2>&1) || exit_code=$?
-
-if (( exit_code == 0 )); then
-  jq -nc \
-    --arg out "$output" \
-    --arg cmd "$cmd" \
-    '{
-      "tests_ok": true,
-      "tests_output": ("Ran: " + $cmd + "\n\n" + $out),
-      "_next": "end_success"
-    }'
-else
-  jq -nc \
-    --arg out "$output" \
-    --arg cmd "$cmd" \
-    --argjson rc "$exit_code" \
-    '{
-      "tests_ok": false,
-      "tests_output": ("Ran: " + $cmd + "\nExit code: " + ($rc | tostring) + "\n\n" + $out),
-      "_next": "fix_loop_gate"
-    }'
-fi

assets/agents/coder/tools.sh

@@ -14,6 +14,99 @@ _project_dir() {
   (cd "${dir}" 2>/dev/null && pwd) || echo "${dir}"
 }
 
+# Normalize a path to be relative to project root.
+# Strips the project_dir prefix if the LLM passes an absolute path.
+# Usage: local rel_path; rel_path=$(_normalize_path "/abs/or/rel/path")
+_normalize_path() {
+  local input_path="$1"
+  local project_dir
+  project_dir=$(_project_dir)
+
+  if [[ "${input_path}" == /* ]]; then
+    input_path="${input_path#"${project_dir}"/}"
+  fi
+
+  input_path="${input_path#./}"
+  echo "${input_path}"
+}
+
+# @cmd Read a file's contents before modifying
+# @option --path! Path to the file (relative to project root)
+read_file() {
+  local file_path
+	# shellcheck disable=SC2154
+  file_path=$(_normalize_path "${argc_path}")
+  local project_dir
+  project_dir=$(_project_dir)
+  local full_path="${project_dir}/${file_path}"
+  
+  if [[ ! -f "${full_path}" ]]; then
+    warn "File not found: ${file_path}" >> "$LLM_OUTPUT"
+    return 0
+  fi
+  
+  {
+  	info "Reading: ${file_path}"
+  	echo ""
+  	cat "${full_path}"
+  } >> "$LLM_OUTPUT"
+}
+
+# @cmd Write complete file contents
+# @option --path! Path for the file (relative to project root)
+# @option --content! Complete file contents to write
+write_file() {
+  local file_path
+  file_path=$(_normalize_path "${argc_path}")
+  # shellcheck disable=SC2154
+  local content="${argc_content}"
+  local project_dir
+  project_dir=$(_project_dir)
+  local full_path="${project_dir}/${file_path}"
+  
+  mkdir -p "$(dirname "${full_path}")"
+  printf '%s' "${content}" > "${full_path}"
+  
+  green "Wrote: ${file_path}" >> "$LLM_OUTPUT"
+}
+
+# @cmd Find files similar to a given path (for pattern matching)
+# @option --path! Path to find similar files for
+find_similar_files() {
+  local file_path
+  file_path=$(_normalize_path "${argc_path}")
+  local project_dir
+  project_dir=$(_project_dir)
+  
+  local ext="${file_path##*.}"
+  local dir
+  dir=$(dirname "${file_path}")
+  
+  info "Similar files to: ${file_path}" >> "$LLM_OUTPUT"
+  echo "" >> "$LLM_OUTPUT"
+  
+  local results
+  results=$(find "${project_dir}/${dir}" -maxdepth 1 -type f -name "*.${ext}" \
+    ! -name "$(basename "${file_path}")" \
+    ! -name "*test*" \
+    ! -name "*spec*" \
+    2>/dev/null | sed "s|^${project_dir}/||" | head -3)
+  
+  if [[ -z "${results}" ]]; then
+    results=$(find "${project_dir}/src" -type f -name "*.${ext}" \
+      ! -name "*test*" \
+      ! -name "*spec*" \
+      -not -path '*/target/*' \
+      2>/dev/null | sed "s|^${project_dir}/||" | head -3)
+  fi
+  
+  if [[ -n "${results}" ]]; then
+    echo "${results}" >> "$LLM_OUTPUT"
+  else
+    warn "No similar files found" >> "$LLM_OUTPUT"
+  fi
+}
+
 # @cmd Verify the project builds successfully
 verify_build() {
   local project_dir
@@ -96,3 +189,28 @@ get_project_structure() {
   } >> "$LLM_OUTPUT"
 }
 
+# @cmd Search for content in the codebase
+# @option --pattern! Pattern to search for
+search_code() {
+	# shellcheck disable=SC2154
+  local pattern="${argc_pattern}"
+  local project_dir
+  project_dir=$(_project_dir)
+  
+  info "Searching: ${pattern}" >> "$LLM_OUTPUT"
+  echo "" >> "$LLM_OUTPUT"
+  
+  local results
+  results=$(grep -rn "${pattern}" "${project_dir}" 2>/dev/null | \
+    grep -v '/target/' | \
+    grep -v '/node_modules/' | \
+    grep -v '/.git/' | \
+    sed "s|^${project_dir}/||" | \
+    head -20) || true
+  
+  if [[ -n "${results}" ]]; then
+    echo "${results}" >> "$LLM_OUTPUT"
+  else
+    warn "No matches" >> "$LLM_OUTPUT"
+  fi
+}

assets/agents/deep-research/README.md

@@ -1,274 +0,0 @@
-# deep-research
-
-A deep web research agent, built as a Loki graph agent. It plans an
-investigation, decomposes it into sub-questions researched in
-parallel, grounds the work in a local knowledge corpus, vets the
-credibility of cited sources, runs a reflexion self-critique loop to
-revise weak findings, delegates the final write-up to a focused
-sub-agent, checks that the cited sources are reachable, and gates the
-result behind human approval.
-
-Unlike a regular agent (which takes a goal and improvises the steps),
-this agent runs a fixed graph: every request goes through the same
-`plan -> parallel research -> vet -> critique -> synthesize -> verify -> approve`
-pipeline.
-
-This agent is also the **canonical reference for the Loki graph
-system**: it exercises every node type (`script`, `llm`, `rag`, `map`,
-`agent`, `input`, `approval`, `end`) and both static fan-out and
-dynamic `map` fan-out. If you are learning how to build a graph
-agent, this is the file to read alongside the
-[Graph-Agents wiki](https://github.com/Dark-Alex-17/loki/wiki/Graph-Agents).
-
-## Workflow
-
-17 nodes. `->` is the static route; a script node can also route
-dynamically via `_next`. The `▶▶` line is a parallel super-step —
-those branches run concurrently:
-
-```
-parse_request (script)              -> bootstrap_research   (or -> ask_topic if no topic)
-ask_topic (input)                   -> bootstrap_research
-bootstrap_research (script)         -> [plan, knowledge_lookup]   ▶▶ parallel
-plan (llm + output_schema)          -> research_each_question
-knowledge_lookup (rag)              -> research_each_question
-research_each_question (map)        -> combine_findings    (spawns one branch per question)
-  └─ research_one_question (llm)    (atomic; runs N×, joins at map)
-combine_findings (script)           -> vet_sources
-vet_sources (llm + custom tool)     -> critique
-critique (llm)                      -> reflexion_gate
-reflexion_gate (script)             -> synthesize  (or -> research_each_question: reflexion loop)
-synthesize (agent: report-writer)   -> verify_sources
-verify_sources (script)             -> approve
-approve (approval)                  -> end_accepted          ("accept")
-                                    -> end_rejected          ("reject")
-                                    -> incorporate_feedback   (any free-form answer)
-incorporate_feedback (script)       -> research_each_question (the human-feedback loop)
-```
-
-### Node-type breakdown
-
-| Type | Nodes |
-|---|---|
-| `script` (Python) | `parse_request`, `bootstrap_research`, `combine_findings`, `reflexion_gate`, `verify_sources`, `incorporate_feedback` |
-| `llm` (tools: `[]`) | `plan`, `critique` |
-| `llm` (with tool whitelist) | `research_one_question`, `vet_sources` |
-| `rag` | `knowledge_lookup` — local corpus retrieval |
-| `map` | `research_each_question` — dynamic fan-out per sub-question |
-| `agent` | `synthesize` — spawns the `report-writer` sub-agent |
-| `input` | `ask_topic` |
-| `approval` | `approve` |
-| `end` | `end_accepted`, `end_rejected` |
-
-## Parallel execution
-
-The graph has two parallel super-steps where Loki's BSP scheduler runs
-branches concurrently.
-
-**1. Context loading (`plan` ‖ `knowledge_lookup`)** — after
-`bootstrap_research`, the LLM planner (which decomposes the topic into
-sub-questions) and the RAG retrieval over the local `knowledge/`
-corpus run side by side. They write disjoint state keys (`plan` writes
-`research_plan` and `questions`; `knowledge_lookup` writes
-`local_context` and `local_sources`) so no reducer is needed.
-
-**2. Per-question research (`research_each_question` map)** — the
-plan emits a `questions` array (3-5 entries, enforced by its
-`output_schema`). The `map` node spawns one parallel branch per
-question (`max_concurrency: 3`). Each branch is an isolated
-`research_one_question` LLM invocation with web tools, instructed to
-investigate exactly its assigned question. Outputs collect into
-`question_findings` in input order, then `combine_findings` joins
-them into a single `findings` Markdown document for downstream nodes.
-
-`settings.max_concurrency: 4` is the graph-wide cap; the per-`map`
-override (`max_concurrency: 3` on `research_each_question`) is
-deliberately lower to leave headroom for the planner's tool calls
-running alongside RAG.
-
-## Local knowledge corpus
-
-`knowledge_lookup` is a `rag` node — it runs hybrid (vector + keyword)
-retrieval over every file in `knowledge/`. The directory ships with a
-small `research-style-notes.md` so the RAG node has something to
-retrieve against on a clean install; drop your own Markdown notes,
-PDFs, or text files into `knowledge/` to bias the research toward
-your local context.
-
-The knowledge base is built once, at agent-load time, into
-`~/.config/loki/agents/deep-research/knowledge_lookup.yaml`. Because
-the node fully specifies its build config (`embedding_model`,
-`chunk_size`, `chunk_overlap`), the build is non-interactive. Delete
-that cached file after adding or changing knowledge to force a
-rebuild.
-
-## Sub-agent: report-writer
-
-The `synthesize` node is an `agent` node that spawns the
-`report-writer` sub-agent (`assets/agents/report-writer/`). This is
-the agent-as-tool pattern: the orchestrating graph delegates the
-writing phase to a focused sub-agent dedicated to coherent prose,
-while the research phase uses different (typically cheaper) LLM nodes
-for fast-and-many-question investigation.
-
-The `report-writer` sub-agent has no tools — it cannot access the
-web, cannot search, and cannot invent facts. It reads only the
-findings it is given and produces a final Markdown report preserving
-every inline citation. See `assets/agents/report-writer/README.md`
-for details.
-
-## Tools and tool scoping
-
-This agent demonstrates Loki's three tool sources and how an `llm`
-node's `tools:` whitelist scopes them per node.
-
-The agent's full tool universe, declared in `graph.yaml`:
-
-- **Global tools** (`global_tools`): `web_search_loki`,
-  `fetch_url_via_curl`, `search_arxiv` - Loki's built-in tool scripts.
-- **MCP server** (`mcp_servers`): `ddg-search` - a DuckDuckGo web
-  search MCP server. Referenced in a whitelist as `mcp:ddg-search`.
-- **Custom agent tool** (`tools.sh`): `classify_source` - a
-  deterministic source-credibility classifier shipped with this agent.
-
-No node receives all of these. Each `llm` node's `tools:` whitelist
-narrows the universe to exactly what that step needs:
-
-| Node | `tools:` whitelist | Draws from |
-|---|---|---|
-| `plan`, `critique` | `[]` | nothing - pure reasoning |
-| `research_one_question` | `web_search_loki`, `fetch_url_via_curl`, `search_arxiv`, `mcp:ddg-search` | global tools + MCP |
-| `vet_sources` | `classify_source` | the custom tool only |
-
-`research_one_question` (each parallel branch of the map) can search
-and fetch but cannot classify sources; `vet_sources` can classify
-sources but cannot touch the web. That separation is the point of the
-`tools:` whitelist: a node gets only the tools its job calls for,
-never the agent's full set.
-
-The `classify_source` custom tool (`tools.sh`) takes a URL and returns
-a credibility tier (government, academic, preprint, organization,
-unverified) derived from the host and top-level domain. It is
-deterministic - exactly the kind of logic a tool should own rather than
-the LLM guessing.
-
-Web search may require API-key configuration; see the
-[Tools](https://github.com/Dark-Alex-17/loki/wiki/Tools) docs.
-`fetch_url_via_curl`, `search_arxiv`, and `classify_source` work
-without a key.
-
-## Setup
-
-`research_one_question` (each parallel branch of the `map`) uses the
-`ddg-search` MCP server via `mcp:ddg-search`. It is one of Loki's
-default MCP servers; make sure it is registered in
-`~/.config/loki/mcp.json` (run `loki --install mcp_config` to restore
-the default template if it is missing). If `ddg-search` is unavailable,
-the branches still have their global web-search tools to fall back on.
-
-The `synthesize` node spawns the `report-writer` sub-agent. Both
-agents ship with `loki agents install`; if you install one manually,
-install both so the agent reference resolves.
-
-## Reflexion
-
-The agent has two loops, both built with script nodes that route via
-`_next`. The engine allows back-edges at runtime; the validator only
-rejects cycles built from static `next` / `routes` edges, so script
-`_next` loops are always allowed.
-
-**Automated reflexion loop.** After the parallel research map and
-`vet_sources`, the `critique` node reviews the merged findings
-against the research plan and the source credibility assessment, and
-emits `VERDICT: PASS` or `VERDICT: REVISE` with specific feedback.
-`reflexion_gate.py` then:
-
-- `PASS` -> continue to `synthesize`.
-- `REVISE`, budget remaining -> loop back to `research_each_question`,
-  with the critique injected as `research_feedback` so every parallel
-  branch sees it on the retry.
-- `REVISE`, budget spent -> continue to `synthesize` anyway (the human
-  approval step is the final backstop).
-
-The budget is `MAX_REFLEXION_REVISIONS` in `reflexion_gate.py`
-(default 2, so the research map runs at most 3 times per pass).
-
-**Human-feedback loop.** At `approve` the user answers `accept`,
-`reject`, or types their own feedback. A free-form answer routes via
-the approval node's `on_other` to `incorporate_feedback.py`, which
-folds that text into `research_feedback` and loops back to
-`research_each_question` for another parallel pass.
-
-`settings.max_loop_iterations` (40) is the engine's infinite-loop
-backstop: it caps the total visits to any single node.
-
-## Running
-
-```sh
-loki agents install                  # ships deep-research
-loki -a deep-research "How does HTTP/3 differ from HTTP/2?"
-loki -a deep-research "Recent advances in solid-state batteries"
-loki -a deep-research                # no prompt -> triggers ask_topic
-```
-
-## Anti-hallucination
-
-- `research_one_question` (each map branch) is instructed to back
-  every claim with a real retrieved source and never to fabricate
-  URLs, titles, or DOIs.
-- `vet_sources` classifies every cited source so weak sources are
-  visible to the critique step.
-- `critique` independently reviews the merged findings and sends weak
-  or uncited work back for another parallel research pass.
-- `synthesize` (the `report-writer` sub-agent) is grounded: it may use
-  only the gathered findings and must keep each claim's inline source.
-  It has no tools and cannot browse the web.
-- `verify_sources` probes every cited URL / DOI with an HTTP HEAD
-  request and reports which are unreachable, so the human reviewer
-  sees broken citations before approving.
-
-## Customizing
-
-- **Loop budget.** `MAX_REFLEXION_REVISIONS` in `reflexion_gate.py`.
-- **Map concurrency.** The `research_each_question` node's
-  `max_concurrency: 3` caps simultaneous web-research branches.
-  Raise to investigate more questions in parallel; lower to be gentle
-  on rate-limited providers.
-- **Per-node model.** Add `model: anthropic:...` to any `llm` node.
-  Cheap models work well for `plan` / `critique` / `vet_sources`; the
-  heavy intelligence is needed in `research_one_question` and the
-  `report-writer` sub-agent.
-- **Tool scope.** Narrow the `research_one_question` node's `tools:`
-  list to constrain where each branch looks (for example, drop
-  `web_search_loki` and `mcp:ddg-search` to force arXiv-only
-  research).
-- **Local knowledge.** Drop files into `knowledge/` to bias every
-  research branch toward your local context (see the *Local
-  knowledge corpus* section above).
-- **Different writer.** Replace `agent: report-writer` on the
-  `synthesize` node with the name of any other agent. The
-  orchestrator does not care what kind of agent the writer is.
-- **Skip approval.** Point both `approve` routes at `end_accepted`,
-  or wire `verify_sources` straight to an `end` node.
-
-## Files
-
-```
-assets/agents/deep-research/
-  graph.yaml                    - agent config + 17-node workflow
-  tools.sh                      - classify_source custom tool
-  README.md                     - this file
-  knowledge/
-    README.md                   - corpus-format notes
-    research-style-notes.md     - starter knowledge file (replace with your notes)
-  scripts/
-    parse_request.py            - _next: bootstrap_research, or ask_topic if no topic
-    bootstrap_research.py       - fan-out source: next [plan, knowledge_lookup]
-    combine_findings.py         - joins map output (question_findings) into findings
-    reflexion_gate.py           - _next: research_each_question (revise) or synthesize
-    verify_sources.py           - HTTP HEAD on cited URLs / DOIs
-    incorporate_feedback.py     - _next: research_each_question, with user feedback
-```
-
-See also `assets/agents/report-writer/` — the sub-agent the
-`synthesize` node spawns.

assets/agents/deep-research/graph.yaml

@@ -1,293 +0,0 @@
-name: deep-research
-description: |
-  Deep web research workflow. Plans an investigation, decomposes it
-  into sub-questions researched in parallel, grounds the work in a
-  local knowledge corpus, vets the credibility of cited sources, runs
-  a reflexion self-critique loop to revise weak or incomplete findings,
-  delegates the final write-up to a focused sub-agent, checks that the
-  cited sources are reachable, and gates the result behind human
-  approval. A reviewer's free-form feedback at the approval step feeds
-  back into another research pass.
-
-  This is the canonical Loki graph-agent reference: it exercises every
-  node type (script, llm, rag, map, agent, input, approval, end) and
-  both static fan-out and dynamic map fan-out.
-
-version: "1.0"
-
-temperature: 0.0
-
-global_tools:
-  - web_search_loki.sh
-  - fetch_url_via_curl.sh
-  - search_arxiv.sh
-
-mcp_servers:
-  - ddg-search
-
-conversation_starters:
-  - "How does HTTP/3 differ from HTTP/2?"
-  - "Summarize recent advances in solid-state battery chemistry"
-
-settings:
-  max_loop_iterations: 40
-  log_state_snapshots: false
-  validate_before_run: true
-  max_concurrency: 4
-
-initial_state:
-  research_feedback: ""
-  research_attempts: 0
-  local_context: ""
-  local_sources: ""
-
-start: parse_request
-
-nodes:
-
-  parse_request:
-    id: parse_request
-    type: script
-    script: scripts/parse_request.py
-    next: bootstrap_research
-
-  ask_topic:
-    id: ask_topic
-    type: input
-    question: "What would you like me to research?"
-    validation: "len(input) > 0"
-    state_updates:
-      topic: "{{input}}"
-    next: bootstrap_research
-
-  bootstrap_research:
-    id: bootstrap_research
-    type: script
-    script: scripts/bootstrap_research.py
-    next: [plan, knowledge_lookup]
-
-  plan:
-    id: plan
-    type: llm
-    instructions: |
-      You are a research planner. Given a topic, produce a focused
-      research plan and decompose it into 3-5 specific sub-questions
-      that can each be researched independently in parallel.
-
-      The plan is a short narrative naming the key questions and the
-      kinds of sources that would be authoritative. The sub-questions
-      are precise, self-contained queries (each one is sent on its own
-      to a separate research worker, so they must be answerable
-      without each other's context).
-    prompt: "Research topic: {{topic}}"
-    tools: []
-    output_schema:
-      type: object
-      properties:
-        research_plan:
-          type: string
-          description: A short plan narrative.
-        questions:
-          type: array
-          items: { type: string }
-          minItems: 1
-          maxItems: 6
-          description: 3-5 specific, self-contained sub-questions.
-      required: [research_plan, questions]
-    next: research_each_question
-
-  knowledge_lookup:
-    id: knowledge_lookup
-    type: rag
-    documents:
-      - ./knowledge/
-    query: "{{topic}}"
-    top_k: 6
-    chunk_size: 1000
-    chunk_overlap: 100
-    state_updates:
-      local_context: "{{output.context}}"
-      local_sources: "{{output.sources}}"
-    next: research_each_question
-
-  research_each_question:
-    id: research_each_question
-    type: map
-    over: "{{questions}}"
-    as: question
-    branch: research_one_question
-    collect_into: question_findings
-    max_concurrency: 3
-    next: combine_findings
-
-  research_one_question:
-    id: research_one_question
-    type: llm
-    instructions: |
-      You are a web research assistant. Investigate the SINGLE question
-      given to you using your tools: search the web, fetch and read
-      pages, and search arXiv for academic sources.
-
-      Rules:
-        - Every factual claim must be backed by a real source you
-          actually retrieved. Never fabricate URLs, page titles,
-          authors, or DOIs.
-        - Prefer primary and authoritative sources over aggregators.
-        - Where sources disagree, report the disagreement rather than
-          papering over it.
-        - Put the URL (or DOI) inline next to each claim it supports.
-
-      Return organized findings in plain text. Do not include
-      meta-commentary about the process.
-    prompt: |
-      Research question: {{question}}
-
-      Local context that may help:
-      {{local_context}}
-
-      {{research_feedback}}
-    tools:
-      - web_search_loki
-      - fetch_url_via_curl
-      - search_arxiv
-      - mcp:ddg-search
-    max_iterations: 10
-    max_attempts: 2
-    temperature: 0.1
-
-  combine_findings:
-    id: combine_findings
-    type: script
-    script: scripts/combine_findings.py
-    next: vet_sources
-
-  vet_sources:
-    id: vet_sources
-    type: llm
-    instructions: |
-      You assess the credibility of the sources cited in a set of
-      research findings. For every distinct source URL in the findings,
-      call the `classify_source` tool to get its credibility tier. Then
-      summarize: which claims rest on HIGH-credibility sources, and
-      which rest on PREPRINT or UNVERIFIED sources and so need
-      corroboration. Do NOT do any new research -- assess only what is
-      already cited.
-    prompt: |
-      Findings to assess:
-      {{findings}}
-    tools:
-      - classify_source
-    max_iterations: 15
-    state_updates:
-      source_assessment: "{{output}}"
-    next: critique
-
-  critique:
-    id: critique
-    type: llm
-    instructions: |
-      You are a meticulous research reviewer. Judge whether the
-      findings below are good enough to synthesize a complete,
-      well-supported report that answers the research plan.
-
-      Mark the findings REVISE if ANY of these hold:
-        - A research-plan question is unanswered or only weakly
-          addressed.
-        - A factual claim has no source, or cites a source that looks
-          fabricated.
-        - The findings lean on a single source where corroboration is
-          needed.
-        - A key claim rests only on a PREPRINT or UNVERIFIED source,
-          per the source credibility assessment below.
-        - An obvious counter-perspective or recent development is
-          missing.
-      Otherwise mark them PASS.
-
-      Respond in EXACTLY this format, nothing else:
-
-      VERDICT: <PASS or REVISE>
-      FEEDBACK: <if REVISE, be specific and actionable -- name the gaps
-      and what kind of source would close them; if PASS, write "none">
-    prompt: |
-      Research plan:
-      {{research_plan}}
-
-      Findings under review:
-      {{findings}}
-
-      Source credibility assessment:
-      {{source_assessment}}
-    tools: []
-    state_updates:
-      critique: "{{output}}"
-    next: reflexion_gate
-
-  reflexion_gate:
-    id: reflexion_gate
-    type: script
-    script: scripts/reflexion_gate.py
-    next: synthesize
-
-  synthesize:
-    id: synthesize
-    type: agent
-    agent: report-writer
-    prompt: |
-      Research topic: {{topic}}
-
-      Findings (organized by sub-question, with inline citations):
-      {{findings}}
-
-      Source credibility assessment:
-      {{source_assessment}}
-
-      Produce the final report following your instructions.
-    timeout: 300
-    state_updates:
-      report: "{{output}}"
-    next: verify_sources
-
-  verify_sources:
-    id: verify_sources
-    type: script
-    script: scripts/verify_sources.py
-    next: approve
-
-  approve:
-    id: approve
-    type: approval
-    question: |
-      Research report on: {{topic}}
-
-      {{report}}
-
-      ----
-      {{source_check}}
-      ----
-
-      Accept this report? Pick "accept" or "reject", or type specific
-      feedback to send the research back for another pass.
-    options:
-      - "accept"
-      - "reject"
-    routes:
-      "accept": end_accepted
-      "reject": end_rejected
-    on_other: incorporate_feedback
-    state_updates:
-      decision: "{{choice}}"
-
-  incorporate_feedback:
-    id: incorporate_feedback
-    type: script
-    script: scripts/incorporate_feedback.py
-
-  end_accepted:
-    id: end_accepted
-    type: end
-    output: "{{report}}"
-
-  end_rejected:
-    id: end_rejected
-    type: end
-    output: "Research on '{{topic}}' was rejected and discarded."

assets/agents/deep-research/knowledge/README.md

@@ -1,23 +0,0 @@
-# Local knowledge corpus for deep-research
-
-The `knowledge_lookup` node in `graph.yaml` is a `rag` node that runs
-hybrid (vector + keyword) retrieval over every file in this directory.
-Drop your own notes, papers (PDFs), Markdown docs, or text files here
-and they will be indexed into a per-agent knowledge base on first run.
-
-Loki supports common file types out of the box: `.md`, `.txt`, `.pdf`,
-`.html`, and others. Subdirectories are walked recursively.
-
-A small starter file (`research-style-notes.md`) ships so the RAG
-node has something non-empty to retrieve against on a clean install.
-Replace or extend it with your own materials to bias the research
-phase toward your local context.
-
-To force the knowledge base to rebuild after you add or change files,
-delete the cached index:
-
-```sh
-rm ~/.config/loki/agents/deep-research/knowledge_lookup.yaml
-```
-
-The next run will rebuild from the current contents of this directory.

assets/agents/deep-research/knowledge/research-style-notes.md

@@ -1,49 +0,0 @@
-# Research style notes
-
-These are general principles the `deep-research` agent should keep in
-mind regardless of topic. Replace this file with your own notes if you
-want to bias retrieval toward your local context.
-
-## What "good research" means here
-
-- **Every factual claim cites a source you actually retrieved.** Never
-  fabricate URLs, page titles, authors, or DOIs.
-- **Primary sources beat aggregators.** Prefer the original paper, the
-  RFC, the standards body, or the manufacturer over a blog summarizing
-  them.
-- **Corroboration matters where stakes are high.** If a single source
-  makes a strong claim, look for a second independent source before
-  taking it as established.
-- **Disagreement is information, not noise.** If two credible sources
-  disagree, report the disagreement and the reasoning on each side.
-- **Old does not mean wrong.** A 2014 RFC is still authoritative if no
-  newer one has obsoleted it; check before assuming a source is stale.
-
-## Source-tier heuristics
-
-The `vet_sources` node uses these rough tiers to weigh credibility.
-The custom tool `classify_source` (see `tools.sh`) implements this
-deterministically by hostname / TLD.
-
-- **HIGH:** government domains (`.gov`, `.mil`), academic institutions
-  (`.edu`, university subdomains), peer-reviewed journals, standards
-  bodies (IETF/RFCs, W3C, ISO, IEEE, NIST), and primary documents from
-  the entities being researched (e.g. a vendor's official spec page).
-- **PREPRINT:** arXiv, bioRxiv, medRxiv, SSRN. Useful but not yet
-  peer-reviewed; treat numeric claims with extra caution.
-- **ORGANIZATION:** established nonprofits, standards-adjacent groups,
-  industry consortia. Reliable for their stated mission but may have a
-  perspective.
-- **UNVERIFIED:** general web pages, blogs, news aggregators, social
-  media. Useful for leads but should not be the only source for a
-  factual claim.
-
-## Common pitfalls to flag in critique
-
-- A claim cited only to a PREPRINT or UNVERIFIED source on a numeric
-  or contested point.
-- A research-plan question that the findings address only obliquely.
-- "Findings" that paraphrase a single source three times rather than
-  triangulating.
-- Citation collisions where two sources are listed but turn out to
-  be the same study reported via different aggregators.

assets/agents/deep-research/scripts/bootstrap_research.py

@@ -1,18 +0,0 @@
-#!/usr/bin/env python3
-"""Fan-out source for context loading.
-
-Has no logic of its own. Exists so the static `next: [plan, knowledge_lookup]`
-list on this node fans out into two parallel branches (the LLM planner and
-the RAG knowledge lookup) as a single super-step. The validator requires
-declared parallel-branch script outputs, so we emit an empty JSON object
-explicitly here.
-"""
-import json
-
-
-def main():
-    print(json.dumps({}))
-
-
-if __name__ == "__main__":
-    main()

assets/agents/deep-research/scripts/combine_findings.py

@@ -1,39 +0,0 @@
-#!/usr/bin/env python3
-"""Join the per-question map outputs into a single `findings` string.
-
-The `research_each_question` map writes `question_findings` (an array,
-one entry per sub-question, in input order). Downstream nodes
-(`vet_sources`, `critique`, `synthesize`) read `{{findings}}` as a
-single block, so this script renders the array as a Markdown document
-with one section per question.
-"""
-import json
-import os
-
-
-def load_state():
-    path = os.environ.get("GRAPH_STATE_FILE")
-    if path:
-        with open(path) as f:
-            return json.load(f)
-    return json.loads(os.environ.get("GRAPH_STATE", "{}"))
-
-
-def main():
-    state = load_state()
-    questions = state.get("questions") or []
-    per_question = state.get("question_findings") or []
-
-    sections = []
-    for idx, q in enumerate(questions):
-        body = per_question[idx] if idx < len(per_question) else ""
-        if isinstance(body, dict) or isinstance(body, list):
-            body = json.dumps(body, indent=2)
-        sections.append(f"## {q}\n\n{body}")
-
-    findings = "\n\n".join(sections) if sections else "No findings gathered."
-    print(json.dumps({"findings": findings}))
-
-
-if __name__ == "__main__":
-    main()

assets/agents/deep-research/scripts/incorporate_feedback.py

@@ -1,41 +0,0 @@
-#!/usr/bin/env python3
-"""Fold a reviewer's free-form feedback back into the research loop.
-
-Runs when the user answers the approval step with their own text
-instead of "accept" or "reject". That text (saved by the approval node
-as `decision`) becomes `research_feedback`, and the graph loops back to
-`research_each_question` for another informed pass (each sub-question is
-re-researched in parallel with the new feedback in context). The
-reflexion counter is reset so the user-driven pass gets a fresh revision
-budget.
-
-Routing (`_next`): always research_each_question.
-"""
-import json
-import os
-
-
-def load_state():
-    path = os.environ.get("GRAPH_STATE_FILE")
-    if path:
-        with open(path) as f:
-            return json.load(f)
-    return json.loads(os.environ.get("GRAPH_STATE", "{}"))
-
-
-def main():
-    state = load_state()
-    feedback = (state.get("decision") or "").strip()
-    output = {
-        "_next": "research_each_question",
-        "research_attempts": 0,
-        "research_feedback": (
-            "The user reviewed the report and asked for changes. Treat "
-            "this as the top priority for the next pass:\n\n" + feedback
-        ),
-    }
-    print(json.dumps(output))
-
-
-if __name__ == "__main__":
-    main()

assets/agents/deep-research/scripts/parse_request.py

@@ -1,35 +0,0 @@
-#!/usr/bin/env python3
-"""Entry router for deep-research.
-
-Reads the caller's prompt from state. If it contains a usable research
-topic, stores it as `topic` and falls through to the static `next`
-(plan). If the prompt is empty, routes to `ask_topic` so the user can
-supply one interactively.
-
-Routing (`_next`):
-  - prompt present -> (no _next; static next: plan)
-  - prompt empty   -> ask_topic
-"""
-import json
-import os
-
-
-def load_state():
-    path = os.environ.get("GRAPH_STATE_FILE")
-    if path:
-        with open(path) as f:
-            return json.load(f)
-    return json.loads(os.environ.get("GRAPH_STATE", "{}"))
-
-
-def main():
-    state = load_state()
-    prompt = (state.get("initial_prompt") or "").strip()
-    if prompt:
-        print(json.dumps({"topic": prompt}))
-    else:
-        print(json.dumps({"_next": "ask_topic"}))
-
-
-if __name__ == "__main__":
-    main()

assets/agents/deep-research/scripts/reflexion_gate.py

@@ -1,76 +0,0 @@
-#!/usr/bin/env python3
-"""Reflexion gate for deep-research.
-
-Runs after `critique` has reviewed the current research findings. If the
-critique's verdict is REVISE and the reflexion budget is not spent,
-loops back to `research` with the critique attached as
-`research_feedback`, so the retry is informed rather than a blind
-re-run. Otherwise it proceeds to `synthesize`.
-
-Routing (`_next`):
-  - verdict PASS                     -> synthesize
-  - verdict REVISE, budget remaining -> research_each_question  (+ research_feedback)
-  - verdict REVISE, budget spent     -> synthesize
-
-Reflexion is a best-effort quality booster, not a hard gate: once the
-budget is spent the workflow proceeds anyway, and the human approval
-step is the final backstop.
-"""
-import json
-import os
-import re
-
-# Automated revision passes allowed. `research` runs at most
-# MAX_REFLEXION_REVISIONS + 1 times per user pass. Bump to allow more.
-MAX_REFLEXION_REVISIONS = 2
-
-
-def load_state():
-    path = os.environ.get("GRAPH_STATE_FILE")
-    if path:
-        with open(path) as f:
-            return json.load(f)
-    return json.loads(os.environ.get("GRAPH_STATE", "{}"))
-
-
-def as_int(value, default=0):
-    try:
-        return int(value)
-    except (TypeError, ValueError):
-        return default
-
-
-def parse_verdict(critique):
-    """Pull PASS/REVISE from the critique's `VERDICT:` line. Defaults to
-    PASS when no verdict line is found, so a malformed critique lets the
-    workflow proceed instead of burning the whole revision budget."""
-    match = re.search(r"VERDICT:\s*([A-Za-z]+)", critique, re.IGNORECASE)
-    if not match:
-        return "PASS"
-    return match.group(1).upper()
-
-
-def main():
-    state = load_state()
-    critique = state.get("critique") or ""
-    verdict = parse_verdict(critique)
-    attempts = as_int(state.get("research_attempts"))
-
-    if verdict == "REVISE" and attempts < MAX_REFLEXION_REVISIONS:
-        feedback = (
-            "A reviewer judged the previous research pass incomplete. "
-            "Address every point in the critique below:\n\n" + critique
-        )
-        output = {
-            "_next": "research_each_question",
-            "research_attempts": attempts + 1,
-            "research_feedback": feedback,
-        }
-    else:
-        output = {"_next": "synthesize"}
-
-    print(json.dumps(output))
-
-
-if __name__ == "__main__":
-    main()

assets/agents/deep-research/scripts/verify_sources.py

@@ -1,69 +0,0 @@
-#!/usr/bin/env python3
-"""Check that the sources cited in the research report are reachable.
-
-Scans the final report for URLs and DOIs, probes each with a HEAD
-request, and writes a `source_check` summary into state so the human
-reviewer sees broken citations at the approval step.
-
-Times out per request so a slow source cannot stall the graph.
-"""
-import json
-import os
-import re
-import urllib.error
-import urllib.request
-
-DOI_RE = re.compile(r"\b(10\.\d{4,9}/[-._;()/:A-Z0-9]+)", re.IGNORECASE)
-URL_RE = re.compile(r"https?://[^\s)\]\}\"'>]+")
-
-
-def load_state():
-    path = os.environ.get("GRAPH_STATE_FILE")
-    if path:
-        with open(path) as f:
-            return json.load(f)
-    return json.loads(os.environ.get("GRAPH_STATE", "{}"))
-
-
-def reachable(url, timeout=5.0):
-    req = urllib.request.Request(url, method="HEAD")
-    try:
-        with urllib.request.urlopen(req, timeout=timeout) as resp:
-            return 200 <= resp.status < 400
-    except urllib.error.HTTPError as e:
-        return 200 <= e.code < 400
-    except Exception:
-        return False
-
-
-def main():
-    state = load_state()
-    report = state.get("report") or ""
-
-    urls = sorted({u.rstrip(".,;)") for u in URL_RE.findall(report)})
-    dois = sorted(set(DOI_RE.findall(report)))
-
-    results = []
-    for url in urls:
-        ok = reachable(url)
-        results.append(f"  {'OK' if ok else 'UNREACHABLE'}  {url}")
-    for doi in dois:
-        url = f"https://doi.org/{doi}"
-        if url in urls:
-            continue
-        ok = reachable(url)
-        results.append(f"  {'OK' if ok else 'UNREACHABLE'}  DOI {doi} ({url})")
-
-    if not results:
-        summary = "No web sources were cited in the report."
-    else:
-        summary = (
-            f"Source reachability ({len(results)} checked):\n"
-            + "\n".join(results)
-        )
-
-    print(json.dumps({"source_check": summary}))
-
-
-if __name__ == "__main__":
-    main()

assets/agents/deep-research/tools.sh

@@ -1,39 +0,0 @@
-#!/usr/bin/env bash
-
-set -e
-
-# @env LLM_OUTPUT=/dev/stdout The output path
-
-# @cmd Classify the credibility tier of a web source from its URL.
-# A deterministic check based on the host and top-level domain. Use it
-# to weigh how much trust to place in a source before relying on it.
-# @option --url!  The full source URL to classify
-classify_source() {
-    # shellcheck disable=SC2154
-    local url="$argc_url"
-    local host="${url#*://}"
-    host="${host%%/*}"
-    host="${host##*@}"
-    host="${host%%:*}"
-    host="$(printf '%s' "$host" | tr '[:upper:]' '[:lower:]')"
-
-    local tier
-    case "$host" in
-        '')
-            tier="UNKNOWN - no host could be parsed from the URL" ;;
-        *.gov | *.gov.* | *.mil)
-            tier="HIGH - government source" ;;
-        *.edu | *.edu.* | *.ac.*)
-            tier="HIGH - academic institution" ;;
-        arxiv.org | *.arxiv.org | biorxiv.org | *.biorxiv.org | medrxiv.org | *.medrxiv.org | ssrn.com | *.ssrn.com)
-            tier="PREPRINT - not yet peer reviewed, corroborate before citing" ;;
-        wikipedia.org | *.wikipedia.org)
-            tier="TERTIARY - encyclopedia, good for orientation not citation" ;;
-        *.org | *.org.*)
-            tier="MEDIUM - organization site, check for institutional bias" ;;
-        *)
-            tier="UNVERIFIED - general web source, corroborate before citing" ;;
-    esac
-
-    printf '%s: %s\n' "${host:-<none>}" "$tier" >> "$LLM_OUTPUT"
-}

assets/agents/jira-helper/README.md

@@ -0,0 +1,14 @@
+# Jira AI Agent
+
+## Overview
+
+The Jira AI Agent is designed to assist with managing tasks within Jira projects, providing capabilities such as 
+creating, searching, updating, assigning, linking, and commenting on issues. Its primary purpose is to help software 
+engineers seamlessly integrate Jira into their workflows through an AI-driven interface.
+
+## Configuration
+This agent uses the official [Atlassian MCP Server](https://github.com/atlassian/atlassian-mcp-server). To use it, 
+ensure you have Node.js v18+ installed to run the local MCP proxy (`mcp-remote`).
+
+The server uses OAuth 2.0 so it will automatically open your browser for you to sign in to your account. No manual 
+configuration is necessary!

assets/agents/jira-helper/config.yaml

@@ -0,0 +1,37 @@
+name: Jira Agent
+description: An AI agent that can assist with Jira tasks such as creating issues, searching for issues, and updating issues.
+version: 0.1.0
+agent_session: temp
+mcp_servers:
+  - atlassian
+instructions: |
+  You are a AI agent designed to assist with managing Jira tasks and helping software engineers utilize and integrate 
+  Jira into their workflows. You can create, search, update, assign, link, and comment on issues in Jira.
+  
+  ## Create Issue (MANDATORY when creating a issue)
+  When a user prompts you to create a Jira issue:
+  1. Prompt the user for what Jira project they want the ticket created in
+  2. If the ticket type requires a parent issue:
+    a. Query Jira for potentially relevant parents
+    b. Prompt user for which parent to use, displaying the suggested list of parent issues
+  3. Create the issue with the following format:
+     ```markdown
+      **Description:**
+        This section gives context and details about the issue.
+      **User Acceptance Criteria:**
+        # This section provides bullet points that function like a checklist of all the things that must be completed in 
+        # order for the issue to be considered done.
+        * Example criteria one
+        * Example criteria two
+     ```
+  4. Ask the user if the issue should be assigned to them
+    a. If yes, then assign the user to the newly created issue
+
+
+  Available tools:
+  {{__tools__}}
+conversation_starters:
+  - What are the latest issues in my Jira project?
+  - Can you create a new Jira issue for me?
+  - What are my open Jira issues?
+  - Can you search for issues with the label "bug" in my Jira project?

assets/agents/report-writer/README.md

@@ -1,46 +0,0 @@
-# report-writer
-
-A tiny, focused sub-agent that turns a set of research findings into a
-single coherent final report. Reads only what it is given — does not
-do independent research, does not access the web, does not invent
-facts. It exists as a focused tool for orchestrating agents to
-delegate the writing phase to.
-
-## Why a separate agent?
-
-This is an example of the **agent-as-tool** pattern in graph agents.
-The `deep-research` graph agent's `synthesize` node is an `agent` node
-that spawns this one (see `assets/agents/deep-research/graph.yaml`).
-Separating the role has two practical benefits:
-
-- The orchestrating agent can use a cheap model (or a high-temperature
-  exploratory one) for the research phase, while letting the writing
-  phase use a different (typically lower-temperature, possibly larger)
-  model dedicated to coherent prose.
-- The writing prompt is owned by this agent's `config.yaml` rather
-  than buried inside another agent's graph. You can polish it
-  independently without touching the research flow.
-
-## Standalone use
-
-You can also use this agent directly if you have a set of findings you
-want polished:
-
-```sh
-loki -a report-writer "Topic: X. Findings: <paste findings here>"
-```
-
-It will produce a single Markdown report following the rules in its
-system prompt: executive summary at the top, grouped sections by
-related sub-questions, every inline citation preserved verbatim, and a
-final "Open questions / disagreements" section.
-
-## What it will NOT do
-
-- Search the web, fetch URLs, query an MCP server, or use any tool.
-  It has no tools configured.
-- Invent facts beyond what is in the findings you give it.
-- Strip or rewrite citations.
-
-These constraints are the point of the agent existing: a writer that
-the orchestrator can trust to stay in its lane.

assets/agents/report-writer/config.yaml

@@ -1,34 +0,0 @@
-name: report-writer
-description: Polishes research findings into a clear, citation-preserving final report
-version: 1.0.0
-temperature: 0.2
-
-instructions: |
-  You are a technical writer. You will be given:
-    - a research topic
-    - a set of findings, organized per sub-question, with inline
-      citations next to each claim
-    - a source-credibility assessment of the cited sources
-
-  Your job is to produce a single, well-organized final report:
-
-  Rules:
-    - Use ONLY the findings provided. Do not introduce facts from
-      your own memory. Do not speculate beyond what the findings
-      support.
-    - Preserve every inline citation. If a sentence in the findings
-      had a URL or DOI, the equivalent sentence in your report must
-      keep the same citation.
-    - Lead with a 2-3 sentence executive summary at the top.
-    - Organize the body so that related sub-questions are grouped,
-      not strictly one section per question. The findings are raw
-      material; the report should read as a single coherent answer
-      to the original topic.
-    - End with a short "Open questions / disagreements" section
-      naming anything the findings flagged as unresolved or
-      contested.
-
-  Output plain Markdown. No metadata, no JSON wrapper.
-
-conversation_starters:
-  - "Polish these findings into a cited report"

assets/agents/sisyphus/README.md

@@ -18,15 +18,16 @@ Sisyphus acts as the primary entry point, capable of handling complex tasks by c
 - 🛠️ **Tool Integration**: Seamlessly uses system tools for building, testing, and file manipulation.
 
 ## Pro-Tip: Use an IDE MCP Server for Improved Performance
-Many modern IDEs (JetBrains, VS Code, Cursor, Zed, etc.) expose MCP servers that let LLMs use IDE tools directly. Using
-one dramatically improves the performance of coding agents. If you have one, add it to your loki config (see the
-[MCP Server docs](../../../docs/function-calling/MCP-SERVERS.md)) and reference it in this agent's `mcp_servers:` list:
+Many modern IDEs now include MCP servers that let LLMs perform operations within the IDE itself and use IDE tools. Using
+an IDE's MCP server dramatically improves the performance of coding agents. So if you have an IDE, try adding that MCP
+server to your config (see the [MCP Server docs](../../../docs/function-calling/MCP-SERVERS.md) to see how to configure
+them), and modify the agent definition to look like this:
 
 ```yaml
 # ...
 
 mcp_servers:
-  - your-ide-mcp-server
+  - jetbrains
 
 global_tools:
   - fs_read.sh

assets/agents/sisyphus/config.yaml

@@ -119,21 +119,20 @@ instructions: |
   1. todo__init --goal "Add user profiles API endpoint"
   2. todo__add --task "Explore existing API patterns"
   3. todo__add --task "Implement profile endpoint"
-  4. agent__spawn --agent explore --prompt "Find existing API endpoint patterns, route structures, and controller conventions. Include code snippets."
-  5. agent__spawn --agent explore --prompt "Find existing data models and database query patterns. Include code snippets."
-  6. agent__collect --id <id1>
-  7. agent__collect --id <id2>
-  8. todo__done --id 1
-  9. agent__spawn --agent coder --prompt "<structured prompt using Coder Delegation Format above, including code snippets from explore results>"
-  10. agent__collect --id <coder_id>
-  11. todo__done --id 2
+  4. todo__add --task "Verify with build/test"
+  5. agent__spawn --agent explore --prompt "Find existing API endpoint patterns, route structures, and controller conventions. Include code snippets."
+  6. agent__spawn --agent explore --prompt "Find existing data models and database query patterns. Include code snippets."
+  7. agent__collect --id <id1>
+  8. agent__collect --id <id2>
+  9. todo__done --id 1
+  10. agent__spawn --agent coder --prompt "<structured prompt using Coder Delegation Format above, including code snippets from explore results>"
+  11. agent__collect --id <coder_id>
+  12. todo__done --id 2
+  13. run_build
+  14. run_tests
+  15. todo__done --id 3
   ```
 
-  Note: the `coder` agent is a graph agent that runs verification (build +
-  tests) and a bounded fix-loop internally. You do NOT need to spawn a
-  separate build/test step. A `CODER_COMPLETE` outcome means build and
-  tests already passed.
-
   ### Example 2: Architecture/design question (explore + oracle in parallel)
 
   User: "How should I structure the authentication for this app?"
@@ -173,22 +172,6 @@ instructions: |
   10. **Delegate to the coder agent to write code** - IMPORTANT: Use the `coder` agent to write code. Do not try to write code yourself except for trivial changes
   11. **Always output a summary of changes when finished** - Make it clear to user's that you've completed your tasks
 
-  ## Coder Outcomes
-
-  The `coder` agent is a graph agent that runs the implement -> verify_build
-  -> verify_tests -> fix_loop pipeline internally. It always returns one of
-  three sentinel outcomes:
-
-  - `CODER_COMPLETE` - implementation succeeded with build + tests green.
-    Continue with any follow-up todos.
-  - `CODER_REJECTED` - user rejected the plan at the approval gate (only
-    triggered for high-complexity plans). Do NOT re-spawn coder blindly;
-    ask the user what to change first.
-  - `CODER_FAILED` - the fix-loop exhausted its budget without producing
-    green build/tests. The failure output includes the last build and tests
-    output. Surface this to the user; consider spawning `oracle` for
-    diagnosis if the failure is unclear.
-
   ## When to Do It Yourself
 
   - Simple command execution

assets/functions/scripts/run-agent.sh

@@ -73,11 +73,11 @@ def to_args:
     to_entries | .[] |
     (.key | split("_") | join("-")) as $key |
     if .value | type == "array" then
-        .value | .[] | "--\($key)=\(. | escape_shell_word)"
+        .value | .[] | "--\($key) \(. | escape_shell_word)"
     elif .value | type == "boolean" then
         if .value then "--\($key)" else "" end
     else
-        "--\($key)=\(.value | escape_shell_word)"
+        "--\($key) \(.value | escape_shell_word)"
     end;
 [ to_args ] | join(" ")
 EOF

assets/functions/scripts/run-tool.sh

@@ -70,11 +70,11 @@ def to_args:
     to_entries | .[] |
     (.key | split("_") | join("-")) as $key |
     if .value | type == "array" then
-        .value | .[] | "--\($key)=\(. | escape_shell_word)"
+        .value | .[] | "--\($key) \(. | escape_shell_word)"
     elif .value | type == "boolean" then
         if .value then "--\($key)" else "" end
     else
-        "--\($key)=\(.value | escape_shell_word)"
+        "--\($key) \(.value | escape_shell_word)"
     end;
 [ to_args ] | join(" ")
 EOF

assets/roles/atlassian.md

@@ -1,8 +0,0 @@
----
-enabled_mcp_servers: atlassian
----
-You are the librarian for the company's Confluence and Jira knowledge bases. Your job is to help users find and retrieve
-information from these platforms. Use all tools at your disposal to answer user queries.
-
-Available Tools:
-{{__tools__}}

config.agent.example.yaml

@@ -17,18 +17,16 @@ agent_session: null              # Set a session to use when starting the agent.
 name: <agent-name>               # Name of the agent, used in the UI and logs
 description: <description>       # Description of the agent, used in the UI
 version: 1                       # Version of the agent
-# Auto-Continue (Todo System)
-# The auto-continue system provides built-in task tracking for improved reliability.
-# When enabled, the model can create todo lists and the system will automatically
-# prompt it to continue when incomplete tasks remain.
-# See the [Todo System documentation](https://github.com/Dark-Alex-17/loki/wiki/TODO-System) for more information
+# Todo System & Auto-Continuation
+# These settings help smaller models handle multi-step tasks more reliably.
+# See docs/TODO-SYSTEM.md for detailed documentation.
 auto_continue: false             # Enable automatic continuation when incomplete todos remain
 max_auto_continues: 10           # Maximum number of automatic continuations before stopping
 inject_todo_instructions: true   # Inject the default todo tool usage instructions into the agent's system prompt
 continuation_prompt: null        # Custom prompt used when auto-continuing (optional; uses default if null)
 # Sub-Agent Spawning System
 # Enable this agent to spawn and manage child agents in parallel.
-# See https://github.com/Dark-Alex-17/loki/wiki/Agents for detailed documentation.
+# See docs/AGENTS.md for detailed documentation.
 can_spawn_agents: false          # Enable the agent to spawn child agents
 max_concurrent_agents: 4         # Maximum number of agents that can run simultaneously
 max_agent_depth: 3               # Maximum nesting depth for sub-agents (prevents runaway spawning)

config.example.yaml

@@ -27,18 +27,18 @@ sync_models_url: >               # URL to sync model changes from
   https://raw.githubusercontent.com/Dark-Alex-17/loki/refs/heads/main/models.yaml
 
 # ---- REPL Prompt ----
-# Custom REPL left/right prompts; see the [REPL Prompt Documentation](https://github.com/Dark-Alex-17/loki/wiki/REPL-Prompt) for more information
+# Custom REPL left/right prompts; see the [REPL Prompt Documentation](./docs/REPL-PROMPT.md) for more information
 left_prompt:
   '{color.red}{model}){color.green}{?session {?agent {agent}>}{session}{?role /}}{!session {?agent {agent}>}}{role}{?rag @{rag}}{color.cyan}{?session )}{!session >}{color.reset} '
 right_prompt:
   '{color.purple}{?session {?consume_tokens {consume_tokens}({consume_percent}%)}{!consume_tokens {consume_tokens}}}{color.reset}'
 
 # ---- Vault ----
-# See the [Vault documentation](https://github.com/Dark-Alex-17/loki/wiki/Vault) for more information on the Loki vault
+# See the [Vault documentation](./docs/VAULT.md) for more information on the Loki vault
 vault_password_file: null        # Path to a file containing the password for the Loki vault (cannot be a secret template)
 
 # ---- Function Calling ----
-# See the [Tools documentation](https://github.com/Dark-Alex-17/loki/wiki/Tools) for more details
+# See the [Tools documentation](./docs/function-calling/TOOLS.md) for more details
 function_calling: true           # Enables or disables function calling (Globally).
 mapping_tools:                   # Alias for a tool or toolset
   fs: 'fs_cat,fs_ls,fs_mkdir,fs_rm,fs_write,fs_read,fs_glob,fs_grep'
@@ -64,6 +64,7 @@ visible_tools:                   # Which tools are visible to be compiled (and a
 #  - get_current_weather.py
 #  - get_current_weather.ts
   - get_current_weather.sh
+  - query_jira_issues.sh
 #  - search_arxiv.sh
 #  - search_wikipedia.sh
 #  - search_wolframalpha.sh
@@ -74,24 +75,14 @@ visible_tools:                   # Which tools are visible to be compiled (and a
 #  - web_search_tavily.sh
 
 # ---- MCP Servers ----
-# See the [MCP Servers documentation](https://github.com/Dark-Alex-17/loki/wiki/MCP-Servers) for more details
+# See the [MCP Servers documentation](./docs/MCP-SERVERS.md) for more details
 mcp_server_support: true         # Enables or disables MCP servers (globally).
 mapping_mcp_servers:             # Alias for an MCP server or set of servers
   git: github,gitmcp
 enabled_mcp_servers: null        # Which MCP servers to enable by default (e.g. 'github,slack,ddg-search')
 
-# ---- Auto-Continue (Todo System) ----
-# The auto-continue system provides built-in task tracking for improved reliability.
-# When enabled, the model can create todo lists and the system will automatically
-# prompt it to continue when incomplete tasks remain.
-# See the [Todo System documentation](https://github.com/Dark-Alex-17/loki/wiki/TODO-System) for more information
-auto_continue: false              # Enable automatic continuation when incomplete todos remain (default: false)
-max_auto_continues: 10            # Maximum number of automatic continuations before stopping (default: 10)
-inject_todo_instructions: true    # Inject default todo usage instructions into the system prompt (default: true)
-continuation_prompt: null         # Custom prompt used when auto-continuing. If null, uses built-in default
-
 # ---- Session ----
-# See the [Session documentation](https://github.com/Dark-Alex-17/loki/wiki/Sessions) for more information
+# See the [Session documentation](./docs/SESSIONS.md) for more information
 save_session: null               # Controls the persistence of the session. If true, auto save; if false, don't auto-save save; if null, ask the user what to do
 compression_threshold: 4000      # Compress the session when the token count reaches or exceeds this threshold
 summarization_prompt: >          # The text prompt used for creating a concise summary of session message
@@ -100,7 +91,7 @@ summary_context_prompt: >        # The text prompt used for including the summar
   'This is a summary of the chat history as a recap: '
 
 # ---- RAG ----
-# See the [RAG Docs](https://github.com/Dark-Alex-17/loki/wiki/RAG) for more details.
+# See the [RAG Docs](./docs/RAG.md) for more details.
 rag_embedding_model: null        # Specifies the embedding model used for context retrieval
 rag_reranker_model: null         # Specifies the reranker model used for sorting retrieved documents; Loki uses Reciprocal Rank Fusion by default
 rag_top_k: 5                     # Specifies the number of documents to retrieve for answering queries
@@ -146,7 +137,7 @@ document_loaders:
     sh -c "yek $1 --json | jq 'map({ path: .filename, contents: .content })'"
 
 # ---- Clients ----
-# See the [Clients documentation](https://github.com/Dark-Alex-17/loki/wiki/Clients) for more details
+# See the [Clients documentation](./docs/clients/CLIENTS.md) for more details
 clients:
   # All clients have the following configuration:
   # - type: xxxx

config.role.example.md

@@ -1,9 +1,5 @@
 ---
-############################################
-## Everything in this section is optional ##
-############################################
-
-# Role Configuration
+# Everything in this section is optional
 name: <role-name>                     # The name of the role
 model: openai:gpt-4o                  # The model to use for this role
 temperature: 0.2                      # The temperature to use for this role when querying the model
@@ -12,14 +8,5 @@ enabled_tools: fs_ls,fs_cat           # A comma-separated list of tools to enabl
 enabled_mcp_servers: github,gitmcp    # A comma-separated list of MCP servers to enable for this role
 prompt: null                          # A custom prompt to use for this role that will immediately query
                                       # the model for output instead of using the instructions below
-# Auto-Continue (Todo System)
-# The auto-continue system provides built-in task tracking for improved reliability.
-# When enabled, the model can create todo lists and the system will automatically
-# prompt it to continue when incomplete tasks remain.
-# See the [Todo System documentation](https://github.com/Dark-Alex-17/loki/wiki/TODO-System) for more information
-auto_continue: false                  # Enable automatic continuation when incomplete todos remain (default: false)
-max_auto_continues: 10                # Maximum number of automatic continuations before stopping (default: 10)
-inject_todo_instructions: true        # Inject default todo tool usage instructions into the system prompt (default: true)
-continuation_prompt: null             # Custom prompt used when auto-continuing. If null, uses built-in default
 ---
 You are an expert at doing things. This is where you write the instructions for the role.

graph.example.yaml

@@ -1,427 +0,0 @@
-# Graph-based agent definition (full-featured reference)
-# Location: <loki-config-dir>/agents/<agent-name>/graph.yaml
-#
-# A graph agent is defined by this file alone. An agent directory contains
-# either a config.yaml (a normal LLM-loop agent) or a graph.yaml (a graph
-# agent), never both. The presence of graph.yaml is what makes the agent
-# a graph agent.
-#
-# This file is a reference: it documents every available field, themed
-# around a deep web research workflow with parallel retrieval. It is not
-# a runnable agent as-is. The `agent:`, `script:`, and `documents:` values
-# point at things that would need to exist for a real agent. For a real,
-# runnable deep-research graph agent, see assets/agents/deep-research/.
-#
-# Full documentation:
-#   https://github.com/Dark-Alex-17/loki/wiki/Graph-Agents
-
-# ---------------------------------------------------------------------------
-# Identity
-# ---------------------------------------------------------------------------
-name: deep-research-example        # Agent name (should match the directory name)
-description: |                     # Free-form prose describing the workflow
-  A reference workflow: triage a research request, retrieve local
-  context, branch on a script decision, run either a sub-agent or an
-  LLM research step, then gate the result behind human approval.
-version: "1.0"                     # Graph schema version. Only "1.0" is accepted.
-
-# ---------------------------------------------------------------------------
-# Agent-level config (all optional)
-# The same knobs a normal agent's config.yaml carries. In a graph agent they
-# live here instead of in a config.yaml.
-# ---------------------------------------------------------------------------
-model: claude:claude-sonnet-4-6    # Default model for `llm` nodes that don't override it
-temperature: 0.0                   # Default sampling temperature for `llm` nodes
-top_p: null                        # Default sampling top-p for `llm` nodes
-
-global_tools:                      # Tool universe an `llm` node's `tools:` whitelist draws from
-  - web_search_loki.sh
-  - fetch_url_via_curl.sh
-
-mcp_servers:                       # MCP servers an `llm` node may reference via `mcp:<server>`
-  - ddg-search
-
-conversation_starters:             # Suggested prompts surfaced in the UI
-  - "Research the current state of WebAssembly outside the browser"
-
-# ---------------------------------------------------------------------------
-# Agent variables (optional)
-# Declared the same way as a normal agent's config.yaml `variables:` block.
-# Each variable becomes available to:
-#   - LLM nodes via the template form `{{name}}` once seeded into state
-#     (see initial_state below).
-#   - Script nodes via the env var `LLM_AGENT_VAR_<UPPER_NAME>`.
-# Values may be overridden at runtime with
-#   `loki -a <agent> --agent-variable <name> <value> "..."`.
-# ---------------------------------------------------------------------------
-variables:
-  - name: project_dir
-    description: |
-      Absolute path to the project directory.
-    default: "."
-
-# ---------------------------------------------------------------------------
-# Execution settings (all optional)
-# ---------------------------------------------------------------------------
-settings:
-  max_loop_iterations: 100   # Per-node visit cap. If one node id is entered more
-                             # than this many times, execution aborts. Default 100.
-  timeout: 600               # Optional wall-clock cap (seconds) on the whole run,
-                             # checked between node transitions.
-  log_state_snapshots: true  # Log state before each node (debug/trace). Default true.
-  validate_before_run: true  # Run the graph validator at startup. Default true.
-  max_concurrency: 4         # Cap on simultaneously running branches in any
-                             # super-step (static fan-out OR a `map` node).
-                             # Default 4. Per-`map` overrides this. See Parallel
-                             # Execution below.
-
-# ---------------------------------------------------------------------------
-# Reducers (optional, required whenever two parallel branches write the same
-# state key in the same super-step; otherwise the validator errors at load).
-#
-# A reducer says how two values for the same key get merged. Built-ins:
-#   append    list += [value]              (single value appended to a list)
-#   extend    list += value (a list)       (list-of-lists flattened by one level)
-#   concat    "a\nb"                       (string join with newline separator)
-#   sum       a + b                        (numeric add; ints stay ints)
-#   max       max(a, b)
-#   min       min(a, b)
-#   merge     {**a, **b}                   (dict union, RHS wins on key collision)
-#   overwrite last-write-wins              (explicit opt-in; B's value replaces A's)
-#
-# Keys not listed here have an implicit "single writer per super-step" rule:
-# the validator rejects any graph where two parallel branches both write a
-# key with no reducer.
-# ---------------------------------------------------------------------------
-reducers:
-  sources: append             # The diamond below writes `sources` from both
-                              # branches; append accumulates them into a list.
-  context: concat             # Each branch contributes prose; concat joins them.
-
-# ---------------------------------------------------------------------------
-# Seed state (optional)
-# Values placed into graph state before any node runs; reference anywhere via
-# {{key}}.
-#
-# Note: `initial_prompt` is seeded automatically by Loki with the
-# caller's prompt. So there's no need to set it here.
-# ---------------------------------------------------------------------------
-initial_state:
-  audience: "general reader"
-  # Seed an empty default for any key that a strict field (a node prompt /
-  # instructions / question / End output) references but that is only set on
-  # some paths. `refinement` is set only if the `refine` input node runs;
-  # seeding it "" keeps `finalize`'s strict prompt from failing on the
-  # approve-directly path.
-  refinement: ""
-
-# ---------------------------------------------------------------------------
-# Entry point
-# ---------------------------------------------------------------------------
-start: triage                # ID of the first node to run (must exist in `nodes`)
-
-# ---------------------------------------------------------------------------
-# Nodes
-# Each node is keyed by its id. The `id:` inside a node must match its key
-# (it may also be omitted and thus Loki fills it in from the key).
-#
-# Node types: agent | script | approval | input | llm | rag | map | end
-# ---------------------------------------------------------------------------
-nodes:
-
-  # --- llm node -----------------------------------------------------------
-  # A one-shot LLM call (with an optional bounded tool-call loop). Runs in a
-  # fresh isolated context. Tools are strictly opt-in (see `tools`).
-  triage:
-    id: triage
-    type: llm
-    description: Classify the research request and extract its topic.
-    instructions: |            # Optional system prompt (templated against state)
-      You triage research requests for a {{audience}} audience.
-    prompt: |                  # Required user prompt (templated against state)
-      Classify this request and extract the core research topic:
-      {{initial_prompt}}
-    tools: []                  # Tool whitelist. Omitted or [] = no tools at all.
-                               # A list narrows to exactly those entries.
-    output_schema:             # Optional JSON Schema. The output is parsed to JSON
-      type: object             # and its top-level object keys auto-merge into state
-      properties:              # (so `topic` / `needs_deep_dive` become {{topic}} etc).
-        topic: { type: string }
-        needs_deep_dive: { type: boolean }
-      required: [topic, needs_deep_dive]
-    state_updates:             # {{output}} = this node's result (here, the parsed object)
-      triage_result: "{{output}}"
-    # --- Polymorphic `next` -----------------------------------------------
-    # A single string runs the next node sequentially (e.g. `next: retrieve`).
-    # A list runs all listed nodes in parallel as one BSP super-step
-    # (for more info on BSP, see https://en.wikipedia.org/wiki/Bulk_synchronous_parallel).
-    # Their writes are merged via `reducers:` at the join. Branches converge
-    # implicitly when they all route to the same downstream node (here,
-    # `synthesize`). See the diamond:
-    #
-    #          triage
-    #          /     \
-    #     retrieve  web_search   (run concurrently)
-    #          \     /
-    #         synthesize         (join; fires once after both finish)
-    next: [retrieve, web_search]
-
-  # --- rag node (parallel branch 1 of the diamond) ------------------------
-  # Hybrid (vector + keyword) retrieval against a per-node knowledge base.
-  # The knowledge base is built once, at agent load time, into
-  # <agent-dir>/retrieve.yaml (named after this node's id).
-  retrieve:
-    id: retrieve
-    type: rag
-    documents:                 # Required. Files, directories, URLs, loader paths.
-      - ./knowledge/           #   relative paths resolve against the agent directory
-      - https://example.com/reference
-    query: "{{topic}}"         # Retrieval query (templated). Default: {{initial_prompt}}.
-    top_k: 5                   # Chunks to retrieve. Default = the KB's own top_k.
-    timeout: 120               # Retrieval timeout in seconds. Default 120.
-    # Knowledge-base build config (optional; used only when the KB is first
-    # built). When embedding_model + chunk_size + chunk_overlap are all set,
-    # the KB builds with no interactive prompts (works in non-interactive runs).
-    embedding_model: openai:text-embedding-3-small
-    chunk_size: 1000
-    chunk_overlap: 100
-    reranker_model: null       # Optional reranker for hybrid-search results
-    batch_size: 100            # Optional embedding-request batch size
-    state_updates:             # {{output}} = { context: <str>, sources: [<path>, ...] }
-      context: "{{output.context}}"   # writes `context` -> `reducers.context = concat`
-      sources: "{{output.sources}}"   # writes `sources` -> `reducers.sources = append`
-    next: synthesize           # Joins with web_search at `synthesize`.
-
-  # --- llm node (parallel branch 2 of the diamond) ------------------------
-  # Runs concurrently with `retrieve`. Both branches write `context` and
-  # `sources`; the validator confirms both keys have a reducer declared, and
-  # the BSP scheduler merges them at the join.
-  web_search:
-    id: web_search
-    type: llm
-    instructions: "You are a web researcher. Cite every claim."
-    prompt: "Web research: {{topic}}. Return findings and sources."
-    tools:
-      - web_search_loki
-      - mcp:ddg-search
-    output_schema:
-      type: object
-      properties:
-        context: { type: string }
-        sources:
-          type: array
-          items: { type: string }
-      required: [context, sources]
-    # When `output_schema` is set, top-level keys auto-merge into state, so
-    # `context` and `sources` are produced without needing `state_updates`.
-    next: synthesize           # Joins with retrieve at `synthesize`.
-
-  # --- script node (the diamond's join; also dispatches) -----------------
-  # Runs a .sh / .py / .ts script. The script receives state via the
-  # GRAPH_STATE env var (inline JSON) or GRAPH_STATE_FILE (path to a JSON
-  # file, used when state exceeds 32 KiB). Exactly one is set. It must print
-  # a single JSON object on stdout: keys merge into state, and the reserved
-  # `_next` key (if present) overrides routing.
-  #
-  # The script also receives these env vars (parity with bash tools called
-  # from normal agents):
-  #   GRAPH_STATE / GRAPH_STATE_FILE  state payload (one of the two is set)
-  #   LLM_ROOT_DIR                    loki config dir
-  #   LLM_PROMPT_UTILS_FILE           path to .shared/prompt-utils.sh
-  #   LLM_AGENT_DATA_DIR              this agent's data directory
-  #   LLM_AGENT_VAR_<NAME>            one per declared `variables:` entry
-  #   PATH                            with loki's functions bin dir prepended
-  #   CLICOLOR_FORCE / FORCE_COLOR    so child tools emit ANSI colors
-  # The script's working directory is loki's invocation CWD (not the agent
-  # directory), matching the behavior of bash tools.
-  #
-  # This node fires once: after both `retrieve` and `web_search` finish.
-  # The BSP scheduler dedups the two incoming edges into a single frontier
-  # entry, applies the staged branch writes through the reducers, then runs
-  # this node against the merged state. Inside the script, `context` is the
-  # concatenated text of both branches and `sources` is the combined list.
-  synthesize:
-    id: synthesize
-    type: script
-    script: scripts/synthesize.py  # Path relative to the agent directory
-    timeout: 30                # Seconds. Default 30.
-    state_updates:             # Applied after the stdout JSON is merged
-      decided_for: "{{topic}}"
-    next: summarize            # Default route if the script emits no `_next`
-    fallback: summarize        # Route taken if the script fails (crash / bad JSON)
-    # This script is expected to emit `_next: deep_dive` (or `_next: subjects_map`
-    # to demonstrate the map node below), or no `_next` (then `next` is used).
-    # Targets reached only via the script's dynamic `_next` get an
-    # "unreachable" warning from the validator. This is expected for `_next`-routed
-    # targets.
-
-  # --- agent node ---------------------------------------------------------
-  # Spawns a full Loki sub-agent and waits for it. The child uses its own
-  # tool stack. Agent nodes have no `tools:` field. No schema hint is
-  # injected even when `output_schema` is set (unlike llm nodes).
-  deep_dive:
-    id: deep_dive
-    type: agent
-    agent: deep-research       # Name of an existing Loki agent to spawn
-    prompt: |                  # User message sent to the child (templated)
-      Research {{topic}} in depth. Existing context:
-      {{context}}
-    timeout: 600               # Optional wall-clock cap, seconds. Default 300.
-    output_schema:             # Optional. Same extraction as llm nodes
-      type: object
-      properties:
-        summary: { type: string }
-        findings:
-          type: array
-          items: { type: string }
-      required: [summary, findings]
-    state_updates:
-      research: "{{output}}"
-    next: review               # Required for agent nodes
-
-  # --- map node (Dynamic fan-out. Think: LangGraph's `Send` API) ----------------
-  # Spawns one parallel sub-branch per item in `over`. Each sub-branch runs
-  # the node referenced by `branch:` with the item bound to `as:`. Outputs
-  # collect into the array named by `collect_into:`, preserving input order.
-  #
-  # Reach via `synthesize`'s `_next: subjects_map`. The producer is expected
-  # to have written a list at `subjects` (e.g. an upstream LLM node with an
-  # `output_schema` returning {"subjects": ["a", "b", "c"]}).
-  subjects_map:
-    id: subjects_map
-    type: map
-    over: "{{subjects}}"        # Required. List expression resolved from state.
-                                # Empty list is allowed. It means no branches spawn,
-                                # and thus `collect_into` is written as [].
-    as: subject                 # Required. Per-branch state key holding the
-                                # current item. Read with {{subject}} inside
-                                # the branch node's prompt.
-    branch: research_subject    # Required. Node id to invoke per item.
-                                # Must point to an llm | agent | rag | script
-                                # node satisfying the map branch contract:
-                                #   - no `next:` (atomic, joined at map exit)
-                                #   - no `state_updates:` other than via the
-                                #     map's `collect_into` channel
-                                #   - no `output_schema:` (top-level merge
-                                #     would clash with collect_into)
-                                # Validator enforces all three.
-    collect_into: subject_findings  # Required. State key for the array of
-                                    # per-branch outputs, in input order
-                                    # (not spawn-finish order).
-    max_concurrency: 3          # Optional per-map cap. Defaults to
-                                # settings.max_concurrency above.
-    output_key: output          # Optional. State key the branch's output
-                                # appears under. Default "output". Useful
-                                # only if the branch reads its own bound
-                                # name back (rare).
-    next: aggregate_subjects    # Where to go after all sub-branches finish.
-
-  # Branch node for subjects_map. Each invocation receives a different
-  # `subject` in state. The branch is "atomic", meaning it cannot route on
-  # its own; the surrounding `map` joins after all invocations finish.
-  research_subject:
-    id: research_subject
-    type: llm
-    instructions: "Research one subject deeply for a {{audience}} audience."
-    prompt: "Research {{subject}}: pull the key facts and one citation."
-    tools:
-      - web_search_loki
-    # No `next:`, `state_updates:`, or `output_schema:` here. Map branches
-    # have a strict contract (see `subjects_map.branch` comment).
-
-  # Aggregator that runs after the map joins. Reads the collected list.
-  aggregate_subjects:
-    id: aggregate_subjects
-    type: llm
-    instructions: "Combine N per-subject reports into one cohesive summary."
-    prompt: |
-      Per-subject reports (in original input order):
-      {{subject_findings}}
-    state_updates:
-      research: "{{output}}"
-    next: review
-
-  # --- llm node with a narrowed tool whitelist ----------------------------
-  summarize:
-    id: summarize
-    type: llm
-    instructions: "You write concise research summaries for a {{audience}} audience."
-    prompt: "Summarize the topic {{topic}}, using your tools as needed."
-    tools:                     # Narrow whitelist: exactly these entries, nothing else
-      - web_search_loki        #   an exact global-tool / custom-tool name
-      - mcp:ddg-search         #   `mcp:<server>` includes that server's functions
-    model: claude:claude-haiku-4-5  # Optional per-node model override
-    temperature: 0.3           # Optional per-node sampling override
-    max_attempts: 2            # Retry count on transient errors only. Default 1.
-    max_iterations: 10         # Tool-call-loop turn cap. Default 10.
-    fallback: review           # Route here if all attempts fail
-    timeout: 300               # Optional node wall-clock cap, seconds (unset = no timeout)
-    state_updates:
-      research: "{{output}}"
-    next: review               # Required for llm nodes: the success route
-
-  # --- approval node ------------------------------------------------------
-  # Human-in-the-loop checkpoint. `user__ask` always offers a free-form
-  # "type your own answer" option, so `on_other` is required.
-  review:
-    id: review
-    type: approval
-    question: |
-      Proposed research result for {{topic}}:
-      {{research}}
-
-      Approve?
-    options:                   # The listed choices shown to the user
-      - "yes"
-      - "no"
-    routes:                    # Map each listed option to its next node
-      "yes": finalize
-      "no": rejected_end
-    on_other: refine           # Required: route for ANY answer not in `routes`
-    state_updates:
-      decision: "{{choice}}"   # {{choice}} = the chosen option or the free-form text
-
-  # --- input node ---------------------------------------------------------
-  # Collects a free-form string from the user.
-  refine:
-    id: refine
-    type: input
-    question: "What should be changed about the research result?"
-    default: "tighten the summary"  # Optional: used if the user submits empty input.
-                                    # Note: a substituted default is not re-validated,
-                                    # so make sure it would satisfy `validation`.
-    validation: "len(input) > 0"   # Optional length predicate: len(input) <op> N,
-                                   # <op> in > >= < <= == . Length only -- no regex.
-    state_updates:
-      refinement: "{{input}}"  # {{input}} = the user's text
-    next: finalize             # Required for input nodes: the success route
-
-  # --- llm node (final synthesis) -----------------------------------------
-  finalize:
-    id: finalize
-    type: llm
-    prompt: |
-      Produce the final research report for {{topic}}.
-      Result so far: {{research}}
-      Requested refinement (if any): {{refinement}}
-    state_updates:
-      final_report: "{{output}}"
-    next: done
-
-  # --- end nodes ----------------------------------------------------------
-  # Terminate the graph. `output` (templated, lenient interpolation) becomes
-  # the graph's final result. A graph needs at least one `end` node.
-  done:
-    id: done
-    type: end
-    state_updates:             # Optional: applied before `output` is rendered
-      status: "completed"
-    output: |
-      [{{status}}] {{final_report}}
-
-      Sources: {{sources}}
-
-  rejected_end:
-    id: rejected_end
-    type: end
-    output: "Research on {{topic}} was not approved."

models.yaml

@@ -487,6 +487,14 @@
           thinking:
             type: enabled
             budget_tokens: 16000
+    - name: claude-3-5-haiku-20241022
+      max_input_tokens: 200000
+      max_output_tokens: 8192
+      require_max_tokens: true
+      input_price: 0.8
+      output_price: 4
+      supports_vision: true
+      supports_function_calling: true
 
 # Links:
 #  - https://docs.mistral.ai/getting-started/models/models_overview/

src/cli/completer.rs

@@ -1,11 +1,9 @@
 use crate::client::{ModelType, list_models};
 use crate::config::paths;
 use crate::config::{AppConfig, Config, list_agents, list_sessions};
-use crate::utils::list_file_names;
 use crate::vault::Vault;
 use clap_complete::{CompletionCandidate, Shell, generate};
 use clap_complete_nushell::Nushell;
-use std::env;
 use std::ffi::OsStr;
 use std::io;
 
@@ -96,36 +94,9 @@ pub(super) fn macro_completer(current: &OsStr) -> Vec<CompletionCandidate> {
         .collect()
 }
 
-fn extract_agent_from_args() -> Option<String> {
-    let args: Vec<String> = env::args().collect();
-    let mut i = 0;
-    while i < args.len() {
-        let arg = &args[i];
-
-        if let Some(value) = arg.strip_prefix("--agent=") {
-            return Some(value.to_string());
-        }
-
-        if (arg == "--agent" || arg == "-a") && i + 1 < args.len() {
-            return Some(args[i + 1].clone());
-        }
-
-        i += 1;
-    }
-    None
-}
-
 pub(super) fn session_completer(current: &OsStr) -> Vec<CompletionCandidate> {
     let cur = current.to_string_lossy();
-
-    let sessions = if let Some(agent_name) = extract_agent_from_args() {
-        let sessions_dir = paths::agent_data_dir(&agent_name).join("sessions");
-        list_file_names(sessions_dir, ".yaml")
-    } else {
-        list_sessions()
-    };
-
-    sessions
+    list_sessions()
         .into_iter()
         .filter(|s| s.starts_with(&*cur))
         .map(CompletionCandidate::new)

src/cli/mod.rs

@@ -4,10 +4,9 @@ use crate::cli::completer::{
     ShellCompletion, agent_completer, macro_completer, model_completer, rag_completer,
     role_completer, secrets_completer, session_completer,
 };
-use crate::config::{AssetCategory, InstallFilter};
 use anyhow::{Context, Result};
 use clap::ValueHint;
-use clap::{Parser, crate_authors, crate_description, crate_version};
+use clap::{Parser, crate_authors, crate_description, crate_name, crate_version};
 use clap_complete::ArgValueCompleter;
 use is_terminal::IsTerminal;
 use std::io::{Read, stdin};
@@ -15,7 +14,7 @@ use std::io::{Read, stdin};
 #[derive(Parser, Debug)]
 #[command(author, version, about, long_about = None)]
 #[command(
-	name = "loki",
+	name = crate_name!(),
 	author = crate_authors!(),
 	version = crate_version!(),
 	about = crate_description!(),
@@ -83,18 +82,6 @@ pub struct Cli {
     /// Build all configured Bash tool scripts
     #[arg(long)]
     pub build_tools: bool,
-    /// Reinstall bundled assets, overwriting any local changes
-    #[arg(long, value_name = "CATEGORY", value_enum)]
-    pub install: Option<AssetCategory>,
-    /// Install assets from a remote git repository (URL may be suffixed with #<ref>)
-    #[arg(long, value_name = "GIT_URL")]
-    pub install_from: Option<String>,
-    /// Restrict --install-from to a single asset category
-    #[arg(long, value_name = "CATEGORY", value_enum, requires = "install_from")]
-    pub filter: Option<InstallFilter>,
-    /// Overwrite all conflicts without prompting (used with --install-from)
-    #[arg(long, requires = "install_from")]
-    pub install_force: bool,
     /// Sync models updates
     #[arg(long)]
     pub sync_models: bool,
@@ -146,12 +133,6 @@ pub struct Cli {
     /// Generate static shell completion scripts
     #[arg(long, value_name = "SHELL", value_enum)]
     pub completions: Option<ShellCompletion>,
-    /// Update Loki to the latest release, or to a specific version
-    #[arg(long, value_name = "VERSION")]
-    pub update: Option<Option<String>>,
-    /// With --update, update even if Loki was installed via a package manager
-    #[arg(long, requires = "update")]
-    pub force: bool,
 }
 
 impl Cli {
@@ -411,31 +392,4 @@ mod tests {
         let cli = parse(&["--macro", "my-macro"]);
         assert_eq!(cli.macro_name, Some("my-macro".to_string()));
     }
-
-    #[test]
-    fn parse_update_flag_no_value() {
-        let cli = parse(&["--update"]);
-
-        assert_eq!(cli.update, Some(None));
-    }
-
-    #[test]
-    fn parse_update_flag_with_version() {
-        let cli = parse(&["--update", "v0.4.0"]);
-
-        assert_eq!(cli.update, Some(Some("v0.4.0".to_string())));
-    }
-
-    #[test]
-    fn parse_update_with_force() {
-        let cli = parse(&["--update", "--force"]);
-
-        assert_eq!(cli.update, Some(None));
-        assert!(cli.force);
-    }
-
-    #[test]
-    fn parse_force_without_update_fails() {
-        assert!(Cli::try_parse_from(["loki", "--force"]).is_err());
-    }
 }

src/client/claude.rs

@@ -117,38 +117,33 @@ async fn prepare_chat_completions(
 /// So this function injects the Claude Code system prompt into the request
 /// body to make it a valid request.
 fn inject_oauth_system_prompt(body: &mut Value) {
-    let existing_text = match body.get("system") {
-        Some(Value::String(s)) => {
-            if s.starts_with(CLAUDE_CODE_PREFIX) {
-                return;
-            }
-            (!s.is_empty()).then(|| s.clone())
-        }
-        Some(Value::Array(blocks)) => {
-            let already_injected = blocks.iter().any(|b| {
-                b.get("text")
-                    .and_then(|t| t.as_str())
-                    .map(|t| t.starts_with(CLAUDE_CODE_PREFIX))
-                    .unwrap_or(false)
+    let prefix_block = json!({
+        "type": "text",
+        "text": CLAUDE_CODE_PREFIX,
+    });
+
+    match body.get("system") {
+        Some(Value::String(existing)) => {
+            let existing_block = json!({
+                "type": "text",
+                "text": existing,
             });
-            if already_injected {
-                return;
-            }
-            let joined: Vec<String> = blocks
-                .iter()
-                .filter_map(|b| b.get("text").and_then(|t| t.as_str()).map(String::from))
-                .collect();
-            (!joined.is_empty()).then(|| joined.join("\n\n"))
+            body["system"] = json!([prefix_block, existing_block]);
         }
-        _ => None,
-    };
-
-    let merged = match existing_text {
-        Some(rest) => format!("{}\n\n{}", CLAUDE_CODE_PREFIX, rest),
-        None => CLAUDE_CODE_PREFIX.to_string(),
-    };
-
-    body["system"] = json!([{ "type": "text", "text": merged }]);
+        Some(Value::Array(_)) => {
+            if let Some(arr) = body["system"].as_array_mut() {
+                let already_injected = arr
+                    .iter()
+                    .any(|block| block["text"].as_str() == Some(CLAUDE_CODE_PREFIX));
+                if !already_injected {
+                    arr.insert(0, prefix_block);
+                }
+            }
+        }
+        _ => {
+            body["system"] = json!([prefix_block]);
+        }
+    }
 }
 
 pub async fn claude_chat_completions(

src/client/common.rs

@@ -1,6 +1,6 @@
 use super::*;
 
-use crate::config::{RenderMode, paths};
+use crate::config::paths;
 use crate::{
     config::{AppConfig, Input, RequestContext},
     function::{FunctionDeclaration, ToolCall, ToolResult, eval_tool_calls},
@@ -418,8 +418,7 @@ pub async fn call_chat_completions(
     abort_signal: AbortSignal,
 ) -> Result<(String, Vec<ToolResult>)> {
     let is_child_agent = ctx.current_depth > 0;
-    let suppress_spinner = is_child_agent || ctx.render_mode == RenderMode::Silent;
-    let spinner_message = if suppress_spinner { "" } else { "Generating" };
+    let spinner_message = if is_child_agent { "" } else { "Generating" };
     let ret = abortable_run_with_spinner(
         client.chat_completions(input.clone()),
         spinner_message,
@@ -460,14 +459,10 @@ pub async fn call_chat_completions_streaming(
 ) -> Result<(String, Vec<ToolResult>)> {
     let (tx, rx) = unbounded_channel();
     let mut handler = SseHandler::new(tx, abort_signal.clone());
-    let silent = ctx.render_mode == RenderMode::Silent;
-    if silent {
-        handler.set_silent(true);
-    }
 
     let (send_ret, render_ret) = tokio::join!(
         client.chat_completions_streaming(input, &mut handler),
-        render_stream(rx, client.app_config(), abort_signal.clone(), silent),
+        render_stream(rx, client.app_config(), abort_signal.clone()),
     );
 
     if handler.abort().aborted() {

src/client/message.rs

@@ -94,21 +94,21 @@ impl MessageContent {
         match self {
             MessageContent::Text(text) => multiline_text(text),
             MessageContent::Array(list) => {
-                let (mut concatenated_text, mut files) = (String::new(), vec![]);
+                let (mut concated_text, mut files) = (String::new(), vec![]);
                 for item in list {
                     match item {
                         MessageContentPart::Text { text } => {
-                            concatenated_text = format!("{concatenated_text} {text}")
+                            concated_text = format!("{concated_text} {text}")
                         }
                         MessageContentPart::ImageUrl { image_url } => {
                             files.push(resolve_url_fn(&image_url.url))
                         }
                     }
                 }
-                if !concatenated_text.is_empty() {
-                    concatenated_text = format!(" -- {}", multiline_text(&concatenated_text))
+                if !concated_text.is_empty() {
+                    concated_text = format!(" -- {}", multiline_text(&concated_text))
                 }
-                format!(".file {}{}", files.join(" "), concatenated_text)
+                format!(".file {}{}", files.join(" "), concated_text)
             }
             MessageContent::ToolCalls(MessageContentToolCalls {
                 tool_results, text, ..
@@ -227,14 +227,9 @@ pub fn patch_messages(messages: &mut Vec<Message>, model: &Model) {
 }
 
 pub fn extract_system_message(messages: &mut Vec<Message>) -> Option<String> {
-    if messages.is_empty() {
-        return None;
-    }
-
     if messages[0].role.is_system() {
         let system_message = messages.remove(0);
         return Some(system_message.content.to_text());
     }
-
     None
 }

src/client/stream.rs

@@ -2,9 +2,9 @@ use super::{ToolCall, catch_error};
 use crate::utils::AbortSignal;
 
 use anyhow::{Context, Result, anyhow, bail};
-use eventsource_stream::Eventsource;
 use futures_util::{Stream, StreamExt};
-use reqwest::{RequestBuilder, header};
+use reqwest::RequestBuilder;
+use reqwest_eventsource::{Error as EventSourceError, Event, RequestBuilderExt};
 use serde_json::Value;
 use tokio::sync::mpsc::UnboundedSender;
 
@@ -16,7 +16,6 @@ pub struct SseHandler {
     last_tool_calls: Vec<ToolCall>,
     max_call_repeats: usize,
     call_repeat_chain_len: usize,
-    silent: bool,
 }
 
 impl SseHandler {
@@ -29,24 +28,14 @@ impl SseHandler {
             last_tool_calls: Vec::new(),
             max_call_repeats: 2,
             call_repeat_chain_len: 3,
-            silent: false,
         }
     }
 
-    pub fn set_silent(&mut self, silent: bool) {
-        self.silent = silent;
-    }
-
     pub fn text(&mut self, text: &str) -> Result<()> {
         if text.is_empty() {
             return Ok(());
         }
         self.buffer.push_str(text);
-
-        if self.silent {
-            return Ok(());
-        }
-
         let ret = self
             .sender
             .send(SseEvent::Text(text.to_string()))
@@ -204,46 +193,11 @@ pub async fn sse_stream<F>(builder: RequestBuilder, mut handle: F) -> Result<()>
 where
     F: FnMut(SseMessage) -> Result<bool>,
 {
-    let res = builder
-        .header(header::ACCEPT, "text/event-stream")
-        .header(header::CACHE_CONTROL, "no-store")
-        .send()
-        .await?;
-    let status = res.status();
-    if !status.is_success() {
-        let text = res.text().await?;
-        let data: Value = match text.parse() {
-            Ok(data) => data,
-            Err(_) => {
-                bail!(
-                    "Invalid response data: {text} (status: {})",
-                    status.as_u16()
-                );
-            }
-        };
-        catch_error(&data, status.as_u16())?;
-        return Ok(());
-    }
-
-    let content_type = res
-        .headers()
-        .get(header::CONTENT_TYPE)
-        .and_then(|value| value.to_str().ok())
-        .map(|value| value.to_string());
-    let is_event_stream = content_type
-        .as_deref()
-        .map(|ct| ct.starts_with("text/event-stream"))
-        .unwrap_or(false);
-    if !is_event_stream {
-        let header_value = content_type.unwrap_or_default();
-        let text = res.text().await?;
-        bail!("Invalid response event-stream. content-type: {header_value}, data: {text}");
-    }
-
-    let mut es = res.bytes_stream().boxed().eventsource();
+    let mut es = builder.eventsource()?;
     while let Some(event) = es.next().await {
         match event {
-            Ok(message) => {
+            Ok(Event::Open) => {}
+            Ok(Event::Message(message)) => {
                 let message = SseMessage {
                     event: message.event,
                     data: message.data,
@@ -253,7 +207,33 @@ where
                 }
             }
             Err(err) => {
-                bail!("{err}");
+                match err {
+                    EventSourceError::StreamEnded => {}
+                    EventSourceError::InvalidStatusCode(status, res) => {
+                        let text = res.text().await?;
+                        let data: Value = match text.parse() {
+                            Ok(data) => data,
+                            Err(_) => {
+                                bail!(
+                                    "Invalid response data: {text} (status: {})",
+                                    status.as_u16()
+                                );
+                            }
+                        };
+                        catch_error(&data, status.as_u16())?;
+                    }
+                    EventSourceError::InvalidContentType(header_value, res) => {
+                        let text = res.text().await?;
+                        bail!(
+                            "Invalid response event-stream. content-type: {}, data: {text}",
+                            header_value.to_str().unwrap_or_default()
+                        );
+                    }
+                    _ => {
+                        bail!("{}", err);
+                    }
+                }
+                es.close();
             }
         }
     }

src/config/agent.rs

@@ -11,8 +11,6 @@ use crate::config::prompts::{
     DEFAULT_SPAWN_INSTRUCTIONS, DEFAULT_TEAMMATE_INSTRUCTIONS, DEFAULT_TODO_INSTRUCTIONS,
     DEFAULT_USER_INTERACTION_INSTRUCTIONS,
 };
-use crate::graph::{Graph, GraphParser, NodeType};
-use crate::rag::RagInitConfig;
 use crate::vault::SECRET_RE;
 use anyhow::{Context, Result};
 use fancy_regex::Captures;
@@ -39,13 +37,12 @@ pub struct Agent {
     session_dynamic_instructions: Option<String>,
     functions: Functions,
     rag: Option<Arc<Rag>>,
-    graph_rags: HashMap<String, Arc<Rag>>,
     model: Model,
     vault: GlobalVault,
 }
 
 impl Agent {
-    pub fn install_builtin_agents(force: bool) -> Result<()> {
+    pub fn install_builtin_agents() -> Result<()> {
         info!(
             "Installing built-in agents in {}",
             paths::agents_data_dir().display()
@@ -65,7 +62,7 @@ impl Agent {
             #[cfg_attr(not(unix), expect(unused))]
             let is_script = matches!(file_extension.as_deref(), Some("sh") | Some("py"));
 
-            if file_path.exists() && !force {
+            if file_path.exists() {
                 debug!(
                     "Agent file already exists, skipping: {}",
                     file_path.display()
@@ -100,28 +97,10 @@ impl Agent {
         let loaders = app.document_loaders.clone();
         let rag_path = paths::agent_rag_file(name, DEFAULT_AGENT_NAME);
         let config_path = paths::agent_config_file(name);
-        let graph_path = paths::agent_graph_file(name);
-        let mut graph_for_rag: Option<Graph> = None;
-        let mut agent_config = match (config_path.exists(), graph_path.exists()) {
-            (true, true) => bail!(
-                "Agent '{name}' has both config.yaml and graph.yaml. A graph agent \
-                 is defined by graph.yaml alone; a normal agent by config.yaml alone. \
-                 Remove one of the two files."
-            ),
-            (true, false) => AgentConfig::load(&config_path)?,
-            (false, true) => {
-                let parser = GraphParser::new(&agent_data_dir);
-                let graph = parser
-                    .load_from_file(&graph_path)
-                    .with_context(|| format!("Failed to load graph.yaml for agent '{name}'"))?;
-                let config = AgentConfig::from_graph(name, &graph);
-                graph_for_rag = Some(graph);
-                config
-            }
-            (false, false) => bail!(
-                "Agent '{name}' has neither a config.yaml nor a graph.yaml at '{}'",
-                agent_data_dir.display()
-            ),
+        let mut agent_config = if config_path.exists() {
+            AgentConfig::load(&config_path)?
+        } else {
+            bail!("Agent config file not found at '{}'", config_path.display())
         };
         let mut functions = Functions::init_agent(name, &agent_config.global_tools)?;
 
@@ -159,16 +138,44 @@ impl Agent {
                     .prompt()?;
             }
             if ans {
-                let document_paths =
-                    resolve_document_paths(&agent_config.documents, &loaders, &agent_data_dir)?;
+                let mut document_paths = vec![];
+                for path in &agent_config.documents {
+                    if is_url(path) {
+                        document_paths.push(path.to_string());
+                    } else if is_loader_protocol(&loaders, path) {
+                        let (protocol, document_path) = path
+                            .split_once(':')
+                            .with_context(|| "Invalid loader protocol path")?;
+                        let resolved_path = resolve_home_dir(document_path);
+                        let new_path = if Path::new(&resolved_path).is_relative() {
+                            safe_join_path(&agent_data_dir, resolved_path)
+                                .ok_or_else(|| anyhow!("Invalid document path: '{path}'"))?
+                        } else {
+                            PathBuf::from(&resolved_path)
+                        };
+                        document_paths.push(format!("{}:{}", protocol, new_path.display()));
+                    } else if Path::new(&resolve_home_dir(path)).is_relative() {
+                        let new_path = safe_join_path(&agent_data_dir, path)
+                            .ok_or_else(|| anyhow!("Invalid document path: '{path}'"))?;
+                        document_paths.push(new_path.display().to_string())
+                    } else {
+                        document_paths.push(path.to_string())
+                    }
+                }
                 let key = RagKey::Agent(name.to_string());
                 let app_clone = app.clone();
                 let rag_path_clone = rag_path.clone();
-                let abort = abort_signal.clone();
                 let rag = app_state
                     .rag_cache
                     .load_with(key, || async move {
-                        Rag::init(&app_clone, "rag", &rag_path_clone, &document_paths, abort).await
+                        Rag::init(
+                            &app_clone,
+                            "rag",
+                            &rag_path_clone,
+                            &document_paths,
+                            abort_signal,
+                        )
+                        .await
                     })
                     .await?;
                 Some(rag)
@@ -179,23 +186,6 @@ impl Agent {
             None
         };
 
-        let graph_rags = match &graph_for_rag {
-            Some(graph) => {
-                init_graph_rags(
-                    app,
-                    app_state,
-                    name,
-                    graph,
-                    &agent_data_dir,
-                    &loaders,
-                    info_flag,
-                    abort_signal.clone(),
-                )
-                .await?
-            }
-            None => HashMap::new(),
-        };
-
         if agent_config.auto_continue {
             functions.append_todo_functions();
         }
@@ -218,7 +208,6 @@ impl Agent {
             session_dynamic_instructions: None,
             functions,
             rag,
-            graph_rags,
             model,
             vault: app_state.vault.clone(),
         })
@@ -298,13 +287,10 @@ impl Agent {
             .display()
             .to_string()
             .into();
-        let config_path = paths::agent_config_file(&self.name);
-        let definition_file = if config_path.exists() {
-            config_path
-        } else {
-            paths::agent_graph_file(&self.name)
-        };
-        value["config_file"] = definition_file.display().to_string().into();
+        value["config_file"] = paths::agent_config_file(&self.name)
+            .display()
+            .to_string()
+            .into();
         let data = serde_yaml::to_string(&value)?;
         Ok(data)
     }
@@ -325,10 +311,6 @@ impl Agent {
         self.rag.clone()
     }
 
-    pub fn graph_rag(&self, node_id: &str) -> Option<Arc<Rag>> {
-        self.graph_rags.get(node_id).cloned()
-    }
-
     pub fn append_mcp_meta_functions(&mut self, mcp_servers: Vec<String>) {
         self.functions.append_mcp_meta_functions(mcp_servers);
     }
@@ -433,14 +415,6 @@ impl Agent {
         self.config.max_auto_continues
     }
 
-    pub fn inject_todo_instructions(&self) -> bool {
-        self.config.inject_todo_instructions
-    }
-
-    pub fn continuation_prompt_value(&self) -> Option<String> {
-        self.config.continuation_prompt.clone()
-    }
-
     pub fn can_spawn_agents(&self) -> bool {
         self.config.can_spawn_agents
     }
@@ -465,6 +439,18 @@ impl Agent {
         self.config.escalation_timeout
     }
 
+    pub fn continuation_prompt(&self) -> String {
+        self.config.continuation_prompt.clone().unwrap_or_else(|| {
+            formatdoc! {"
+                [SYSTEM REMINDER - TODO CONTINUATION]
+                You have incomplete tasks. Rules:
+                1. BEFORE marking a todo done: verify the work compiles/works. No premature completion.
+                2. If a todo is broad (e.g. \"implement X and implement Y\"): break it into specific subtasks FIRST using todo__add, then work on those.\n\
+                3. Each todo should be atomic and be \"single responsibility\" - completable in one focused action.
+                4. Continue with the next pending item now. Call tools immediately."}
+        })
+    }
+
     pub fn compression_threshold(&self) -> Option<usize> {
         self.config.compression_threshold
     }
@@ -668,25 +654,6 @@ impl AgentConfig {
         Ok(agent_config)
     }
 
-    pub fn from_graph(dir_name: &str, graph: &Graph) -> Self {
-        AgentConfig {
-            name: dir_name.to_string(),
-            model_id: graph.model.clone(),
-            temperature: graph.temperature,
-            top_p: graph.top_p,
-            description: graph.description.clone(),
-            global_tools: graph.global_tools.clone(),
-            mcp_servers: graph.mcp_servers.clone(),
-            conversation_starters: graph.conversation_starters.clone(),
-            variables: graph.variables.clone(),
-            can_spawn_agents: graph.has_agent_node(),
-            max_concurrent_agents: default_max_concurrent_agents(),
-            max_agent_depth: default_max_agent_depth(),
-            escalation_timeout: default_escalation_timeout(),
-            ..AgentConfig::default()
-        }
-    }
-
     fn load_envs(&mut self, app: &AppConfig) {
         let name = &self.name;
         let with_prefix = |v: &str| normalize_env_name(&format!("{name}_{v}"));
@@ -783,136 +750,6 @@ pub struct AgentVariable {
     pub value: String,
 }
 
-fn resolve_document_paths(
-    documents: &[String],
-    loaders: &HashMap<String, String>,
-    agent_data_dir: &Path,
-) -> Result<Vec<String>> {
-    let mut document_paths = vec![];
-    for path in documents {
-        if is_url(path) {
-            document_paths.push(path.to_string());
-        } else if is_loader_protocol(loaders, path) {
-            let (protocol, document_path) = path
-                .split_once(':')
-                .with_context(|| "Invalid loader protocol path")?;
-            let resolved_path = resolve_home_dir(document_path);
-            let new_path = if Path::new(&resolved_path).is_relative() {
-                safe_join_path(agent_data_dir, resolved_path)
-                    .ok_or_else(|| anyhow!("Invalid document path: '{path}'"))?
-            } else {
-                PathBuf::from(&resolved_path)
-            };
-
-            document_paths.push(format!("{}:{}", protocol, new_path.display()));
-        } else if Path::new(&resolve_home_dir(path)).is_relative() {
-            let new_path = safe_join_path(agent_data_dir, path)
-                .ok_or_else(|| anyhow!("Invalid document path: '{path}'"))?;
-            document_paths.push(new_path.display().to_string())
-        } else {
-            document_paths.push(path.to_string())
-        }
-    }
-    Ok(document_paths)
-}
-
-#[allow(clippy::too_many_arguments)]
-async fn init_graph_rags(
-    app: &AppConfig,
-    app_state: &AppState,
-    agent_name: &str,
-    graph: &Graph,
-    agent_data_dir: &Path,
-    loaders: &HashMap<String, String>,
-    info_flag: bool,
-    abort_signal: AbortSignal,
-) -> Result<HashMap<String, Arc<Rag>>> {
-    let mut rags = HashMap::new();
-    if info_flag {
-        return Ok(rags);
-    }
-
-    for (node_id, node) in &graph.nodes {
-        let NodeType::Rag(rag_node) = &node.node_type else {
-            continue;
-        };
-        let rag_path = paths::agent_rag_file(agent_name, node_id);
-        let key = RagKey::GraphNode {
-            agent: agent_name.to_string(),
-            node: node_id.clone(),
-        };
-        let rag = if rag_path.exists() {
-            let app_clone = app.clone();
-            let path_clone = rag_path.clone();
-            let name_clone = node_id.clone();
-            app_state
-                .rag_cache
-                .load_with(key, || async move {
-                    Rag::load(&app_clone, &name_clone, &path_clone)
-                })
-                .await?
-        } else {
-            let config = RagInitConfig {
-                embedding_model: rag_node.embedding_model.clone(),
-                chunk_size: rag_node.chunk_size,
-                chunk_overlap: rag_node.chunk_overlap,
-                reranker_model: rag_node.reranker_model.clone(),
-                top_k: rag_node.top_k,
-                batch_size: rag_node.batch_size,
-            };
-            let fully_specified = config.embedding_model.is_some()
-                && config.chunk_size.is_some()
-                && config.chunk_overlap.is_some();
-            if !fully_specified {
-                if !*IS_STDOUT_TERMINAL {
-                    bail!(
-                        "Agent '{agent_name}' requires RAG for rag node '{node_id}', but its \
-                         knowledge base is not built and the node does not fully specify how \
-                         to build it. Set `embedding_model`, `chunk_size`, and `chunk_overlap` \
-                         on the node, or run the agent once interactively."
-                    );
-                }
-
-                let ans = Confirm::new(&format!(
-                    "Initialize RAG knowledge base for rag node '{node_id}'?"
-                ))
-                .with_default(true)
-                .prompt()?;
-
-                if !ans {
-                    bail!(
-                        "Agent '{agent_name}' has rag node '{node_id}' but its RAG was not \
-                         initialized. RAG initialization is required for this agent."
-                    );
-                }
-            }
-
-            let document_paths =
-                resolve_document_paths(&rag_node.documents, loaders, agent_data_dir)?;
-            let app_clone = app.clone();
-            let path_clone = rag_path.clone();
-            let name_clone = node_id.clone();
-            let abort = abort_signal.clone();
-            app_state
-                .rag_cache
-                .load_with(key, || async move {
-                    Rag::init_with_config(
-                        &app_clone,
-                        &name_clone,
-                        &path_clone,
-                        &document_paths,
-                        &config,
-                        abort,
-                    )
-                    .await
-                })
-                .await?
-        };
-        rags.insert(node_id.clone(), rag);
-    }
-    Ok(rags)
-}
-
 pub fn list_agents() -> Vec<String> {
     let agents_data_dir = paths::agents_data_dir();
     if !agents_data_dir.exists() {
@@ -1039,88 +876,4 @@ variables:
         assert!(config.inject_todo_instructions);
         assert!(config.inject_spawn_instructions);
     }
-
-    #[test]
-    fn from_graph_maps_agent_level_fields() {
-        let yaml = formatdoc! {r#"
-            name: graph_name_ignored
-            description: A graph agent
-            model: claude:claude-sonnet-4-6
-            temperature: 0.3
-            top_p: 0.8
-            global_tools:
-              - fetch_pdf.sh
-            mcp_servers:
-              - pubmed-search
-            conversation_starters:
-              - "Start here"
-            start: e
-            nodes:
-              e:
-                id: e
-                type: end
-                output: done
-            "#};
-        let graph: Graph = serde_yaml::from_str(&yaml).unwrap();
-
-        let config = AgentConfig::from_graph("my-agent-dir", &graph);
-
-        assert_eq!(config.name, "my-agent-dir");
-        assert_eq!(config.description, "A graph agent");
-        assert_eq!(config.model_id.as_deref(), Some("claude:claude-sonnet-4-6"));
-        assert_eq!(config.temperature, Some(0.3));
-        assert_eq!(config.top_p, Some(0.8));
-        assert_eq!(config.global_tools, vec!["fetch_pdf.sh"]);
-        assert_eq!(config.mcp_servers, vec!["pubmed-search"]);
-        assert_eq!(config.conversation_starters, vec!["Start here"]);
-    }
-
-    #[test]
-    fn from_graph_derives_can_spawn_agents_from_agent_nodes() {
-        let with_agent = formatdoc! {r#"
-            name: g
-            start: a
-            nodes:
-              a:
-                id: a
-                type: agent
-                agent: helper
-                prompt: hi
-                next: e
-              e:
-                id: e
-                type: end
-                output: done
-            "#};
-        let graph: Graph = serde_yaml::from_str(&with_agent).unwrap();
-        assert!(AgentConfig::from_graph("d", &graph).can_spawn_agents);
-
-        let no_agent =
-            "name: g\nstart: x\nnodes:\n  x:\n    id: x\n    type: end\n    output: ok\n";
-        let graph: Graph = serde_yaml::from_str(no_agent).unwrap();
-        assert!(!AgentConfig::from_graph("d", &graph).can_spawn_agents);
-    }
-
-    #[test]
-    fn from_graph_keeps_defaults_for_llm_loop_fields() {
-        let yaml = "name: g\nstart: x\nnodes:\n  x:\n    id: x\n    type: end\n    output: ok\n";
-        let graph: Graph = serde_yaml::from_str(yaml).unwrap();
-
-        let config = AgentConfig::from_graph("d", &graph);
-
-        assert!(!config.auto_continue);
-        assert!(config.instructions.is_empty());
-        assert!(config.documents.is_empty());
-        assert!(!config.inject_todo_instructions);
-        assert!(!config.inject_spawn_instructions);
-        assert_eq!(config.max_auto_continues, 0);
-        assert_eq!(config.summarization_threshold, 0);
-
-        assert_eq!(
-            config.max_concurrent_agents,
-            default_max_concurrent_agents()
-        );
-        assert_eq!(config.max_agent_depth, default_max_agent_depth());
-        assert_eq!(config.escalation_timeout, default_escalation_timeout());
-    }
 }

src/config/app_config.rs

@@ -39,11 +39,6 @@ pub struct AppConfig {
     pub mapping_mcp_servers: IndexMap<String, String>,
     pub enabled_mcp_servers: Option<String>,
 
-    pub auto_continue: bool,
-    pub max_auto_continues: usize,
-    pub inject_todo_instructions: bool,
-    pub continuation_prompt: Option<String>,
-
     pub repl_prelude: Option<String>,
     pub cmd_prelude: Option<String>,
     pub agent_session: Option<String>,
@@ -100,11 +95,6 @@ impl Default for AppConfig {
             mapping_mcp_servers: Default::default(),
             enabled_mcp_servers: None,
 
-            auto_continue: false,
-            max_auto_continues: 10,
-            inject_todo_instructions: true,
-            continuation_prompt: None,
-
             repl_prelude: None,
             cmd_prelude: None,
             agent_session: None,
@@ -162,11 +152,6 @@ impl AppConfig {
             mapping_mcp_servers: config.mapping_mcp_servers,
             enabled_mcp_servers: config.enabled_mcp_servers,
 
-            auto_continue: config.auto_continue,
-            max_auto_continues: config.max_auto_continues,
-            inject_todo_instructions: config.inject_todo_instructions,
-            continuation_prompt: config.continuation_prompt,
-
             repl_prelude: config.repl_prelude,
             cmd_prelude: config.cmd_prelude,
             agent_session: config.agent_session,

src/config/macros.rs

@@ -85,7 +85,7 @@ impl Macro {
         Ok(value)
     }
 
-    pub fn install_macros(force: bool) -> Result<()> {
+    pub fn install_macros() -> Result<()> {
         info!(
             "Installing built-in macros in {}",
             paths::macros_dir().display()
@@ -98,7 +98,7 @@ impl Macro {
             let content = unsafe { std::str::from_utf8_unchecked(&embedded_file.data) };
             let file_path = paths::macros_dir().join(file.as_ref());
 
-            if file_path.exists() && !force {
+            if file_path.exists() {
                 debug!(
                     "Macro file already exists, skipping: {}",
                     file_path.display()

src/config/mcp_factory.rs

@@ -109,13 +109,12 @@ impl McpFactory {
 mod tests {
     use super::*;
     use crate::mcp::{JsonField, McpServer, McpTransportType};
-    use indexmap::IndexMap;
     use std::collections::HashMap;
 
     fn stdio_spec(
         command: &str,
         args: Option<Vec<String>>,
-        env: Option<IndexMap<String, JsonField>>,
+        env: Option<HashMap<String, JsonField>>,
     ) -> McpServer {
         McpServer {
             transport_type: McpTransportType::Stdio,
@@ -131,7 +130,7 @@ mod tests {
     fn remote_spec(
         transport: McpTransportType,
         url: &str,
-        headers: Option<IndexMap<String, String>>,
+        headers: Option<HashMap<String, String>>,
     ) -> McpServer {
         McpServer {
             transport_type: transport,
@@ -146,7 +145,7 @@ mod tests {
 
     #[test]
     fn key_from_stdio_spec_captures_command_args_env() {
-        let mut env = IndexMap::new();
+        let mut env = HashMap::new();
         env.insert("TOKEN".into(), JsonField::Str("abc".into()));
         let spec = stdio_spec("npx", Some(vec!["-y".into(), "server".into()]), Some(env));
         let key = McpServerKey::from_spec("my-server", &spec);
@@ -164,7 +163,7 @@ mod tests {
 
     #[test]
     fn key_from_stdio_spec_sorts_args_and_env() {
-        let mut env = IndexMap::new();
+        let mut env = HashMap::new();
         env.insert("Z_VAR".into(), JsonField::Str("z".into()));
         env.insert("A_VAR".into(), JsonField::Int(42));
         let spec = stdio_spec(
@@ -223,7 +222,7 @@ mod tests {
 
     #[test]
     fn key_from_remote_sse_spec_with_sorted_headers() {
-        let mut hdrs = IndexMap::new();
+        let mut hdrs = HashMap::new();
         hdrs.insert("Z-Key".into(), "z-val".into());
         hdrs.insert("A-Key".into(), "a-val".into());
         let spec = remote_spec(McpTransportType::Sse, "http://sse.example.com", Some(hdrs));
@@ -265,7 +264,7 @@ mod tests {
 
     #[test]
     fn key_env_bool_and_int_coerce_to_string() {
-        let mut env = IndexMap::new();
+        let mut env = HashMap::new();
         env.insert("FLAG".into(), JsonField::Bool(true));
         env.insert("PORT".into(), JsonField::Int(3000));
         let spec = stdio_spec("cmd", None, Some(env));

src/config/mod.rs

@@ -2,7 +2,6 @@ mod agent;
 mod app_config;
 mod app_state;
 mod input;
-mod install_remote;
 mod macros;
 mod mcp_factory;
 pub(crate) mod paths;
@@ -13,24 +12,19 @@ mod role;
 mod session;
 pub(crate) mod todo;
 mod tool_scope;
-mod update;
 
-pub use self::agent::{
-    Agent, AgentVariable, AgentVariables, complete_agent_variables, list_agents,
-};
+pub use self::agent::{Agent, AgentVariables, complete_agent_variables, list_agents};
 #[allow(unused_imports)]
 pub use self::app_config::AppConfig;
 #[allow(unused_imports)]
 pub use self::app_state::AppState;
 pub use self::input::Input;
-pub use self::install_remote::{install_remote, install_remote_from_repl_args};
 #[allow(unused_imports)]
-pub use self::request_context::{RenderMode, RequestContext};
+pub use self::request_context::RequestContext;
 pub use self::role::{
     CODE_ROLE, CREATE_TITLE_ROLE, EXPLAIN_SHELL_ROLE, Role, RoleLike, SHELL_ROLE,
 };
 use self::session::Session;
-pub use self::update::run_self_update;
 use crate::client::{
     ClientConfig, MessageContentToolCalls, Model, ModelType, OPENAI_COMPATIBLE_PROVIDERS,
     ProviderModels, create_client_config, list_client_types,
@@ -72,7 +66,6 @@ const DARK_THEME: &[u8] = include_bytes!("../../assets/monokai-extended.theme.bi
 const LIGHT_THEME: &[u8] = include_bytes!("../../assets/monokai-extended-light.theme.bin");
 
 const CONFIG_FILE_NAME: &str = "config.yaml";
-const AGENT_GRAPH_FILE_NAME: &str = "graph.yaml";
 const ROLES_DIR_NAME: &str = "roles";
 const MACROS_DIR_NAME: &str = "macros";
 const ENV_FILE_NAME: &str = ".env";
@@ -86,26 +79,6 @@ const GLOBAL_TOOLS_DIR_NAME: &str = "tools";
 const GLOBAL_TOOLS_UTILS_DIR_NAME: &str = "utils";
 const BASH_PROMPT_UTILS_FILE_NAME: &str = "prompt-utils.sh";
 const MCP_FILE_NAME: &str = "mcp.json";
-const DEFAULT_VISIBLE_TOOLS: [&str; 18] = [
-    "execute_command.sh",
-    "execute_py_code.py",
-    "execute_sql_code.sh",
-    "fetch_url_via_curl.sh",
-    "fs_cat.sh",
-    "fs_glob.sh",
-    "fs_grep.sh",
-    "fs_ls.sh",
-    "fs_mkdir.sh",
-    "fs_patch.sh",
-    "fs_read.sh",
-    "fs_rm.sh",
-    "fs_write.sh",
-    "get_current_time.sh",
-    "get_current_weather.sh",
-    "search_wikipedia.sh",
-    "search_arxiv.sh",
-    "web_search_loki.sh",
-];
 
 const CLIENTS_FIELD: &str = "clients";
 
@@ -148,11 +121,6 @@ pub struct Config {
     pub mapping_mcp_servers: IndexMap<String, String>,
     pub enabled_mcp_servers: Option<String>,
 
-    pub auto_continue: bool,
-    pub max_auto_continues: usize,
-    pub inject_todo_instructions: bool,
-    pub continuation_prompt: Option<String>,
-
     pub repl_prelude: Option<String>,
     pub cmd_prelude: Option<String>,
     pub agent_session: Option<String>,
@@ -209,11 +177,6 @@ impl Default for Config {
             mapping_mcp_servers: Default::default(),
             enabled_mcp_servers: None,
 
-            auto_continue: false,
-            max_auto_continues: 10,
-            inject_todo_instructions: true,
-            continuation_prompt: None,
-
             repl_prelude: None,
             cmd_prelude: None,
             agent_session: None,
@@ -247,110 +210,12 @@ impl Default for Config {
 }
 
 pub fn install_builtins() -> Result<()> {
-    Functions::install_builtin_global_tools(false)?;
-    Agent::install_builtin_agents(false)?;
-    Macro::install_macros(false)?;
+    Functions::install_builtin_global_tools()?;
+    Agent::install_builtin_agents()?;
+    Macro::install_macros()?;
     Ok(())
 }
 
-#[derive(Debug, Clone, Copy, PartialEq, Eq, clap::ValueEnum)]
-pub enum AssetCategory {
-    Agents,
-    Macros,
-    Functions,
-    #[value(name = "mcp_config")]
-    McpConfig,
-}
-
-impl AssetCategory {
-    pub const NAMES: [&'static str; 4] = ["agents", "macros", "functions", "mcp_config"];
-
-    pub fn parse(name: &str) -> Option<Self> {
-        match name {
-            "agents" => Some(Self::Agents),
-            "macros" => Some(Self::Macros),
-            "functions" => Some(Self::Functions),
-            "mcp_config" => Some(Self::McpConfig),
-            _ => None,
-        }
-    }
-}
-
-#[derive(Debug, Clone, Copy, PartialEq, Eq, clap::ValueEnum)]
-pub enum InstallFilter {
-    Agents,
-    Roles,
-    Macros,
-    Functions,
-    #[value(name = "mcp_config")]
-    McpConfig,
-}
-
-impl InstallFilter {
-    pub const NAMES: [&'static str; 5] = ["agents", "roles", "macros", "functions", "mcp_config"];
-
-    pub fn parse(name: &str) -> Option<Self> {
-        match name {
-            "agents" => Some(Self::Agents),
-            "roles" => Some(Self::Roles),
-            "macros" => Some(Self::Macros),
-            "functions" => Some(Self::Functions),
-            "mcp_config" => Some(Self::McpConfig),
-            _ => None,
-        }
-    }
-}
-
-pub fn install_assets(category: AssetCategory) -> Result<()> {
-    let (label, target) = match category {
-        AssetCategory::Agents => ("agents", paths::agents_data_dir()),
-        AssetCategory::Macros => ("macros", paths::macros_dir()),
-        AssetCategory::Functions => ("functions", paths::functions_dir()),
-        AssetCategory::McpConfig => ("MCP config", paths::mcp_config_file()),
-    };
-
-    if !confirm_asset_overwrite(category, label, &target)? {
-        println!("Aborted. No files were changed.");
-        return Ok(());
-    }
-
-    match category {
-        AssetCategory::Agents => Agent::install_builtin_agents(true)?,
-        AssetCategory::Macros => Macro::install_macros(true)?,
-        AssetCategory::Functions => Functions::install_builtin_global_tools(true)?,
-        AssetCategory::McpConfig => Functions::install_mcp_config()?,
-    }
-
-    println!("Reinstalled bundled {label} ({})", target.display());
-
-    Ok(())
-}
-
-fn confirm_asset_overwrite(category: AssetCategory, label: &str, target: &Path) -> Result<bool> {
-    if !*IS_STDOUT_TERMINAL {
-        return Ok(true);
-    }
-    let body = match category {
-        AssetCategory::McpConfig => format!(
-            "This replaces your MCP server configuration at {} with this \
-             build's bundled template. Your configured MCP servers (and any \
-             custom secret references they contain) will be lost.",
-            target.display()
-        ),
-        _ => format!(
-            "Reinstalling bundled {label} overwrites every bundled {label} in \
-             {} with this build's packaged versions. Local changes to bundled \
-             {label} will be lost; {label} you created yourself are left \
-             untouched.",
-            target.display()
-        ),
-    };
-    let prompt = format!("{} {body}\nContinue? [y/N] ", warning_text("WARNING:"));
-    let answer = read_single_key(&['y', 'Y', 'n', 'N'], 'n', &prompt)?;
-
-    Ok(matches!(answer, 'y' | 'Y'))
-}
-
 pub fn default_sessions_dir() -> PathBuf {
     match env::var(get_env_name("sessions_dir")) {
         Ok(value) => PathBuf::from(value),
@@ -609,18 +474,6 @@ pub async fn create_config_file(config_path: &Path) -> Result<()> {
     let (model, clients_config) = create_client_config(client, &vault).await?;
     config["model"] = model.into();
     config["vault_password_file"] = vault.password_file()?.display().to_string().into();
-    config["stream"] = json!(true);
-    config["save"] = json!(true);
-    config["keybindings"] = json!("vi");
-    config["wrap"] = json!("auto");
-    config["wrap_code"] = json!(false);
-    config["function_calling_support"] = json!(true);
-    config["enabled_tools"] = json!(null);
-    config["visible_tools"] = json!(DEFAULT_VISIBLE_TOOLS);
-    config["mcp_server_support"] = json!(true);
-    config["enabled_mcp_servers"] = json!(null);
-    config["highlight"] = json!(true);
-    config["light_theme"] = json!(false);
     config[CLIENTS_FIELD] = clients_config;
 
     let config_data = serde_yaml::to_string(&config).with_context(|| "Failed to create config")?;

src/config/paths.rs

@@ -1,9 +1,8 @@
 use super::role::Role;
 use super::{
-    AGENT_GRAPH_FILE_NAME, AGENTS_DIR_NAME, BASH_PROMPT_UTILS_FILE_NAME, CONFIG_FILE_NAME,
-    ENV_FILE_NAME, FUNCTIONS_BIN_DIR_NAME, FUNCTIONS_DIR_NAME, GLOBAL_TOOLS_DIR_NAME,
-    GLOBAL_TOOLS_UTILS_DIR_NAME, MACROS_DIR_NAME, MCP_FILE_NAME, ModelsOverride, RAGS_DIR_NAME,
-    ROLES_DIR_NAME,
+    AGENTS_DIR_NAME, BASH_PROMPT_UTILS_FILE_NAME, CONFIG_FILE_NAME, ENV_FILE_NAME,
+    FUNCTIONS_BIN_DIR_NAME, FUNCTIONS_DIR_NAME, GLOBAL_TOOLS_DIR_NAME, GLOBAL_TOOLS_UTILS_DIR_NAME,
+    MACROS_DIR_NAME, MCP_FILE_NAME, ModelsOverride, RAGS_DIR_NAME, ROLES_DIR_NAME,
 };
 use crate::client::ProviderModels;
 use crate::utils::{get_env_name, list_file_names, normalize_env_name};
@@ -128,10 +127,6 @@ pub fn agent_data_dir(name: &str) -> PathBuf {
     }
 }
 
-pub fn agent_graph_file(agent_name: &str) -> PathBuf {
-    agent_data_dir(agent_name).join(AGENT_GRAPH_FILE_NAME)
-}
-
 pub fn agent_config_file(name: &str) -> PathBuf {
     match env::var(format!("{}_CONFIG_FILE", normalize_env_name(name))) {
         Ok(value) => PathBuf::from(value),

src/config/rag_cache.rs

@@ -9,7 +9,6 @@ use std::sync::{Arc, Weak};
 pub enum RagKey {
     Named(String),
     Agent(String),
-    GraphNode { agent: String, node: String },
 }
 
 #[derive(Default)]

src/config/request_context.rs

@@ -1,14 +1,14 @@
+use super::MessageContentToolCalls;
 use super::rag_cache::{RagCache, RagKey};
 use super::session::Session;
 use super::todo::TodoList;
 use super::tool_scope::{McpRuntime, ToolScope};
 use super::{
-    AGENTS_DIR_NAME, Agent, AgentVariables, AppConfig, AppState, AssetCategory, CREATE_TITLE_ROLE,
-    Input, InstallFilter, LEFT_PROMPT, LastMessage, MESSAGES_FILE_NAME, RIGHT_PROMPT, Role,
-    RoleLike, SESSIONS_DIR_NAME, SUMMARIZATION_PROMPT, SUMMARY_CONTEXT_PROMPT, StateFlags,
-    TEMP_ROLE_NAME, TEMP_SESSION_NAME, WorkingMode, ensure_parent_exists, list_agents, paths,
+    AGENTS_DIR_NAME, Agent, AgentVariables, AppConfig, AppState, CREATE_TITLE_ROLE, Input,
+    LEFT_PROMPT, LastMessage, MESSAGES_FILE_NAME, RIGHT_PROMPT, Role, RoleLike, SESSIONS_DIR_NAME,
+    SUMMARIZATION_PROMPT, SUMMARY_CONTEXT_PROMPT, StateFlags, TEMP_ROLE_NAME, TEMP_SESSION_NAME,
+    WorkingMode, ensure_parent_exists, list_agents, paths,
 };
-use super::{MessageContentToolCalls, prompts};
 use crate::client::{Model, ModelType, list_models};
 use crate::function::{
     FunctionDeclaration, Functions, ToolCallTracker, ToolResult,
@@ -27,33 +27,16 @@ use crate::utils::{
     list_file_names, now, render_prompt, temp_file,
 };
 
-use crate::graph;
 use anyhow::{Context, Error, Result, bail};
-#[cfg(test)]
-use indexmap::IndexMap;
 use indoc::formatdoc;
 use inquire::{Confirm, MultiSelect, Text, list_option::ListOption, validator::Validation};
 use parking_lot::RwLock;
 use std::collections::{HashMap, HashSet};
+use std::env;
 use std::fs::{File, OpenOptions, read_dir, read_to_string, remove_dir_all, remove_file};
 use std::io::Write;
 use std::path::{Path, PathBuf};
 use std::sync::Arc;
-use std::{env, fs};
-
-pub struct AutoContinueConfig {
-    pub enabled: bool,
-    pub max_continues: usize,
-    pub inject_instructions: bool,
-    pub continuation_prompt: Option<String>,
-}
-
-#[derive(Debug, Clone, Copy, PartialEq, Eq, Default)]
-pub enum RenderMode {
-    #[default]
-    Streaming,
-    Silent,
-}
 
 pub struct RequestContext {
     pub app: Arc<AppState>,
@@ -83,8 +66,6 @@ pub struct RequestContext {
     pub auto_continue_count: usize,
     pub todo_list: TodoList,
     pub last_continuation_response: Option<String>,
-
-    pub render_mode: RenderMode,
 }
 
 impl RequestContext {
@@ -111,7 +92,6 @@ impl RequestContext {
             auto_continue_count: 0,
             todo_list: TodoList::default(),
             last_continuation_response: None,
-            render_mode: RenderMode::default(),
         }
     }
 
@@ -158,51 +138,9 @@ impl RequestContext {
             auto_continue_count: 0,
             todo_list: TodoList::default(),
             last_continuation_response: None,
-            render_mode: RenderMode::default(),
         })
     }
 
-    /// Forks the context for one parallel branch of a graph super-step.
-    ///
-    /// Each branch gets a fresh, owned clone. Mutations (role swap,
-    /// `before/after_chat_completion`, tool tracker, last_message, etc.) are
-    /// scoped to the branch and discarded when the branch finishes. The
-    /// user-visible state communication happens through the graph's
-    /// `StateManager` (via `fork_for_branch_state` + `diff_against` +
-    /// `apply_branch_writes` reducers), and not through `RequestContext`.
-    ///
-    /// Distinction from `new_for_child`: `new_for_child` builds a fresh context
-    /// for a spawned sub-agent (different agent identity, different supervisor
-    /// hierarchy, depth+1, fresh tool tracker). `fork_for_branch` keeps the
-    /// caller's identity and supervisor hierarchy; it's a sibling clone of the
-    /// same logical agent, running one of N parallel work items.
-    pub fn fork_for_branch(&self) -> Self {
-        Self {
-            app: Arc::clone(&self.app),
-            macro_flag: self.macro_flag,
-            info_flag: self.info_flag,
-            working_mode: self.working_mode,
-            model: self.model.clone(),
-            agent_variables: self.agent_variables.clone(),
-            role: self.role.clone(),
-            session: self.session.clone(),
-            rag: self.rag.clone(),
-            agent: self.agent.clone(),
-            last_message: self.last_message.clone(),
-            tool_scope: self.tool_scope.clone(),
-            supervisor: self.supervisor.clone(),
-            parent_supervisor: self.parent_supervisor.clone(),
-            self_agent_id: self.self_agent_id.clone(),
-            inbox: self.inbox.clone(),
-            escalation_queue: self.escalation_queue.clone(),
-            current_depth: self.current_depth,
-            auto_continue_count: 0,
-            todo_list: self.todo_list.clone(),
-            last_continuation_response: None,
-            render_mode: self.render_mode,
-        }
-    }
-
     pub fn new_for_child(
         app: Arc<AppState>,
         parent: &Self,
@@ -238,7 +176,6 @@ impl RequestContext {
             auto_continue_count: 0,
             todo_list: TodoList::default(),
             last_continuation_response: None,
-            render_mode: parent.render_mode,
         }
     }
 
@@ -586,7 +523,7 @@ impl RequestContext {
     }
 
     pub fn extract_role(&self, app: &AppConfig) -> Role {
-        let mut role = if let Some(session) = self.session.as_ref() {
+        if let Some(session) = self.session.as_ref() {
             session.to_role()
         } else if let Some(agent) = self.agent.as_ref() {
             agent.to_role()
@@ -602,65 +539,6 @@ impl RequestContext {
                 app.enabled_mcp_servers.clone(),
             );
             role
-        };
-
-        if self.agent.is_none() && self.app.config.function_calling_support {
-            let config = self.auto_continue_config();
-            if config.enabled && config.inject_instructions {
-                role.append_to_prompt(prompts::DEFAULT_TODO_INSTRUCTIONS);
-            }
-        }
-
-        role
-    }
-
-    pub fn auto_continue_config(&self) -> AutoContinueConfig {
-        if let Some(agent) = &self.agent {
-            return AutoContinueConfig {
-                enabled: agent.auto_continue_enabled(),
-                max_continues: agent.max_auto_continues(),
-                inject_instructions: agent.inject_todo_instructions(),
-                continuation_prompt: agent.continuation_prompt_value(),
-            };
-        }
-        let app = &self.app.config;
-        let enabled = self
-            .session
-            .as_ref()
-            .and_then(|s| s.auto_continue())
-            .or_else(|| self.role.as_ref().and_then(|r| r.auto_continue()))
-            .unwrap_or(app.auto_continue);
-        let max = self
-            .session
-            .as_ref()
-            .and_then(|s| s.max_auto_continues())
-            .or_else(|| self.role.as_ref().and_then(|r| r.max_auto_continues()))
-            .unwrap_or(app.max_auto_continues);
-        let inject = self
-            .session
-            .as_ref()
-            .and_then(|s| s.inject_todo_instructions())
-            .or_else(|| {
-                self.role
-                    .as_ref()
-                    .and_then(|r| r.inject_todo_instructions())
-            })
-            .unwrap_or(app.inject_todo_instructions);
-        let prompt = self
-            .session
-            .as_ref()
-            .and_then(|s| s.continuation_prompt().map(|v| v.to_string()))
-            .or_else(|| {
-                self.role
-                    .as_ref()
-                    .and_then(|r| r.continuation_prompt().map(|v| v.to_string()))
-            })
-            .or_else(|| app.continuation_prompt.clone());
-        AutoContinueConfig {
-            enabled,
-            max_continues: max,
-            inject_instructions: inject,
-            continuation_prompt: prompt,
         }
     }
 
@@ -869,8 +747,6 @@ impl RequestContext {
                 app.function_calling_support.to_string(),
             ),
             ("mcp_server_support", app.mcp_server_support.to_string()),
-            ("auto_continue", app.auto_continue.to_string()),
-            ("max_auto_continues", app.max_auto_continues.to_string()),
             ("stream", app.stream.to_string()),
             ("save", app.save.to_string()),
             ("keybindings", app.keybindings.clone()),
@@ -1046,12 +922,9 @@ impl RequestContext {
         let app = self.app.config.as_ref();
         let mut functions = vec![];
         if app.function_calling_support {
-            // Compute the set of tool names enabled by the role filter, drawn
-            // from BOTH the tool_scope pool and the agent's pool so that an
-            // explicit `enabled_tools` list (e.g. from a graph LLM node) can
-            // narrow the agent's own custom tools too.
-            let role_filter: Option<HashSet<String>> = role.enabled_tools().map(|enabled_tools| {
-                let mut declaration_names: HashSet<String> = self
+            if let Some(enabled_tools) = role.enabled_tools() {
+                let mut tool_names: HashSet<String> = Default::default();
+                let declaration_names: HashSet<String> = self
                     .tool_scope
                     .functions
                     .declarations()
@@ -1063,32 +936,11 @@ impl RequestContext {
                     })
                     .map(|v| v.name.to_string())
                     .collect();
-
-                if let Some(agent) = &self.agent {
-                    declaration_names.extend(
-                        agent
-                            .functions()
-                            .declarations()
-                            .iter()
-                            .filter(|v| {
-                                !v.name.starts_with(MCP_INVOKE_META_FUNCTION_NAME_PREFIX)
-                                    && !v.name.starts_with(MCP_SEARCH_META_FUNCTION_NAME_PREFIX)
-                                    && !v.name.starts_with(MCP_DESCRIBE_META_FUNCTION_NAME_PREFIX)
-                            })
-                            .map(|v| v.name.to_string()),
-                    );
-                }
-
-                let mut tool_names: HashSet<String> = Default::default();
                 if enabled_tools == "all" {
                     tool_names.extend(declaration_names);
                 } else {
                     for item in enabled_tools.split(',') {
                         let item = item.trim();
-                        if item.is_empty() {
-                            continue;
-                        }
-
                         if let Some(values) = app.mapping_tools.get(item) {
                             tool_names.extend(
                                 values
@@ -1101,10 +953,6 @@ impl RequestContext {
                         }
                     }
                 }
-                tool_names
-            });
-
-            if let Some(ref tool_names) = role_filter {
                 functions = self
                     .tool_scope
                     .functions
@@ -1147,11 +995,6 @@ impl RequestContext {
                             && !v.name.starts_with(MCP_DESCRIBE_META_FUNCTION_NAME_PREFIX)
                     })
                     .collect();
-
-                if let Some(ref tool_names) = role_filter {
-                    agent_functions.retain(|v| tool_names.contains(&v.name));
-                }
-
                 let tool_names: HashSet<String> = agent_functions
                     .iter()
                     .filter_map(|v| {
@@ -1178,88 +1021,63 @@ impl RequestContext {
         let app = self.app.config.as_ref();
         let mut mcp_functions = vec![];
         if app.mcp_server_support {
-            let role_filter: Option<HashSet<String>> =
-                role.enabled_mcp_servers().map(|enabled_mcp_servers| {
-                    let mut mcp_declaration_names: HashSet<String> = self
-                        .tool_scope
-                        .functions
-                        .declarations()
-                        .iter()
-                        .filter(|v| {
-                            v.name.starts_with(MCP_INVOKE_META_FUNCTION_NAME_PREFIX)
-                                || v.name.starts_with(MCP_SEARCH_META_FUNCTION_NAME_PREFIX)
-                                || v.name.starts_with(MCP_DESCRIBE_META_FUNCTION_NAME_PREFIX)
-                        })
-                        .map(|v| v.name.to_string())
-                        .collect();
-                    if let Some(agent) = &self.agent {
-                        mcp_declaration_names.extend(
-                            agent
-                                .functions()
-                                .declarations()
-                                .iter()
-                                .filter(|v| {
-                                    v.name.starts_with(MCP_INVOKE_META_FUNCTION_NAME_PREFIX)
-                                        || v.name.starts_with(MCP_SEARCH_META_FUNCTION_NAME_PREFIX)
-                                        || v.name
-                                            .starts_with(MCP_DESCRIBE_META_FUNCTION_NAME_PREFIX)
-                                })
-                                .map(|v| v.name.to_string()),
-                        );
-                    }
-
-                    let mut server_names: HashSet<String> = Default::default();
-                    if enabled_mcp_servers == "all" {
-                        server_names.extend(mcp_declaration_names);
-                    } else {
-                        for item in enabled_mcp_servers.split(',') {
-                            let item = item.trim();
-                            if item.is_empty() {
-                                continue;
-                            }
-
-                            let item_invoke_name =
-                                format!("{}_{item}", MCP_INVOKE_META_FUNCTION_NAME_PREFIX);
-                            let item_search_name =
-                                format!("{}_{item}", MCP_SEARCH_META_FUNCTION_NAME_PREFIX);
-                            let item_describe_name =
-                                format!("{}_{item}", MCP_DESCRIBE_META_FUNCTION_NAME_PREFIX);
-                            if let Some(values) = app.mapping_mcp_servers.get(item) {
-                                server_names.extend(
-                                    values
-                                        .split(',')
-                                        .flat_map(|v| {
-                                            vec![
-                                                format!(
-                                                    "{}_{}",
-                                                    MCP_INVOKE_META_FUNCTION_NAME_PREFIX,
-                                                    v.to_string()
-                                                ),
-                                                format!(
-                                                    "{}_{}",
-                                                    MCP_SEARCH_META_FUNCTION_NAME_PREFIX,
-                                                    v.to_string()
-                                                ),
-                                                format!(
-                                                    "{}_{}",
-                                                    MCP_DESCRIBE_META_FUNCTION_NAME_PREFIX,
-                                                    v.to_string()
-                                                ),
-                                            ]
-                                        })
-                                        .filter(|v| mcp_declaration_names.contains(v)),
-                                )
-                            } else if mcp_declaration_names.contains(&item_invoke_name) {
-                                server_names.insert(item_invoke_name);
-                                server_names.insert(item_search_name);
-                                server_names.insert(item_describe_name);
-                            }
+            if let Some(enabled_mcp_servers) = role.enabled_mcp_servers() {
+                let mut server_names: HashSet<String> = Default::default();
+                let mcp_declaration_names: HashSet<String> = self
+                    .tool_scope
+                    .functions
+                    .declarations()
+                    .iter()
+                    .filter(|v| {
+                        v.name.starts_with(MCP_INVOKE_META_FUNCTION_NAME_PREFIX)
+                            || v.name.starts_with(MCP_SEARCH_META_FUNCTION_NAME_PREFIX)
+                            || v.name.starts_with(MCP_DESCRIBE_META_FUNCTION_NAME_PREFIX)
+                    })
+                    .map(|v| v.name.to_string())
+                    .collect();
+                if enabled_mcp_servers == "all" {
+                    server_names.extend(mcp_declaration_names);
+                } else {
+                    for item in enabled_mcp_servers.split(',') {
+                        let item = item.trim();
+                        let item_invoke_name =
+                            format!("{}_{item}", MCP_INVOKE_META_FUNCTION_NAME_PREFIX);
+                        let item_search_name =
+                            format!("{}_{item}", MCP_SEARCH_META_FUNCTION_NAME_PREFIX);
+                        let item_describe_name =
+                            format!("{}_{item}", MCP_DESCRIBE_META_FUNCTION_NAME_PREFIX);
+                        if let Some(values) = app.mapping_mcp_servers.get(item) {
+                            server_names.extend(
+                                values
+                                    .split(',')
+                                    .flat_map(|v| {
+                                        vec![
+                                            format!(
+                                                "{}_{}",
+                                                MCP_INVOKE_META_FUNCTION_NAME_PREFIX,
+                                                v.to_string()
+                                            ),
+                                            format!(
+                                                "{}_{}",
+                                                MCP_SEARCH_META_FUNCTION_NAME_PREFIX,
+                                                v.to_string()
+                                            ),
+                                            format!(
+                                                "{}_{}",
+                                                MCP_DESCRIBE_META_FUNCTION_NAME_PREFIX,
+                                                v.to_string()
+                                            ),
+                                        ]
+                                    })
+                                    .filter(|v| mcp_declaration_names.contains(v)),
+                            )
+                        } else if mcp_declaration_names.contains(&item_invoke_name) {
+                            server_names.insert(item_invoke_name);
+                            server_names.insert(item_search_name);
+                            server_names.insert(item_describe_name);
                         }
                     }
-                    server_names
-                });
-
-            if let Some(ref server_names) = role_filter {
+                }
                 mcp_functions = self
                     .tool_scope
                     .functions
@@ -1287,11 +1105,6 @@ impl RequestContext {
                             || v.name.starts_with(MCP_DESCRIBE_META_FUNCTION_NAME_PREFIX)
                     })
                     .collect();
-
-                if let Some(ref server_names) = role_filter {
-                    agent_functions.retain(|v| server_names.contains(&v.name));
-                }
-
                 let tool_names: HashSet<String> = agent_functions
                     .iter()
                     .filter_map(|v| {
@@ -1399,19 +1212,6 @@ impl RequestContext {
         Ok(())
     }
 
-    pub fn edit_mcp_config(&self) -> Result<()> {
-        let mcp_path = paths::mcp_config_file();
-        let editor = self.app.config.editor()?;
-        edit_file(&editor, &mcp_path)?;
-        println!(
-            "NOTE: Remember to restart {} for changes to '{}' to take effect",
-            env!("CARGO_CRATE_NAME"),
-            mcp_path.display(),
-        );
-
-        Ok(())
-    }
-
     pub fn new_role(&self, app: &AppConfig, name: &str) -> Result<()> {
         if self.macro_flag {
             bail!("No role");
@@ -1486,30 +1286,21 @@ impl RequestContext {
             Some(agent) => agent.name(),
             None => bail!("No agent"),
         };
-        let config_path = paths::agent_config_file(agent_name);
-        let graph_path = paths::agent_graph_file(agent_name);
-        let target_path = if !config_path.exists() && graph_path.exists() {
-            graph_path
-        } else {
-            config_path
-        };
-
-        ensure_parent_exists(&target_path)?;
-        if !target_path.exists() {
-            fs::write(
-                &target_path,
+        let agent_config_path = paths::agent_config_file(agent_name);
+        ensure_parent_exists(&agent_config_path)?;
+        if !agent_config_path.exists() {
+            std::fs::write(
+                &agent_config_path,
                 "# see https://github.com/Dark-Alex-17/loki/blob/main/config.agent.example.yaml\n",
             )
-            .with_context(|| format!("Failed to write to '{}'", target_path.display()))?;
+            .with_context(|| format!("Failed to write to '{}'", agent_config_path.display()))?;
         }
-
         let editor = app.editor()?;
-        edit_file(&editor, &target_path)?;
+        edit_file(&editor, &agent_config_path)?;
         println!(
             "NOTE: Remember to reload the agent if there are changes made to '{}'",
-            target_path.display()
+            agent_config_path.display()
         );
-
         Ok(())
     }
 
@@ -1611,24 +1402,12 @@ impl RequestContext {
     }
 
     pub async fn update(&mut self, data: &str, abort_signal: AbortSignal) -> Result<()> {
-        let (key, raw_value) = match data.split_once(char::is_whitespace) {
-            Some((k, v)) => (k, v.trim()),
-            None => bail!("Usage: .set <key> <value>. If value is null, unset key."),
-        };
-
-        if raw_value.is_empty() {
+        let parts: Vec<&str> = data.split_whitespace().collect();
+        if parts.len() != 2 {
             bail!("Usage: .set <key> <value>. If value is null, unset key.");
         }
-
-        let value = match key {
-            "continuation_prompt" => raw_value,
-            _ => {
-                if raw_value.contains(char::is_whitespace) {
-                    bail!("Usage: .set <key> <value>. If value is null, unset key.");
-                }
-                raw_value
-            }
-        };
+        let key = parts[0];
+        let value = parts[1];
         match key {
             "temperature" => {
                 let value = super::parse_value(value)?;
@@ -1743,49 +1522,6 @@ impl RequestContext {
                 let value = value.parse().with_context(|| "Invalid value")?;
                 self.update_app_config(|app| app.highlight = value);
             }
-            "auto_continue" => {
-                let value: bool = value.parse().with_context(|| "Invalid value")?;
-                if value && !self.app.config.function_calling_support {
-                    bail!(
-                        "Cannot enable auto_continue: function calling is disabled. Set 'function_calling_support: true' first."
-                    );
-                }
-                if let Some(session) = self.session.as_mut() {
-                    session.set_auto_continue(Some(value));
-                } else {
-                    self.update_app_config(|app| app.auto_continue = value);
-                }
-                if value
-                    && self.app.config.function_calling_support
-                    && !self.tool_scope.functions.contains("todo__init")
-                {
-                    self.tool_scope.functions.append_todo_functions();
-                }
-            }
-            "max_auto_continues" => {
-                let value: usize = value.parse().with_context(|| "Invalid value")?;
-                if let Some(session) = self.session.as_mut() {
-                    session.set_max_auto_continues(Some(value));
-                } else {
-                    self.update_app_config(|app| app.max_auto_continues = value);
-                }
-            }
-            "inject_todo_instructions" => {
-                let value: bool = value.parse().with_context(|| "Invalid value")?;
-                if let Some(session) = self.session.as_mut() {
-                    session.set_inject_todo_instructions(Some(value));
-                } else {
-                    self.update_app_config(|app| app.inject_todo_instructions = value);
-                }
-            }
-            "continuation_prompt" => {
-                let value: Option<String> = super::parse_value(value)?;
-                if let Some(session) = self.session.as_mut() {
-                    session.set_continuation_prompt(value);
-                } else {
-                    self.update_app_config(|app| app.continuation_prompt = value);
-                }
-            }
             _ => bail!("Unknown key '{key}'"),
         }
         Ok(())
@@ -1855,12 +1591,6 @@ impl RequestContext {
                 }
                 ".rag" => super::map_completion_values(paths::list_rags()),
                 ".agent" => super::map_completion_values(list_agents()),
-                ".install" => {
-                    let mut values: Vec<String> =
-                        AssetCategory::NAMES.iter().map(|s| s.to_string()).collect();
-                    values.push("remote".to_string());
-                    super::map_completion_values(values)
-                }
                 ".macro" => super::map_completion_values(paths::list_macros()),
                 ".starter" => match &self.agent {
                     Some(agent) => agent
@@ -1873,14 +1603,10 @@ impl RequestContext {
                 },
                 ".set" => {
                     let mut values = vec![
-                        "auto_continue",
-                        "continuation_prompt",
                         "temperature",
                         "top_p",
                         "enabled_tools",
                         "enabled_mcp_servers",
-                        "inject_todo_instructions",
-                        "max_auto_continues",
                         "save_session",
                         "compression_threshold",
                         "rag_reranker_model",
@@ -1916,28 +1642,6 @@ impl RequestContext {
                 }
                 _ => vec![],
             };
-        } else if cmd == ".install" && args.first() == Some(&"remote") && args.len() >= 2 {
-            let prev = args.get(args.len() - 2).copied().unwrap_or("");
-            if prev == "--filter" {
-                values = super::map_completion_values(
-                    InstallFilter::NAMES.iter().map(|s| s.to_string()).collect(),
-                );
-            } else {
-                let has_filter = args.iter().enumerate().any(|(i, a)| {
-                    a.starts_with("--filter=") || (*a == "--filter" && i < args.len() - 1)
-                });
-                let has_force = args.contains(&"--force");
-                let mut available: Vec<&str> = vec![];
-
-                if !has_filter {
-                    available.push("--filter");
-                }
-                if !has_force {
-                    available.push("--force");
-                }
-
-                values = super::map_completion_values(available);
-            }
         } else if cmd == ".set" && args.len() == 2 {
             let candidates = match args[0] {
                 "max_output_tokens" => match self.current_model().max_output_tokens() {
@@ -2017,19 +1721,6 @@ impl RequestContext {
                     .map(|v| v.id())
                     .collect(),
                 "highlight" => super::complete_bool(app.highlight),
-                "auto_continue" => {
-                    let config = self.auto_continue_config();
-                    super::complete_bool(config.enabled)
-                }
-                "max_auto_continues" => {
-                    let config = self.auto_continue_config();
-                    vec![config.max_continues.to_string()]
-                }
-                "inject_todo_instructions" => {
-                    let config = self.auto_continue_config();
-                    super::complete_bool(config.inject_instructions)
-                }
-                "continuation_prompt" => vec!["null".to_string()],
                 _ => vec![],
             };
             values = candidates.into_iter().map(|v| (v, None)).collect();
@@ -2044,7 +1735,7 @@ impl RequestContext {
                 .collect();
         } else if cmd == ".agent" {
             if args.len() == 2 {
-                let dir = paths::agent_data_dir(args[0]).join(SESSIONS_DIR_NAME);
+                let dir = paths::agent_data_dir(args[0]).join(super::SESSIONS_DIR_NAME);
                 values = list_file_names(dir, ".yaml")
                     .into_iter()
                     .map(|v| (v, None))
@@ -2119,12 +1810,6 @@ impl RequestContext {
         if self.working_mode.is_repl() {
             functions.append_user_interaction_functions();
         }
-        if self.agent.is_none()
-            && app.function_calling_support
-            && self.auto_continue_config().enabled
-        {
-            functions.append_todo_functions();
-        }
         if !mcp_runtime.is_empty() {
             functions.append_mcp_meta_functions(mcp_runtime.server_names());
         }
@@ -2145,10 +1830,6 @@ impl RequestContext {
         abort_signal: AbortSignal,
     ) -> Result<()> {
         let role = self.retrieve_role(app, name)?;
-        if let Some(session) = self.session.as_mut() {
-            session.guard_empty()?;
-        }
-
         let mcp_servers = if app.mcp_server_support {
             role.enabled_mcp_servers()
         } else {
@@ -2275,14 +1956,6 @@ impl RequestContext {
         )
         .await?;
 
-        let is_graph_agent = graph::agent_has_graph(agent_name);
-        if is_graph_agent && session_name.is_some() {
-            bail!(
-                "Graph-based agent '{agent_name}' does not support sessions. \
-                 The graph manages its own state; re-run without a session."
-            );
-        }
-
         let mcp_servers = if app.mcp_server_support {
             (!agent.mcp_server_names().is_empty()).then(|| agent.mcp_server_names().join(","))
         } else {
@@ -2304,22 +1977,14 @@ impl RequestContext {
             );
         }
 
-        // Graph agents manage their own state; never engage a session,
-        // not even an inherited app-level `agent_session` default.
         let session_name = session_name.map(|v| v.to_string()).or_else(|| {
-            if self.macro_flag || is_graph_agent {
+            if self.macro_flag {
                 None
             } else {
                 agent.agent_session().map(|v| v.to_string())
             }
         });
 
-        if self.session.is_some() {
-            bail!(
-                "Already in a session, please run '.exit session' first to exit the current session."
-            );
-        }
-
         let should_init_supervisor = agent.can_spawn_agents();
         let max_concurrent = agent.max_concurrent_agents();
         let max_depth = agent.max_agent_depth();
@@ -2531,7 +2196,7 @@ impl RequestContext {
             .clone()
             .unwrap_or_else(|| SUMMARY_CONTEXT_PROMPT.into());
 
-        let todo_prefix = if self.auto_continue_config().enabled && !self.todo_list.is_empty() {
+        let todo_prefix = if self.agent.is_some() && !self.todo_list.is_empty() {
             format!(
                 "[ACTIVE TODO LIST]\n{}\n\n",
                 self.todo_list.render_for_model()
@@ -2926,7 +2591,7 @@ mod tests {
         let mcp_config = if server_names.is_empty() {
             None
         } else {
-            let mut servers = IndexMap::new();
+            let mut servers = HashMap::new();
             for name in server_names {
                 servers.insert(
                     name.to_string(),
@@ -3624,246 +3289,4 @@ mod tests {
         create_dir_all(&rags_dir).unwrap();
         assert!(paths::list_rags().is_empty());
     }
-
-    #[test]
-    #[serial]
-    fn use_agent_errors_when_already_in_session() {
-        let _guard = TestConfigDirGuard::new();
-        let mut ctx = create_test_ctx();
-        ctx.session = Some(Session::default());
-
-        let app = ctx.app.config.clone();
-        let agent_name = format!(
-            "test_agent_{}",
-            SystemTime::now()
-                .duration_since(UNIX_EPOCH)
-                .unwrap()
-                .as_nanos()
-        );
-        let agent_dir = paths::agent_data_dir(&agent_name);
-        create_dir_all(&agent_dir).unwrap();
-        write(
-            agent_dir.join("config.yaml"),
-            format!("name: {agent_name}\ninstructions: hi\n"),
-        )
-        .unwrap();
-
-        let abort = utils::create_abort_signal();
-        let result = run_async(ctx.use_agent(&app, &agent_name, Some("test_session"), abort));
-        assert!(result.is_err());
-        assert!(
-            result
-                .unwrap_err()
-                .to_string()
-                .contains("Already in a session")
-        );
-        assert!(
-            ctx.agent.is_none(),
-            "Agent should not be set when session check fails"
-        );
-    }
-
-    #[test]
-    #[serial]
-    fn use_agent_errors_when_already_in_session_even_without_session_name() {
-        let _guard = TestConfigDirGuard::new();
-        let mut ctx = create_test_ctx();
-        ctx.session = Some(Session::default());
-
-        let app = ctx.app.config.clone();
-        let agent_name = format!(
-            "test_agent_{}",
-            SystemTime::now()
-                .duration_since(UNIX_EPOCH)
-                .unwrap()
-                .as_nanos()
-        );
-        let agent_dir = paths::agent_data_dir(&agent_name);
-        create_dir_all(&agent_dir).unwrap();
-        write(
-            agent_dir.join("config.yaml"),
-            format!("name: {agent_name}\ninstructions: hi\n"),
-        )
-        .unwrap();
-
-        let abort = utils::create_abort_signal();
-        let result = run_async(ctx.use_agent(&app, &agent_name, None, abort));
-        assert!(result.is_err());
-        assert!(
-            result
-                .unwrap_err()
-                .to_string()
-                .contains("Already in a session")
-        );
-        assert!(
-            ctx.agent.is_none(),
-            "Agent should not be set when session check fails"
-        );
-    }
-
-    #[test]
-    #[serial]
-    fn use_agent_errors_when_graph_agent_given_explicit_session() {
-        let _guard = TestConfigDirGuard::new();
-        let mut ctx = create_test_ctx();
-
-        let app = ctx.app.config.clone();
-        let agent_name = format!(
-            "test_graph_agent_{}",
-            SystemTime::now()
-                .duration_since(UNIX_EPOCH)
-                .unwrap()
-                .as_nanos()
-        );
-        let agent_dir = paths::agent_data_dir(&agent_name);
-        create_dir_all(&agent_dir).unwrap();
-        write(
-            agent_dir.join("graph.yaml"),
-            format!(
-                "name: {agent_name}\nversion: \"1.0\"\nstart: done\nnodes:\n  done:\n    type: end\n    output: ok\n"
-            ),
-        )
-        .unwrap();
-
-        let abort = utils::create_abort_signal();
-        let result = run_async(ctx.use_agent(&app, &agent_name, Some("test_session"), abort));
-
-        assert!(result.is_err());
-        assert!(
-            result
-                .unwrap_err()
-                .to_string()
-                .contains("does not support sessions")
-        );
-        assert!(
-            ctx.agent.is_none(),
-            "Agent should not be set when the graph-agent session guard fails"
-        );
-    }
-
-    #[test]
-    #[serial]
-    fn use_agent_skips_inherited_session_for_graph_agent() {
-        let _guard = TestConfigDirGuard::new();
-        let mut ctx = create_test_ctx();
-        ctx.update_app_config(|app| app.agent_session = Some("inherited".to_string()));
-
-        let app = ctx.app.config.clone();
-        let agent_name = format!(
-            "test_graph_agent_{}",
-            SystemTime::now()
-                .duration_since(UNIX_EPOCH)
-                .unwrap()
-                .as_nanos()
-        );
-        let agent_dir = paths::agent_data_dir(&agent_name);
-        create_dir_all(&agent_dir).unwrap();
-        write(
-            agent_dir.join("graph.yaml"),
-            format!(
-                "name: {agent_name}\nversion: \"1.0\"\nstart: done\nnodes:\n  done:\n    type: end\n    output: ok\n"
-            ),
-        )
-        .unwrap();
-
-        let abort = utils::create_abort_signal();
-        run_async(ctx.use_agent(&app, &agent_name, None, abort)).unwrap();
-
-        assert!(ctx.agent.is_some(), "Graph agent should load successfully");
-        assert!(
-            ctx.session.is_none(),
-            "Graph agent must not engage a session, not even an inherited default"
-        );
-    }
-
-    fn first_file(dir: &Path) -> Option<PathBuf> {
-        for entry in read_dir(dir).ok()?.flatten() {
-            let path = entry.path();
-            if path.is_dir() {
-                if let Some(found) = first_file(&path) {
-                    return Some(found);
-                }
-            } else {
-                return Some(path);
-            }
-        }
-        None
-    }
-
-    #[test]
-    fn asset_category_parse_maps_known_names() {
-        assert_eq!(AssetCategory::parse("agents"), Some(AssetCategory::Agents));
-        assert_eq!(AssetCategory::parse("macros"), Some(AssetCategory::Macros));
-        assert_eq!(
-            AssetCategory::parse("functions"),
-            Some(AssetCategory::Functions)
-        );
-        assert_eq!(
-            AssetCategory::parse("mcp_config"),
-            Some(AssetCategory::McpConfig)
-        );
-        assert_eq!(AssetCategory::parse("roles"), None);
-        assert_eq!(AssetCategory::parse(""), None);
-    }
-
-    #[test]
-    #[serial]
-    fn install_builtin_agents_force_overwrites_only_with_force() {
-        let _guard = TestConfigDirGuard::new();
-
-        Agent::install_builtin_agents(false).unwrap();
-        let file =
-            first_file(&paths::agents_data_dir()).expect("bundled agents should be installed");
-
-        write(&file, "SENTINEL").unwrap();
-        Agent::install_builtin_agents(false).unwrap();
-        assert_eq!(
-            read_to_string(&file).unwrap(),
-            "SENTINEL",
-            "non-force install must not overwrite an existing file"
-        );
-
-        Agent::install_builtin_agents(true).unwrap();
-        assert_ne!(
-            read_to_string(&file).unwrap(),
-            "SENTINEL",
-            "force install must overwrite the existing file"
-        );
-    }
-
-    #[test]
-    #[serial]
-    fn install_functions_force_preserves_user_mcp_json() {
-        let _guard = TestConfigDirGuard::new();
-
-        Functions::install_builtin_global_tools(false).unwrap();
-        let mcp = paths::mcp_config_file();
-        assert!(mcp.exists(), "mcp.json should be installed on first run");
-
-        write(&mcp, "USER_MCP_CONFIG").unwrap();
-        Functions::install_builtin_global_tools(true).unwrap();
-        assert_eq!(
-            read_to_string(&mcp).unwrap(),
-            "USER_MCP_CONFIG",
-            "force install must NOT overwrite the user's mcp.json"
-        );
-    }
-
-    #[test]
-    #[serial]
-    fn install_mcp_config_overwrites_existing() {
-        let _guard = TestConfigDirGuard::new();
-
-        Functions::install_mcp_config().unwrap();
-        let mcp = paths::mcp_config_file();
-        assert!(mcp.exists(), "install_mcp_config should create mcp.json");
-
-        write(&mcp, "USER_MCP_CONFIG").unwrap();
-        Functions::install_mcp_config().unwrap();
-        assert_ne!(
-            read_to_string(&mcp).unwrap(),
-            "USER_MCP_CONFIG",
-            "install_mcp_config must overwrite the existing mcp.json"
-        );
-    }
 }

src/config/role.rs

@@ -55,14 +55,6 @@ pub struct Role {
     enabled_tools: Option<String>,
     #[serde(skip_serializing_if = "Option::is_none")]
     enabled_mcp_servers: Option<String>,
-    #[serde(skip_serializing_if = "Option::is_none")]
-    auto_continue: Option<bool>,
-    #[serde(skip_serializing_if = "Option::is_none")]
-    max_auto_continues: Option<usize>,
-    #[serde(skip_serializing_if = "Option::is_none")]
-    inject_todo_instructions: Option<bool>,
-    #[serde(skip_serializing_if = "Option::is_none")]
-    continuation_prompt: Option<String>,
 
     #[serde(skip)]
     model: Model,
@@ -98,14 +90,6 @@ impl Role {
                     "enabled_mcp_servers" => {
                         role.enabled_mcp_servers = value.as_str().map(|v| v.to_string())
                     }
-                    "auto_continue" => role.auto_continue = value.as_bool(),
-                    "max_auto_continues" => {
-                        role.max_auto_continues = value.as_u64().map(|v| v as usize)
-                    }
-                    "inject_todo_instructions" => role.inject_todo_instructions = value.as_bool(),
-                    "continuation_prompt" => {
-                        role.continuation_prompt = value.as_str().map(|v| v.to_string())
-                    }
                     _ => (),
                 }
             }
@@ -147,20 +131,6 @@ impl Role {
         if let Some(enabled_mcp_servers) = self.enabled_mcp_servers() {
             metadata.push(format!("enabled_mcp_servers: {enabled_mcp_servers}"));
         }
-        if let Some(auto_continue) = self.auto_continue {
-            metadata.push(format!("auto_continue: {auto_continue}"));
-        }
-        if let Some(max_auto_continues) = self.max_auto_continues {
-            metadata.push(format!("max_auto_continues: {max_auto_continues}"));
-        }
-        if let Some(inject_todo_instructions) = self.inject_todo_instructions {
-            metadata.push(format!(
-                "inject_todo_instructions: {inject_todo_instructions}"
-            ));
-        }
-        if let Some(continuation_prompt) = &self.continuation_prompt {
-            metadata.push(format!("continuation_prompt: {continuation_prompt}"));
-        }
         if metadata.is_empty() {
             format!("{}\n", self.prompt)
         } else if self.prompt.is_empty() {
@@ -255,26 +225,6 @@ impl Role {
         self.prompt.contains(INPUT_PLACEHOLDER)
     }
 
-    pub fn auto_continue(&self) -> Option<bool> {
-        self.auto_continue
-    }
-
-    pub fn max_auto_continues(&self) -> Option<usize> {
-        self.max_auto_continues
-    }
-
-    pub fn inject_todo_instructions(&self) -> Option<bool> {
-        self.inject_todo_instructions
-    }
-
-    pub fn continuation_prompt(&self) -> Option<&str> {
-        self.continuation_prompt.as_deref()
-    }
-
-    pub fn append_to_prompt(&mut self, text: &str) {
-        self.prompt.push_str(text);
-    }
-
     pub fn echo_messages(&self, input: &Input) -> String {
         let input_markdown = input.render();
         if self.is_empty_prompt() {

src/config/session.rs

@@ -32,14 +32,6 @@ pub struct Session {
     save_session: Option<bool>,
     #[serde(skip_serializing_if = "Option::is_none")]
     compression_threshold: Option<usize>,
-    #[serde(skip_serializing_if = "Option::is_none")]
-    auto_continue: Option<bool>,
-    #[serde(skip_serializing_if = "Option::is_none")]
-    max_auto_continues: Option<usize>,
-    #[serde(skip_serializing_if = "Option::is_none")]
-    inject_todo_instructions: Option<bool>,
-    #[serde(skip_serializing_if = "Option::is_none")]
-    continuation_prompt: Option<String>,
 
     #[serde(skip_serializing_if = "Option::is_none")]
     role_name: Option<String>,
@@ -178,18 +170,6 @@ impl Session {
         if let Some(save_session) = self.save_session() {
             data["save_session"] = save_session.into();
         }
-        if let Some(auto_continue) = self.auto_continue() {
-            data["auto_continue"] = auto_continue.into();
-        }
-        if let Some(max_auto_continues) = self.max_auto_continues() {
-            data["max_auto_continues"] = max_auto_continues.into();
-        }
-        if let Some(inject_todo_instructions) = self.inject_todo_instructions() {
-            data["inject_todo_instructions"] = inject_todo_instructions.into();
-        }
-        if let Some(continuation_prompt) = self.continuation_prompt() {
-            data["continuation_prompt"] = continuation_prompt.into();
-        }
         let (tokens, percent) = self.tokens_usage();
         data["total_tokens"] = tokens.into();
         if let Some(max_input_tokens) = self.model().max_input_tokens() {
@@ -245,22 +225,6 @@ impl Session {
             items.push(("compression_threshold", compression_threshold.to_string()));
         }
 
-        if let Some(auto_continue) = self.auto_continue() {
-            items.push(("auto_continue", auto_continue.to_string()));
-        }
-        if let Some(max_auto_continues) = self.max_auto_continues() {
-            items.push(("max_auto_continues", max_auto_continues.to_string()));
-        }
-        if let Some(inject_todo_instructions) = self.inject_todo_instructions() {
-            items.push((
-                "inject_todo_instructions",
-                inject_todo_instructions.to_string(),
-            ));
-        }
-        if let Some(continuation_prompt) = self.continuation_prompt() {
-            items.push(("continuation_prompt", continuation_prompt.to_string()));
-        }
-
         if let Some(max_input_tokens) = self.model().max_input_tokens() {
             items.push(("max_input_tokens", max_input_tokens.to_string()));
         }
@@ -371,50 +335,6 @@ impl Session {
         }
     }
 
-    pub fn auto_continue(&self) -> Option<bool> {
-        self.auto_continue
-    }
-
-    pub fn max_auto_continues(&self) -> Option<usize> {
-        self.max_auto_continues
-    }
-
-    pub fn set_auto_continue(&mut self, value: Option<bool>) {
-        if self.auto_continue != value {
-            self.auto_continue = value;
-            self.dirty = true;
-        }
-    }
-
-    pub fn set_max_auto_continues(&mut self, value: Option<usize>) {
-        if self.max_auto_continues != value {
-            self.max_auto_continues = value;
-            self.dirty = true;
-        }
-    }
-
-    pub fn inject_todo_instructions(&self) -> Option<bool> {
-        self.inject_todo_instructions
-    }
-
-    pub fn continuation_prompt(&self) -> Option<&str> {
-        self.continuation_prompt.as_deref()
-    }
-
-    pub fn set_inject_todo_instructions(&mut self, value: Option<bool>) {
-        if self.inject_todo_instructions != value {
-            self.inject_todo_instructions = value;
-            self.dirty = true;
-        }
-    }
-
-    pub fn set_continuation_prompt(&mut self, value: Option<String>) {
-        if self.continuation_prompt != value {
-            self.continuation_prompt = value;
-            self.dirty = true;
-        }
-    }
-
     pub fn needs_compression(&self, global_compression_threshold: usize) -> bool {
         if self.compressing {
             return false;
@@ -628,6 +548,15 @@ impl Session {
         let mut messages = self.messages.clone();
         if input.continue_output().is_some() {
             return messages;
+        } else if input.regenerate() {
+            while let Some(last) = messages.last() {
+                if !last.role.is_user() {
+                    messages.pop();
+                } else {
+                    break;
+                }
+            }
+            return messages;
         }
         let mut need_add_msg = true;
         let len = messages.len();

src/config/tool_scope.rs

@@ -8,7 +8,6 @@ use serde_json::{Value, json};
 use std::collections::HashMap;
 use std::sync::Arc;
 
-#[derive(Clone)]
 pub struct ToolScope {
     pub functions: Functions,
     pub mcp_runtime: McpRuntime,
@@ -25,7 +24,7 @@ impl Default for ToolScope {
     }
 }
 
-#[derive(Default, Clone)]
+#[derive(Default)]
 pub struct McpRuntime {
     pub servers: HashMap<String, Arc<ConnectedServer>>,
 }

src/config/update.rs

@@ -1,244 +0,0 @@
-use crate::utils::warning_text;
-use anyhow::{Context, Result, bail};
-use dunce::canonicalize;
-use inquire::Confirm;
-use is_terminal::IsTerminal;
-use self_update::Status;
-use self_update::backends::github::Update;
-use std::fs::OpenOptions;
-use std::path::Path;
-use std::{env, fs, io, process};
-
-#[derive(Debug, Clone, Copy, PartialEq, Eq)]
-enum InstallSource {
-    Cargo,
-    Homebrew,
-    Manual,
-}
-
-impl InstallSource {
-    fn is_package_managed(self) -> bool {
-        matches!(self, InstallSource::Cargo | InstallSource::Homebrew)
-    }
-
-    fn label(self) -> &'static str {
-        match self {
-            InstallSource::Cargo => "Cargo",
-            InstallSource::Homebrew => "Homebrew",
-            InstallSource::Manual => "manually-installed",
-        }
-    }
-}
-
-fn classify_install_path(path: &Path) -> InstallSource {
-    let components: Vec<&str> = path
-        .components()
-        .filter_map(|c| c.as_os_str().to_str())
-        .collect();
-
-    if components
-        .windows(2)
-        .any(|w| w[0] == ".cargo" && w[1] == "bin")
-    {
-        return InstallSource::Cargo;
-    }
-
-    if components.contains(&"Cellar") {
-        return InstallSource::Homebrew;
-    }
-    let path_str = path.to_string_lossy();
-    if path_str.starts_with("/opt/homebrew/") || path_str.starts_with("/home/linuxbrew/.linuxbrew/")
-    {
-        return InstallSource::Homebrew;
-    }
-
-    InstallSource::Manual
-}
-
-fn normalize_version(requested: Option<String>) -> Option<String> {
-    let raw = requested?;
-    let trimmed = raw.trim();
-    if trimmed.is_empty() || trimmed.eq_ignore_ascii_case("latest") {
-        return None;
-    }
-    match trimmed.chars().next() {
-        Some('v' | 'V') => Some(trimmed.to_string()),
-        Some(c) if c.is_ascii_digit() => Some(format!("v{trimmed}")),
-        _ => Some(trimmed.to_string()),
-    }
-}
-
-fn is_dir_writable(dir: &Path) -> bool {
-    let probe = dir.join(format!(".loki-update-write-test-{}", process::id()));
-    match OpenOptions::new().write(true).create_new(true).open(&probe) {
-        Ok(_) => {
-            let _ = fs::remove_file(&probe);
-            true
-        }
-        Err(_) => false,
-    }
-}
-
-pub fn run_self_update(requested: Option<String>, force: bool) -> Result<()> {
-    let target_tag = normalize_version(requested);
-
-    let exe_path = env::current_exe()
-        .context("Could not determine the path of the running loki executable")?;
-    let resolved = canonicalize(&exe_path).unwrap_or_else(|_| exe_path.clone());
-    let source = classify_install_path(&resolved);
-
-    if source.is_package_managed() {
-        let body = match source {
-            InstallSource::Homebrew => format!(
-                "Loki appears to be installed via Homebrew ({}).\n\
-                 Updating in place replaces the binary inside Homebrew's Cellar; `brew` will\n\
-                 then report a version that no longer matches the file on disk, and a later\n\
-                 `brew upgrade`/`brew reinstall` may overwrite it or fail.\n\
-                 The clean way to update is:  brew upgrade loki",
-                exe_path.display()
-            ),
-            InstallSource::Cargo => format!(
-                "Loki appears to be installed via `cargo install` ({}).\n\
-                 Updating in place leaves Cargo's records out of sync with the binary on disk.\n\
-                 The clean way to update is:  cargo install --locked loki-ai",
-                exe_path.display()
-            ),
-            InstallSource::Manual => unreachable!("Manual installs are not package-managed"),
-        };
-        println!("{} {body}", warning_text("WARNING:"));
-
-        if force {
-            println!("--force specified; updating anyway.");
-        } else if io::stdin().is_terminal() {
-            let proceed = Confirm::new("Update anyway?")
-                .with_default(false)
-                .prompt()?;
-            if !proceed {
-                println!("Update cancelled.");
-                return Ok(());
-            }
-        } else {
-            bail!(
-                "Refusing to update a {} install. Re-run with --force to override.",
-                source.label()
-            );
-        }
-    }
-
-    if let Some(parent) = exe_path.parent()
-        && !is_dir_writable(parent)
-    {
-        bail!(
-            "No write permission for '{}'. Re-run with elevated permissions (e.g. sudo), \
-             or update Loki through your package manager.",
-            parent.display()
-        );
-    }
-
-    let interactive = io::stdin().is_terminal();
-    let mut builder = Update::configure();
-    builder
-        .repo_owner("Dark-Alex-17")
-        .repo_name("loki")
-        .bin_name("loki")
-        .current_version(env!("CARGO_PKG_VERSION"))
-        .no_confirm(true)
-        .show_download_progress(interactive);
-    if let Some(tag) = &target_tag {
-        builder.target_version_tag(tag.as_str());
-    }
-    let status = builder
-        .build()
-        .context("Failed to configure the self-update")?
-        .update()
-        .context("Self-update failed")?;
-
-    match status {
-        Status::UpToDate(version) => {
-            println!("Loki is already up to date (v{version}).");
-        }
-        Status::Updated(version) => {
-            println!("Loki updated to v{version}. Restart loki to use the new version.");
-        }
-    }
-    Ok(())
-}
-
-#[cfg(test)]
-mod tests {
-    use super::*;
-    use std::path::PathBuf;
-
-    #[test]
-    fn classify_cargo_install() {
-        assert_eq!(
-            classify_install_path(&PathBuf::from("/home/u/.cargo/bin/loki")),
-            InstallSource::Cargo
-        );
-    }
-
-    #[test]
-    fn classify_homebrew_opt_prefix() {
-        assert_eq!(
-            classify_install_path(&PathBuf::from("/opt/homebrew/bin/loki")),
-            InstallSource::Homebrew
-        );
-    }
-
-    #[test]
-    fn classify_homebrew_cellar() {
-        assert_eq!(
-            classify_install_path(&PathBuf::from("/usr/local/Cellar/loki/0.3.0/bin/loki")),
-            InstallSource::Homebrew
-        );
-    }
-
-    #[test]
-    fn classify_homebrew_linuxbrew() {
-        assert_eq!(
-            classify_install_path(&PathBuf::from("/home/linuxbrew/.linuxbrew/bin/loki")),
-            InstallSource::Homebrew
-        );
-    }
-
-    #[test]
-    fn classify_manual_usr_local_bin() {
-        assert_eq!(
-            classify_install_path(&PathBuf::from("/usr/local/bin/loki")),
-            InstallSource::Manual
-        );
-    }
-
-    #[test]
-    fn classify_manual_local_bin() {
-        assert_eq!(
-            classify_install_path(&PathBuf::from("/home/u/.local/bin/loki")),
-            InstallSource::Manual
-        );
-    }
-
-    #[test]
-    fn normalize_version_latest_and_empty_are_none() {
-        assert_eq!(normalize_version(None), None);
-        assert_eq!(normalize_version(Some(String::new())), None);
-        assert_eq!(normalize_version(Some("   ".to_string())), None);
-        assert_eq!(normalize_version(Some("latest".to_string())), None);
-        assert_eq!(normalize_version(Some("LATEST".to_string())), None);
-    }
-
-    #[test]
-    fn normalize_version_prepends_v_for_bare_semver() {
-        assert_eq!(
-            normalize_version(Some("0.4.0".to_string())),
-            Some("v0.4.0".to_string())
-        );
-        assert_eq!(
-            normalize_version(Some("v0.4.0".to_string())),
-            Some("v0.4.0".to_string())
-        );
-        assert_eq!(
-            normalize_version(Some("  v0.4.0  ".to_string())),
-            Some("v0.4.0".to_string())
-        );
-    }
-}

src/function/mod.rs

@@ -51,7 +51,7 @@ enum BinaryType<'a> {
 }
 
 #[derive(Debug, Clone, Copy, PartialEq, Eq, AsRefStr)]
-pub enum Language {
+enum Language {
     Bash,
     Python,
     TypeScript,
@@ -60,13 +60,7 @@ pub enum Language {
 
 impl From<&String> for Language {
     fn from(s: &String) -> Self {
-        Language::from_extension(s)
-    }
-}
-
-impl Language {
-    pub fn from_extension(ext: &str) -> Self {
-        match ext.to_lowercase().as_str() {
+        match s.to_lowercase().as_str() {
             "sh" => Language::Bash,
             "py" => Language::Python,
             "ts" => Language::TypeScript,
@@ -96,17 +90,6 @@ impl Language {
     }
 }
 
-impl Language {
-    pub fn direct_invoker(self) -> Option<(&'static str, &'static [&'static str])> {
-        match self {
-            Language::Bash => Some(("bash", &[])),
-            Language::Python => Some(("python3", &[])),
-            Language::TypeScript => Some(("npx", &["tsx"])),
-            Language::Unsupported => None,
-        }
-    }
-}
-
 fn extract_shebang_runtime(path: &Path) -> Option<String> {
     let file = File::open(path).ok()?;
     let reader = io::BufReader::new(file);
@@ -209,7 +192,7 @@ pub struct Functions {
 }
 
 impl Functions {
-    pub fn install_builtin_global_tools(force: bool) -> Result<()> {
+    pub fn install_builtin_global_tools() -> Result<()> {
         info!(
             "Installing global built-in functions in {}",
             paths::functions_dir().display()
@@ -227,14 +210,14 @@ impl Functions {
             })?;
             let content = unsafe { std::str::from_utf8_unchecked(&embedded_file.data) };
             let file_path = paths::functions_dir().join(file.as_ref());
-            #[cfg_attr(not(unix), expect(unused))]
-            let is_script = file_path
+            let file_extension = file_path
                 .extension()
                 .and_then(OsStr::to_str)
-                .is_some_and(|ext| Language::from_extension(ext) != Language::Unsupported);
+                .map(|s| s.to_lowercase());
+            #[cfg_attr(not(unix), expect(unused))]
+            let is_script = matches!(file_extension.as_deref(), Some("sh") | Some("py"));
 
-            let force_this = force && file.as_ref() != "mcp.json";
-            if file_path.exists() && !force_this {
+            if file_path.exists() {
                 debug!(
                     "Function file already exists, skipping: {}",
                     file_path.display()
@@ -257,22 +240,6 @@ impl Functions {
         Ok(())
     }
 
-    pub fn install_mcp_config() -> Result<()> {
-        let file_path = paths::mcp_config_file();
-        let embedded = FunctionAssets::get("mcp.json")
-            .ok_or_else(|| anyhow!("Failed to load embedded mcp.json"))?;
-        let content = unsafe { std::str::from_utf8_unchecked(&embedded.data) };
-
-        ensure_parent_exists(&file_path)?;
-
-        info!("Reinstalling MCP config file: {}", file_path.display());
-
-        let mut config_file = File::create(&file_path)?;
-        config_file.write_all(content.as_bytes())?;
-
-        Ok(())
-    }
-
     pub fn init(visible_tools: &[String]) -> Result<Self> {
         Self::clear_global_functions_bin_dir()?;
 
@@ -1448,23 +1415,6 @@ mod tests {
         assert!(tc.thought_signature.is_none());
     }
 
-    #[test]
-    fn direct_invoker_maps_each_language() {
-        assert_eq!(
-            Language::Bash.direct_invoker(),
-            Some(("bash", &[] as &[&str]))
-        );
-        assert_eq!(
-            Language::Python.direct_invoker(),
-            Some(("python3", &[] as &[&str]))
-        );
-        assert_eq!(
-            Language::TypeScript.direct_invoker(),
-            Some(("npx", &["tsx"] as &[&str]))
-        );
-        assert_eq!(Language::Unsupported.direct_invoker(), None);
-    }
-
     #[test]
     fn toolcall_with_thought_signature() {
         let tc = ToolCall::new("t".into(), json!({}), None)

src/function/supervisor.rs

@@ -5,7 +5,6 @@ use crate::supervisor::mailbox::{Envelope, EnvelopePayload, Inbox};
 use crate::supervisor::{AgentExitStatus, AgentHandle, AgentResult, Supervisor};
 use crate::utils::{AbortSignal, create_abort_signal};
 
-use crate::graph;
 use anyhow::{Context, Result, anyhow, bail};
 use chrono::Utc;
 use indexmap::IndexMap;
@@ -14,8 +13,6 @@ use parking_lot::RwLock;
 use serde_json::{Value, json};
 use std::pin::Pin;
 use std::sync::Arc;
-use std::time::Duration;
-use tokio::time;
 use uuid::Uuid;
 
 pub const SUPERVISOR_FUNCTION_PREFIX: &str = "agent__";
@@ -327,21 +324,12 @@ pub async fn handle_supervisor_tool(
     }
 }
 
-pub fn run_child_agent(
+fn run_child_agent(
     mut child_ctx: RequestContext,
     initial_input: Input,
     abort_signal: AbortSignal,
 ) -> Pin<Box<dyn Future<Output = Result<String>> + Send>> {
     Box::pin(async move {
-        if graph::active_agent_graph_name(&child_ctx).is_some() {
-            return graph::run_active_agent_graph(
-                &mut child_ctx,
-                &initial_input.text(),
-                abort_signal,
-            )
-            .await;
-        }
-
         let mut accumulated_output = String::new();
         let mut input = initial_input;
         let app = Arc::clone(&child_ctx.app.config);
@@ -384,98 +372,6 @@ pub fn run_child_agent(
     })
 }
 
-/// Spawn an agent synchronously from a graph node and return its accumulated
-/// output. This is similar to `handle_spawn` but runs the child agent in the
-/// current task (no tokio::spawn, no supervisor handle registration) so the
-/// graph executor can sequence agent nodes directly.
-pub async fn run_agent_for_graph(
-    parent_ctx: &mut RequestContext,
-    agent_name: &str,
-    prompt: &str,
-) -> Result<String> {
-    let short_uuid = &Uuid::new_v4().to_string()[..8];
-    let agent_id = format!("graph_agent_{agent_name}_{short_uuid}");
-    let current_depth = parent_ctx.current_depth + 1;
-
-    if let Some(supervisor) = parent_ctx.supervisor.as_ref().cloned() {
-        let max_depth = supervisor.read().max_depth();
-        if current_depth > max_depth {
-            bail!("Max agent depth exceeded ({current_depth}/{max_depth})");
-        }
-    }
-
-    if !parent_ctx.app.config.function_calling_support {
-        bail!("Function calling support must be enabled to spawn agents.");
-    }
-
-    let child_inbox = Arc::new(Inbox::new());
-    parent_ctx.ensure_root_escalation_queue();
-    let child_abort = create_abort_signal();
-
-    let app_config = Arc::clone(&parent_ctx.app.config);
-    let current_model = parent_ctx.current_model().clone();
-    let info_flag = parent_ctx.info_flag;
-    let child_app_state = Arc::new(AppState {
-        config: Arc::new(app_config.as_ref().clone()),
-        vault: parent_ctx.app.vault.clone(),
-        mcp_factory: parent_ctx.app.mcp_factory.clone(),
-        rag_cache: parent_ctx.app.rag_cache.clone(),
-        mcp_config: parent_ctx.app.mcp_config.clone(),
-        mcp_log_path: parent_ctx.app.mcp_log_path.clone(),
-        mcp_registry: parent_ctx.app.mcp_registry.clone(),
-        functions: parent_ctx.app.functions.clone(),
-    });
-
-    let agent = Agent::init(
-        app_config.as_ref(),
-        child_app_state.as_ref(),
-        &current_model,
-        info_flag,
-        agent_name,
-        child_abort.clone(),
-    )
-    .await?;
-
-    let agent_mcp_servers = agent.mcp_server_names().to_vec();
-    let session = agent.agent_session().map(|v| v.to_string());
-    let should_init_supervisor = agent.can_spawn_agents();
-    let agent_max_concurrent = agent.max_concurrent_agents();
-    let agent_max_depth = agent.max_agent_depth();
-
-    let mut child_ctx = RequestContext::new_for_child(
-        Arc::clone(&child_app_state),
-        parent_ctx,
-        current_depth,
-        Arc::clone(&child_inbox),
-        agent_id.clone(),
-    );
-    child_ctx.rag = agent.rag();
-    child_ctx.agent = Some(agent);
-    if should_init_supervisor {
-        child_ctx.supervisor = Some(Arc::new(RwLock::new(Supervisor::new(
-            agent_max_concurrent,
-            agent_max_depth,
-        ))));
-    }
-
-    if let Some(session) = session {
-        child_ctx
-            .use_session(app_config.as_ref(), Some(&session), child_abort.clone())
-            .await?;
-        sync_agent_functions_to_ctx(&mut child_ctx)?;
-    } else {
-        populate_agent_mcp_runtime(&mut child_ctx, &agent_mcp_servers).await?;
-        sync_agent_functions_to_ctx(&mut child_ctx)?;
-        child_ctx.init_agent_shared_variables()?;
-    }
-
-    let input = Input::from_str(&child_ctx, prompt, None);
-
-    debug!("Spawning agent '{agent_name}' for graph node as '{agent_id}'");
-
-    run_child_agent(child_ctx, input, child_abort).await
-}
-
 async fn populate_agent_mcp_runtime(ctx: &mut RequestContext, server_ids: &[String]) -> Result<()> {
     if !ctx.app.config.mcp_server_support {
         return Ok(());
@@ -705,25 +601,11 @@ async fn handle_check(ctx: &mut RequestContext, args: &Value) -> Result<Value> {
 
     match is_finished {
         Some(true) => handle_collect(ctx, args).await,
-        Some(false) => {
-            let mut result = json!({
-                "status": "pending",
-                "id": id,
-                "message": "Agent is still running"
-            });
-
-            if let Some(queue) = ctx.root_escalation_queue()
-                && queue.has_pending()
-            {
-                let summary = queue.pending_summary();
-                result["pending_escalations"] = json!(summary);
-                result["message"] = json!(
-                    "Agent is still running. Child agents have pending escalations that need your reply via agent__reply_escalation."
-                );
-            }
-
-            Ok(result)
-        }
+        Some(false) => Ok(json!({
+            "status": "pending",
+            "id": id,
+            "message": "Agent is still running"
+        })),
         None => Ok(json!({
             "status": "error",
             "message": format!("No agent found with id '{id}'")
@@ -737,48 +619,12 @@ async fn handle_collect(ctx: &mut RequestContext, args: &Value) -> Result<Value>
         .and_then(Value::as_str)
         .ok_or_else(|| anyhow!("'id' is required"))?;
 
-    let supervisor = ctx
-        .supervisor
-        .as_ref()
-        .cloned()
-        .ok_or_else(|| anyhow!("No supervisor active"))?;
-
-    {
-        let sup = supervisor.read();
-        if sup.is_finished(id).is_none() {
-            return Ok(json!({
-                "status": "error",
-                "message": format!("Agent '{id}' not found. Use agent__check to verify it exists and is finished.")
-            }));
-        }
-    }
-
-    loop {
-        let is_finished = {
-            let sup = supervisor.read();
-            sup.is_finished(id).unwrap_or(false)
-        };
-
-        if is_finished {
-            break;
-        }
-
-        if let Some(queue) = ctx.root_escalation_queue()
-            && queue.has_pending()
-        {
-            let summary = queue.pending_summary();
-            return Ok(json!({
-                "status": "pending",
-                "id": id,
-                "message": format!("Agent '{id}' is still running, but child agents have pending escalations that need your reply. Reply via agent__reply_escalation, then call agent__collect again."),
-                "pending_escalations": summary,
-            }));
-        }
-
-        time::sleep(Duration::from_millis(200)).await;
-    }
-
     let handle = {
+        let supervisor = ctx
+            .supervisor
+            .as_ref()
+            .cloned()
+            .ok_or_else(|| anyhow!("No supervisor active"))?;
         let mut sup = supervisor.write();
         sup.take(id)
     };
@@ -803,7 +649,7 @@ async fn handle_collect(ctx: &mut RequestContext, args: &Value) -> Result<Value>
         }
         None => Ok(json!({
             "status": "error",
-            "message": format!("Agent '{id}' completed but could not be collected. It may have been collected by another call.")
+            "message": format!("Agent '{id}' not found. Use agent__check to verify it exists and is finished.")
         })),
     }
 }
@@ -1347,7 +1193,7 @@ mod tests {
             let inbox = Arc::new(Inbox::new());
             let abort = create_abort_signal();
             let join_handle = tokio::spawn(async {
-                time::sleep(Duration::from_secs(60)).await;
+                tokio::time::sleep(std::time::Duration::from_secs(60)).await;
                 Ok(AgentResult {
                     id: "slow".into(),
                     agent_name: "test".into(),

src/function/todo.rs

@@ -94,14 +94,8 @@ pub fn handle_todo_tool(ctx: &mut RequestContext, cmd_name: &str, args: &Value)
         .strip_prefix(TODO_FUNCTION_PREFIX)
         .unwrap_or(cmd_name);
 
-    if !ctx.app.config.function_calling_support {
-        bail!("Cannot use todo tools: function calling is disabled.");
-    }
-    let auto_config = ctx.auto_continue_config();
-    if !auto_config.enabled {
-        bail!(
-            "Auto-continue is not enabled. Set 'auto_continue: true' in your config to use todo tools."
-        );
+    if ctx.agent.is_none() {
+        bail!("No active agent");
     }
 
     match action {

src/function/user_interaction.rs

@@ -2,7 +2,7 @@ use super::{FunctionDeclaration, JsonSchema};
 use crate::config::RequestContext;
 use crate::supervisor::escalation::{EscalationRequest, new_escalation_id};
 
-use anyhow::{Result, anyhow, bail};
+use anyhow::{Result, anyhow};
 use indexmap::IndexMap;
 use inquire::{Confirm, MultiSelect, Select, Text};
 use serde_json::{Value, json};
@@ -155,10 +155,7 @@ fn handle_direct_ask(args: &Value) -> Result<Value> {
     let mut options = parse_options(args)?;
     options.push(CUSTOM_MULTI_CHOICE_ANSWER_OPTION.to_string());
 
-    let mut answer = Select::new(question, options)
-        .without_filtering()
-        .with_help_message("↑↓ to move, enter to select")
-        .prompt()?;
+    let mut answer = Select::new(question, options).prompt()?;
 
     if answer == CUSTOM_MULTI_CHOICE_ANSWER_OPTION {
         answer = Text::new("Custom response:").prompt()?
@@ -208,11 +205,12 @@ async fn handle_escalated(ctx: &RequestContext, action: &str, args: &Value) -> R
         .ok_or_else(|| anyhow!("'question' is required"))?
         .to_string();
 
-    let options: Option<Vec<String>> = if args.get("options").is_some() {
-        Some(parse_options(args)?)
-    } else {
-        None
-    };
+    let options: Option<Vec<String>> = args.get("options").and_then(Value::as_array).map(|arr| {
+        arr.iter()
+            .filter_map(Value::as_str)
+            .map(String::from)
+            .collect()
+    });
 
     let from_agent_id = ctx
         .self_agent_id
@@ -264,24 +262,13 @@ async fn handle_escalated(ctx: &RequestContext, action: &str, args: &Value) -> R
 }
 
 fn parse_options(args: &Value) -> Result<Vec<String>> {
-    let raw = args
-        .get("options")
-        .ok_or_else(|| anyhow!("'options' is required and must be an array of strings"))?;
-
-    let arr: Vec<Value> = match raw {
-        Value::Array(arr) => arr.clone(),
-        Value::String(s) => serde_json::from_str::<Vec<Value>>(s).map_err(|_| {
-            anyhow!(
-                "'options' was a string but did not parse as a JSON array. \
-                 Pass options as a native JSON array, e.g. [\"yes\", \"no\"]."
-            )
-        })?,
-        _ => bail!("'options' is required and must be an array of strings"),
-    };
-
-    Ok(arr
-        .iter()
-        .filter_map(Value::as_str)
-        .map(String::from)
-        .collect())
+    args.get("options")
+        .and_then(Value::as_array)
+        .map(|arr| {
+            arr.iter()
+                .filter_map(Value::as_str)
+                .map(String::from)
+                .collect()
+        })
+        .ok_or_else(|| anyhow!("'options' is required and must be an array of strings"))
 }

src/graph/agent.rs

@@ -1,272 +0,0 @@
-use super::state::StateManager;
-use super::structured;
-use super::types::AgentNode;
-use crate::config::RequestContext;
-use crate::function::supervisor::run_agent_for_graph;
-use anyhow::{Context, Result};
-use serde_json::Value;
-use std::time::Duration;
-use tokio::time::timeout;
-
-const OUTPUT_KEY: &str = "output";
-const DEFAULT_TIMEOUT_SECS: u64 = 300;
-
-pub struct AgentNodeExecutor;
-
-impl AgentNodeExecutor {
-    pub async fn execute(
-        node: &AgentNode,
-        state_manager: &mut StateManager,
-        parent_ctx: &mut RequestContext,
-    ) -> Result<String> {
-        let prompt = state_manager
-            .interpolate(&node.prompt)
-            .with_context(|| format!("Failed to interpolate prompt for agent '{}'", node.agent))?;
-
-        let timeout_dur = Duration::from_secs(node.timeout.unwrap_or(DEFAULT_TIMEOUT_SECS));
-
-        let raw = timeout(
-            timeout_dur,
-            run_agent_for_graph(parent_ctx, &node.agent, &prompt),
-        )
-        .await
-        .with_context(|| {
-            format!(
-                "Agent '{}' timed out after {}s",
-                node.agent,
-                timeout_dur.as_secs()
-            )
-        })?
-        .with_context(|| format!("Agent '{}' failed", node.agent))?;
-
-        let output_value = match &node.output_schema {
-            Some(schema) => structured::extract(&raw, schema, parent_ctx)
-                .await
-                .with_context(|| {
-                    format!(
-                        "Agent '{}' output failed structured-output extraction",
-                        node.agent
-                    )
-                })?,
-            None => Value::String(raw.clone()),
-        };
-
-        apply_state_updates(node, state_manager, &output_value);
-
-        Ok(raw)
-    }
-}
-
-fn apply_state_updates(node: &AgentNode, state_manager: &mut StateManager, output: &Value) {
-    if node.output_schema.is_some()
-        && let Some(obj) = output.as_object()
-    {
-        for (k, v) in obj {
-            state_manager.state_mut().set(k.clone(), v.clone());
-        }
-    }
-
-    let Some(updates) = &node.state_updates else {
-        return;
-    };
-    let prev_output = state_manager.state().get(OUTPUT_KEY).cloned();
-    state_manager
-        .state_mut()
-        .set(OUTPUT_KEY.into(), output.clone());
-
-    for (key, template) in updates {
-        let value = state_manager.interpolate_lenient(template);
-        state_manager
-            .state_mut()
-            .set(key.clone(), Value::String(value));
-    }
-
-    match prev_output {
-        Some(v) => state_manager.state_mut().set(OUTPUT_KEY.into(), v),
-        None => {
-            state_manager
-                .state_mut()
-                .set(OUTPUT_KEY.into(), Value::Null);
-        }
-    }
-}
-
-#[cfg(test)]
-mod tests {
-    use super::super::types::AgentNode;
-    use super::*;
-    use serde_json::json;
-    use std::collections::HashMap;
-
-    fn manager_with(pairs: &[(&str, Value)]) -> StateManager {
-        let mut map = HashMap::new();
-        for (k, v) in pairs {
-            map.insert((*k).into(), v.clone());
-        }
-        StateManager::new(map)
-    }
-
-    fn node_with(prompt: &str, updates: Option<HashMap<String, String>>) -> AgentNode {
-        AgentNode {
-            agent: "test_agent".into(),
-            prompt: prompt.into(),
-            state_updates: updates,
-            output_schema: None,
-            timeout: None,
-        }
-    }
-
-    #[test]
-    fn state_updates_use_output_placeholder() {
-        let node = {
-            let mut u = HashMap::new();
-            u.insert("findings".into(), "{{output}}".into());
-            node_with("hi", Some(u))
-        };
-        let mut state = manager_with(&[]);
-
-        apply_state_updates(&node, &mut state, &json!("agent finished its work"));
-
-        assert_eq!(
-            state.state().get("findings"),
-            Some(&json!("agent finished its work"))
-        );
-    }
-
-    #[test]
-    fn state_updates_can_reference_existing_keys_and_output() {
-        let node = {
-            let mut u = HashMap::new();
-            u.insert("summary".into(), "{{topic}}: {{output}}".into());
-            node_with("hi", Some(u))
-        };
-        let mut state = manager_with(&[("topic", json!("auth"))]);
-
-        apply_state_updates(&node, &mut state, &json!("JWT vs sessions"));
-
-        assert_eq!(
-            state.state().get("summary"),
-            Some(&json!("auth: JWT vs sessions"))
-        );
-    }
-
-    #[test]
-    fn output_key_is_cleaned_up_after_state_updates() {
-        let node = {
-            let mut u = HashMap::new();
-            u.insert("findings".into(), "{{output}}".into());
-            node_with("hi", Some(u))
-        };
-        let mut state = manager_with(&[]);
-
-        apply_state_updates(&node, &mut state, &json!("anything"));
-
-        assert_eq!(state.state().get("output"), Some(&Value::Null));
-    }
-
-    #[test]
-    fn pre_existing_output_value_is_preserved() {
-        let node = {
-            let mut u = HashMap::new();
-            u.insert("greeting".into(), "{{output}}".into());
-            node_with("hi", Some(u))
-        };
-        let mut state = manager_with(&[("output", json!("preserved"))]);
-
-        apply_state_updates(&node, &mut state, &json!("new agent output"));
-
-        assert_eq!(
-            state.state().get("greeting"),
-            Some(&json!("new agent output"))
-        );
-        assert_eq!(state.state().get("output"), Some(&json!("preserved")));
-    }
-
-    #[test]
-    fn no_state_updates_is_a_noop() {
-        let node = node_with("hi", None);
-        let mut state = manager_with(&[("k", json!("v"))]);
-
-        apply_state_updates(&node, &mut state, &json!("ignored"));
-
-        assert_eq!(state.state().get("k"), Some(&json!("v")));
-        assert!(state.state().get("output").is_none());
-    }
-
-    #[test]
-    fn interpolate_lenient_on_state_updates_handles_missing_keys() {
-        let node = {
-            let mut u = HashMap::new();
-            u.insert("decorated".into(), "[{{missing}}] {{output}}".into());
-            node_with("hi", Some(u))
-        };
-        let mut state = manager_with(&[]);
-
-        apply_state_updates(&node, &mut state, &json!("DATA"));
-
-        assert_eq!(state.state().get("decorated"), Some(&json!("[] DATA")));
-    }
-
-    fn node_with_schema(
-        prompt: &str,
-        updates: Option<HashMap<String, String>>,
-        schema: Value,
-    ) -> AgentNode {
-        let mut n = node_with(prompt, updates);
-        n.output_schema = Some(schema);
-        n
-    }
-
-    #[test]
-    fn output_schema_auto_merges_top_level_keys() {
-        let node = node_with_schema("hi", None, json!({"type": "object"}));
-        let mut state = manager_with(&[]);
-        let output = json!({"goal": "do X", "summary": "details"});
-
-        apply_state_updates(&node, &mut state, &output);
-
-        assert_eq!(state.state().get("goal"), Some(&json!("do X")));
-        assert_eq!(state.state().get("summary"), Some(&json!("details")));
-    }
-
-    #[test]
-    fn output_schema_preserves_nested_value_types() {
-        let node = node_with_schema("hi", None, json!({"type": "object"}));
-        let mut state = manager_with(&[]);
-        let output = json!({
-            "tags": ["a", "b"],
-            "config": { "key": "value" },
-            "count": 42
-        });
-
-        apply_state_updates(&node, &mut state, &output);
-
-        assert_eq!(state.state().get("tags"), Some(&json!(["a", "b"])));
-        assert_eq!(state.state().get("config"), Some(&json!({"key": "value"})));
-        assert_eq!(state.state().get("count"), Some(&json!(42)));
-    }
-
-    #[test]
-    fn output_schema_explicit_state_updates_override_auto_merge() {
-        let mut u = HashMap::new();
-        u.insert("goal".into(), "renamed-{{output.goal}}".into());
-        let node = node_with_schema("hi", Some(u), json!({"type": "object"}));
-        let mut state = manager_with(&[]);
-        let output = json!({"goal": "do X"});
-
-        apply_state_updates(&node, &mut state, &output);
-
-        assert_eq!(state.state().get("goal"), Some(&json!("renamed-do X")));
-    }
-
-    #[test]
-    fn no_schema_does_not_auto_merge() {
-        let node = node_with("hi", None);
-        let mut state = manager_with(&[]);
-        let output = json!({"goal": "do X"});
-
-        apply_state_updates(&node, &mut state, &output);
-
-        assert!(state.state().get("goal").is_none());
-    }
-}

src/graph/dispatch.rs

@@ -1,47 +0,0 @@
-use super::{GraphExecutor, GraphParser, agent_has_graph};
-use crate::config::RequestContext;
-use crate::config::paths;
-use crate::utils::AbortSignal;
-use anyhow::{Context, Result, anyhow};
-use log::info;
-use serde_json::Value;
-
-pub fn active_agent_graph_name(ctx: &RequestContext) -> Option<String> {
-    let name = ctx.agent.as_ref()?.name().to_string();
-    agent_has_graph(&name).then_some(name)
-}
-
-pub async fn run_active_agent_graph(
-    ctx: &mut RequestContext,
-    prompt: &str,
-    abort_signal: AbortSignal,
-) -> Result<String> {
-    let agent_name =
-        active_agent_graph_name(ctx).ok_or_else(|| anyhow!("Active agent has no graph.yaml"))?;
-
-    info!("Agent '{agent_name}' has graph.yaml; routing to graph executor");
-
-    let agent_dir = paths::agent_data_dir(&agent_name);
-    let graph_path = paths::agent_graph_file(&agent_name);
-
-    let parser = GraphParser::new(&agent_dir);
-    let mut graph = parser
-        .load_from_file(&graph_path)
-        .with_context(|| format!("Failed to load graph.yaml for agent '{agent_name}'"))?;
-
-    graph
-        .initial_state
-        .insert("initial_prompt".into(), Value::String(prompt.to_string()));
-
-    let executor = GraphExecutor::new(graph, agent_dir);
-    let output = executor
-        .execute(ctx, abort_signal)
-        .await
-        .with_context(|| format!("Graph execution failed for agent '{agent_name}'"))?;
-
-    if let Some(supervisor) = ctx.supervisor.clone() {
-        supervisor.read().cancel_all();
-    }
-
-    Ok(output)
-}

src/graph/executor.rs

@@ -1,796 +0,0 @@
-use super::agent::AgentNodeExecutor;
-use super::llm::{LlmExecutionOutcome, LlmNodeExecutor};
-use super::logging::{GraphLogger, narrate_node_complete, narrate_node_failed};
-use super::map::MapNodeExecutor;
-use super::rag::RagNodeExecutor;
-use super::script::ScriptExecutor;
-use super::staging::BranchWrites;
-use super::state::StateManager;
-use super::types::{EndNode, Graph, Node, NodeType};
-use super::user_interaction::{ApprovalNodeExecutor, InputNodeExecutor};
-use super::validator::{AgentValidationContext, GraphValidator};
-use crate::config::{RenderMode, RequestContext};
-use crate::utils::AbortSignal;
-use anyhow::{Context, Result, anyhow, bail};
-use futures_util::future::join_all;
-use serde_json::Value;
-use std::collections::{HashMap, HashSet};
-use std::path::PathBuf;
-use std::sync::Arc;
-use std::time::{Duration, Instant};
-use tokio::sync::Semaphore;
-
-pub struct GraphExecutor {
-    graph: Graph,
-    base_dir: PathBuf,
-}
-
-impl GraphExecutor {
-    pub fn new(graph: Graph, base_dir: impl Into<PathBuf>) -> Self {
-        Self {
-            graph,
-            base_dir: base_dir.into(),
-        }
-    }
-
-    pub async fn execute(
-        self,
-        ctx: &mut RequestContext,
-        abort_signal: AbortSignal,
-    ) -> Result<String> {
-        let is_nested = ctx.current_depth > 0;
-        let mut logger = GraphLogger::with_visibility(
-            &self.graph.name,
-            self.graph.settings.log_state_snapshots,
-            is_nested,
-        );
-        let result = self.run(&mut logger, ctx, abort_signal).await;
-        if let Err(e) = &result {
-            logger.graph_error(e);
-        }
-        result
-    }
-
-    async fn run(
-        self,
-        logger: &mut GraphLogger,
-        ctx: &mut RequestContext,
-        abort_signal: AbortSignal,
-    ) -> Result<String> {
-        let GraphExecutor { graph, base_dir } = self;
-
-        if graph.settings.validate_before_run {
-            let mut validator = GraphValidator::new(&base_dir);
-            if let Some(agent) = &ctx.agent {
-                validator = validator.with_agent_context(AgentValidationContext::from_agent(
-                    agent,
-                    Arc::clone(&ctx.app.config),
-                ));
-            }
-            let result = validator.validate(&graph);
-            for w in &result.warnings {
-                logger.validation_warning(w.node_id.as_deref(), &w.message);
-            }
-            result.into_result()?;
-        }
-
-        let mut state = StateManager::new(graph.initial_state.clone());
-        let agent_envs = ctx
-            .agent
-            .as_ref()
-            .map(|a| a.variable_envs())
-            .unwrap_or_default();
-        let script_executor = ScriptExecutor::new(&base_dir).with_envs(agent_envs);
-        let max_iterations = graph.settings.max_loop_iterations;
-        let graph_timeout = graph.settings.timeout.map(Duration::from_secs);
-        let max_concurrency = graph.settings.max_concurrency;
-        let graph = Arc::new(graph);
-        let start = Instant::now();
-
-        let mut frontier: HashSet<String> = HashSet::from([graph.start.clone()]);
-        logger.graph_start(&graph.start, graph.nodes.len());
-
-        loop {
-            if frontier.is_empty() {
-                bail!(
-                    "Graph '{}' frontier emptied without reaching an End node",
-                    graph.name
-                );
-            }
-
-            if abort_signal.aborted() {
-                bail!(
-                    "Graph '{}' aborted before super-step with frontier {:?}",
-                    graph.name,
-                    sorted_frontier(&frontier)
-                );
-            }
-            if let Some(t) = graph_timeout
-                && start.elapsed() > t
-            {
-                bail!(
-                    "Graph '{}' timed out after {}s before super-step with frontier {:?}",
-                    graph.name,
-                    t.as_secs(),
-                    sorted_frontier(&frontier)
-                );
-            }
-
-            // Loop-count and visit tracking on live state, BEFORE forking.
-            // This counts every entry to a node toward max_loop_iterations
-            // regardless of how many parallel branches converged on it.
-            for node_id in &frontier {
-                state.state_mut().visit_node(node_id);
-                let visits = state.state().loop_count(node_id);
-                if visits > max_iterations {
-                    bail!(
-                        "Node '{}' visited {} times (max_loop_iterations={}). \
-                         Possible infinite loop.",
-                        node_id,
-                        visits,
-                        max_iterations
-                    );
-                }
-            }
-
-            for node_id in &frontier {
-                let node = graph.get_node(node_id).ok_or_else(|| {
-                    anyhow!("Node '{}' not found in graph '{}'", node_id, graph.name)
-                })?;
-                let visits = state.state().loop_count(node_id);
-                logger.node_entry(node, visits);
-            }
-            let snapshot_label = if frontier.len() == 1 {
-                frontier.iter().next().cloned().unwrap_or_default()
-            } else {
-                format!("super-step {{{}}}", sorted_frontier(&frontier).join(","))
-            };
-            logger.state_snapshot(&snapshot_label, &state);
-
-            let snapshot = state.read_snapshot();
-            let semaphore = Arc::new(Semaphore::new(max_concurrency));
-
-            let frontier_size = frontier.len();
-            let in_super_step = frontier_size > 1;
-            let silent = logger.silent();
-
-            if in_super_step {
-                let mut branches = sorted_frontier(&frontier);
-                branches.sort();
-                logger.super_step_start(&branches);
-            }
-
-            let mut branch_tasks = Vec::with_capacity(frontier_size);
-            for node_id in &frontier {
-                let node = graph
-                    .get_node(node_id)
-                    .ok_or_else(|| {
-                        anyhow!("Node '{}' not found in graph '{}'", node_id, graph.name)
-                    })?
-                    .clone();
-                logger.node_start(&node, in_super_step);
-                let branch_state = state.fork_for_branch_state();
-                let mut branch_ctx = ctx.fork_for_branch();
-                if in_super_step {
-                    branch_ctx.render_mode = RenderMode::Silent;
-                }
-                let script_exec_clone = script_executor.clone();
-                let graph_clone = Arc::clone(&graph);
-                let current = node_id.clone();
-                let sem_clone = semaphore.clone();
-                let abort_clone = abort_signal.clone();
-
-                let task = tokio::spawn(async move {
-                    let _permit = sem_clone
-                        .acquire()
-                        .await
-                        .expect("semaphore should not be closed");
-                    if abort_clone.aborted() {
-                        narrate_node_failed(
-                            silent,
-                            &node,
-                            Duration::default(),
-                            "aborted",
-                            in_super_step,
-                        );
-                        return (
-                            current.clone(),
-                            branch_state,
-                            Err(anyhow!("branch aborted")),
-                            Duration::default(),
-                        );
-                    }
-                    let node_start = Instant::now();
-                    let mut state = branch_state;
-                    let mut ctx = branch_ctx;
-                    let step_ctx = StepContext {
-                        graph: graph_clone.as_ref(),
-                        script_executor: &script_exec_clone,
-                        max_concurrency,
-                        abort_signal: &abort_clone,
-                    };
-                    let result = step(&node, &mut state, &mut ctx, &step_ctx, &current).await;
-                    let elapsed = node_start.elapsed();
-                    match &result {
-                        Ok(StepResult::Continue(targets)) => {
-                            let route = if targets.is_empty() {
-                                None
-                            } else {
-                                Some(targets.join(", "))
-                            };
-                            narrate_node_complete(
-                                silent,
-                                &node,
-                                elapsed,
-                                route.as_deref(),
-                                in_super_step,
-                            );
-                        }
-                        Ok(StepResult::End(_)) => {
-                            narrate_node_complete(
-                                silent,
-                                &node,
-                                elapsed,
-                                Some("END"),
-                                in_super_step,
-                            );
-                        }
-                        Err(e) => {
-                            narrate_node_failed(
-                                silent,
-                                &node,
-                                elapsed,
-                                &e.to_string(),
-                                in_super_step,
-                            );
-                        }
-                    }
-                    (current, state, result, elapsed)
-                });
-                branch_tasks.push(task);
-            }
-
-            let joined = join_all(branch_tasks).await;
-
-            let mut branch_writes: Vec<BranchWrites> = Vec::new();
-            let mut next_frontier: HashSet<String> = HashSet::new();
-            let mut end_results: Vec<(String, StateManager, String)> = Vec::new();
-
-            for join_result in joined {
-                let (node_id, branch_state, step_result, elapsed) =
-                    join_result.map_err(|e| anyhow!("Branch task panicked: {e}"))?;
-                logger.record_timing(&node_id, elapsed);
-
-                let step_outcome = step_result.with_context(|| format!("at node '{node_id}'"))?;
-
-                match step_outcome {
-                    StepResult::Continue(targets) => {
-                        for target in &targets {
-                            logger.routing(&node_id, target);
-                        }
-                        let diff = branch_state.diff_against(snapshot.as_ref());
-                        branch_writes.push(BranchWrites {
-                            node_id: node_id.clone(),
-                            invocation_index: 0,
-                            writes: diff,
-                        });
-                        next_frontier.extend(targets);
-                    }
-                    StepResult::End(output) => {
-                        end_results.push((node_id.clone(), branch_state, output));
-                    }
-                }
-            }
-
-            if end_results.len() > 1 {
-                let mut ids: Vec<String> =
-                    end_results.iter().map(|(id, _, _)| id.clone()).collect();
-                ids.sort();
-                bail!(
-                    "super-step ended with multiple End targets ({}). \
-                     Fan-out branches must converge at a join node before \
-                     terminating. To fix: route all parallel branches to a \
-                     single shared next-node, then terminate from there.",
-                    ids.join(", ")
-                );
-            }
-
-            // Sort by (node_id, invocation_index) so non-commutative reducers
-            // like Concat/Merge produce deterministic output across runs.
-            branch_writes.sort_by(|a, b| {
-                a.node_id
-                    .cmp(&b.node_id)
-                    .then(a.invocation_index.cmp(&b.invocation_index))
-            });
-            state.apply_branch_writes(branch_writes, &graph.reducers)?;
-
-            if let Some((node_id, end_state, output)) = end_results.into_iter().next() {
-                let diff = end_state.diff_against(snapshot.as_ref());
-                state.apply_branch_writes(
-                    vec![BranchWrites {
-                        node_id: node_id.clone(),
-                        invocation_index: 0,
-                        writes: diff,
-                    }],
-                    &graph.reducers,
-                )?;
-                logger.graph_complete(&node_id, start.elapsed());
-                return Ok(output);
-            }
-
-            if in_super_step {
-                logger.super_step_end(&sorted_frontier(&next_frontier));
-            }
-            frontier = next_frontier;
-        }
-    }
-}
-
-fn sorted_frontier(frontier: &HashSet<String>) -> Vec<String> {
-    let mut v: Vec<String> = frontier.iter().cloned().collect();
-    v.sort();
-    v
-}
-
-pub(super) struct StepContext<'a> {
-    pub graph: &'a Graph,
-    pub script_executor: &'a ScriptExecutor,
-    pub max_concurrency: usize,
-    pub abort_signal: &'a AbortSignal,
-}
-
-impl StepContext<'_> {
-    pub fn graph_name(&self) -> &str {
-        &self.graph.name
-    }
-}
-
-enum StepResult {
-    // The set of next-node ids the executor should add to the next super-step's
-    // frontier. A `Vec` of length 1 for sequential routing (default) and the
-    // full target list for fan-out (`next: [a, b, ...]`). Dynamic single-route
-    // decisions (script `_next`, approval routes, LLM/RAG fallback) always emit
-    // a single-element vec.
-    Continue(Vec<String>),
-    End(String),
-}
-
-async fn step(
-    node: &Node,
-    state: &mut StateManager,
-    ctx: &mut RequestContext,
-    step_ctx: &StepContext<'_>,
-    current: &str,
-) -> Result<StepResult> {
-    match &node.node_type {
-        NodeType::Agent(agent_node) => {
-            AgentNodeExecutor::execute(agent_node, state, ctx).await?;
-            let targets = static_next_targets(node, current, "agent")?;
-            Ok(StepResult::Continue(targets))
-        }
-        NodeType::Script(script_node) => {
-            let dynamic = match step_ctx.script_executor.execute(script_node, state).await {
-                Ok(n) => n,
-                Err(e) => {
-                    if let Some(fallback) = &script_node.fallback {
-                        warn!(
-                            "[graph:{}] script '{}' failed, routing to fallback '{}': {}",
-                            step_ctx.graph_name(),
-                            current,
-                            fallback,
-                            e
-                        );
-                        return Ok(StepResult::Continue(vec![fallback.clone()]));
-                    }
-                    return Err(e);
-                }
-            };
-            let targets = match dynamic {
-                Some(n) => vec![n],
-                None => static_next_targets(node, current, "script")?,
-            };
-            Ok(StepResult::Continue(targets))
-        }
-        NodeType::Approval(approval_node) => {
-            let next = ApprovalNodeExecutor::execute(approval_node, state, ctx).await?;
-            Ok(StepResult::Continue(vec![next]))
-        }
-        NodeType::Input(input_node) => {
-            let next_id = first_next_target(node);
-            let next = InputNodeExecutor::execute(input_node, next_id, state, ctx).await?;
-            Ok(StepResult::Continue(vec![next]))
-        }
-        NodeType::Llm(llm_node) => {
-            let outcome = LlmNodeExecutor::execute(llm_node, state, ctx).await?;
-            let targets = match outcome {
-                LlmExecutionOutcome::Continue => static_next_targets(node, current, "llm")?,
-                LlmExecutionOutcome::FellBack(target) => vec![target],
-            };
-            Ok(StepResult::Continue(targets))
-        }
-        NodeType::Rag(rag_node) => {
-            RagNodeExecutor::execute(rag_node, current, state, ctx).await?;
-            let targets = static_next_targets(node, current, "rag")?;
-            Ok(StepResult::Continue(targets))
-        }
-        NodeType::End(end_node) => Ok(StepResult::End(resolve_end_output(end_node, state))),
-        NodeType::Map(map_node) => {
-            let targets = static_next_targets(node, current, "map")?;
-            MapNodeExecutor::execute(map_node, state, ctx, step_ctx, current).await?;
-            Ok(StepResult::Continue(targets))
-        }
-    }
-}
-
-fn static_next_targets(node: &Node, current: &str, kind: &str) -> Result<Vec<String>> {
-    node.next
-        .as_ref()
-        .map(|t| t.as_slice().to_vec())
-        .ok_or_else(|| anyhow!("{kind} node '{current}' has no `next` and is not an end node"))
-}
-
-fn first_next_target(node: &Node) -> Option<&str> {
-    node.next
-        .as_ref()
-        .and_then(|t| t.as_slice().first().map(|s| s.as_str()))
-}
-
-fn resolve_end_output(end_node: &EndNode, state: &mut StateManager) -> String {
-    apply_simple_state_updates(end_node.state_updates.as_ref(), state);
-    state.interpolate_lenient(&end_node.output)
-}
-
-fn apply_simple_state_updates(updates: Option<&HashMap<String, String>>, state: &mut StateManager) {
-    let Some(updates) = updates else {
-        return;
-    };
-    for (key, template) in updates {
-        let value = state.interpolate_lenient(template);
-        state.state_mut().set(key.clone(), Value::String(value));
-    }
-}
-
-#[cfg(test)]
-mod tests {
-    use super::*;
-    use serde_json::json;
-
-    fn state_with(pairs: &[(&str, Value)]) -> StateManager {
-        let mut map = HashMap::new();
-        for (k, v) in pairs {
-            map.insert((*k).into(), v.clone());
-        }
-        StateManager::new(map)
-    }
-
-    fn end_node(output: &str, updates: Option<HashMap<String, String>>) -> EndNode {
-        EndNode {
-            output: output.into(),
-            state_updates: updates,
-        }
-    }
-
-    #[test]
-    fn resolve_end_output_interpolates_template_against_state() {
-        let mut state = state_with(&[("name", json!("alice"))]);
-
-        let node = end_node("done: {{name}}", None);
-
-        assert_eq!(resolve_end_output(&node, &mut state), "done: alice");
-    }
-
-    #[test]
-    fn resolve_end_output_applies_state_updates_before_interpolation() {
-        let mut updates = HashMap::new();
-        updates.insert("summary".into(), "completed for {{user}}".into());
-        let node = end_node("RESULT: {{summary}}", Some(updates));
-
-        let mut state = state_with(&[("user", json!("bob"))]);
-
-        assert_eq!(
-            resolve_end_output(&node, &mut state),
-            "RESULT: completed for bob"
-        );
-        assert_eq!(
-            state.state().get("summary"),
-            Some(&json!("completed for bob"))
-        );
-    }
-
-    #[test]
-    fn resolve_end_output_with_empty_template_returns_empty_string() {
-        let mut state = state_with(&[]);
-
-        let node = end_node("", None);
-
-        assert_eq!(resolve_end_output(&node, &mut state), "");
-    }
-
-    #[test]
-    fn resolve_end_output_lenient_on_missing_keys() {
-        let mut state = state_with(&[]);
-
-        let node = end_node("hello {{unknown}}!", None);
-
-        assert_eq!(resolve_end_output(&node, &mut state), "hello !");
-    }
-
-    #[test]
-    fn apply_simple_state_updates_does_nothing_when_none() {
-        let mut state = state_with(&[("k", json!("v"))]);
-
-        apply_simple_state_updates(None, &mut state);
-
-        assert_eq!(state.state().get("k"), Some(&json!("v")));
-    }
-
-    #[test]
-    fn apply_simple_state_updates_overwrites_existing_values() {
-        let mut updates = HashMap::new();
-        updates.insert("k".into(), "new-{{k}}".into());
-        let mut state = state_with(&[("k", json!("old"))]);
-
-        apply_simple_state_updates(Some(&updates), &mut state);
-
-        assert_eq!(state.state().get("k"), Some(&json!("new-old")));
-    }
-}
-
-#[cfg(test)]
-mod integration_tests {
-    use super::*;
-    use crate::config::{AppState, WorkingMode};
-    use crate::utils::{create_abort_signal, temp_file};
-    use std::fs;
-
-    fn cmd_available(name: &str) -> bool {
-        which::which(name).is_ok()
-    }
-
-    struct TestWorkspace {
-        dir: PathBuf,
-    }
-
-    impl TestWorkspace {
-        fn new() -> Self {
-            let dir = temp_file("-graph-integration-", "");
-            fs::create_dir_all(&dir).unwrap();
-            Self { dir }
-        }
-
-        fn write_script(&self, name: &str, contents: &str) {
-            fs::write(self.dir.join(name), contents).unwrap();
-        }
-    }
-
-    impl Drop for TestWorkspace {
-        fn drop(&mut self) {
-            let _ = fs::remove_dir_all(&self.dir);
-        }
-    }
-
-    fn make_ctx() -> RequestContext {
-        RequestContext::new(Arc::new(AppState::test_default()), WorkingMode::Cmd)
-    }
-
-    #[tokio::test]
-    async fn static_fan_out_merges_branch_writes_via_append_reducer() {
-        if !cmd_available("bash") {
-            eprintln!("skipping: bash not available");
-            return;
-        }
-        let ws = TestWorkspace::new();
-        ws.write_script("dispatcher.sh", "#!/bin/bash\necho '{}'\n");
-        ws.write_script(
-            "worker_a.sh",
-            "#!/bin/bash\necho '{\"results\": \"alpha\"}'\n",
-        );
-        ws.write_script(
-            "worker_b.sh",
-            "#!/bin/bash\necho '{\"results\": \"beta\"}'\n",
-        );
-
-        let yaml = r#"
-name: static_fan_out_test
-start: dispatcher
-reducers:
-  results: append
-nodes:
-  dispatcher:
-    type: script
-    script: dispatcher.sh
-    state_updates: {}
-    next: [worker_a, worker_b]
-  worker_a:
-    type: script
-    script: worker_a.sh
-    state_updates: {}
-    next: join
-  worker_b:
-    type: script
-    script: worker_b.sh
-    state_updates: {}
-    next: join
-  join:
-    type: end
-    output: "{{results}}"
-"#;
-        let graph: Graph = serde_yaml::from_str(yaml).unwrap();
-        let mut ctx = make_ctx();
-        let abort = create_abort_signal();
-        let result = GraphExecutor::new(graph, &ws.dir)
-            .execute(&mut ctx, abort)
-            .await
-            .unwrap_or_else(|e| panic!("executor failed: {e:#}"));
-
-        let parsed: Value = serde_json::from_str(&result)
-            .unwrap_or_else(|_| panic!("expected JSON array, got: {result}"));
-        let arr = parsed.as_array().expect("results should be an array");
-        assert_eq!(arr.len(), 2, "expected 2 elements, got: {result}");
-        let strs: Vec<&str> = arr.iter().filter_map(|v| v.as_str()).collect();
-        assert!(strs.contains(&"alpha"), "missing 'alpha' in {strs:?}");
-        assert!(strs.contains(&"beta"), "missing 'beta' in {strs:?}");
-    }
-
-    #[tokio::test]
-    async fn map_over_list_collects_outputs_in_input_order() {
-        if !cmd_available("python3") {
-            eprintln!("skipping: python3 not available");
-            return;
-        }
-        let ws = TestWorkspace::new();
-        ws.write_script(
-            "doubler.py",
-            r#"#!/usr/bin/env python3
-import os, json
-state = json.loads(os.environ.get("GRAPH_STATE", "{}"))
-val = state["item"]
-print(json.dumps({"output": val * 2}))
-"#,
-        );
-
-        let yaml = r#"
-name: map_input_order_test
-start: fan_out
-initial_state:
-  items: [1, 2, 3, 4, 5]
-nodes:
-  fan_out:
-    type: map
-    over: "{{items}}"
-    as: item
-    branch: doubler
-    collect_into: doubled
-    next: done
-  doubler:
-    type: script
-    script: doubler.py
-    state_updates: {}
-  done:
-    type: end
-    output: "{{doubled}}"
-"#;
-        let graph: Graph = serde_yaml::from_str(yaml).unwrap();
-        let mut ctx = make_ctx();
-        let abort = create_abort_signal();
-        let result = GraphExecutor::new(graph, &ws.dir)
-            .execute(&mut ctx, abort)
-            .await
-            .unwrap_or_else(|e| panic!("executor failed: {e:#}"));
-
-        let parsed: Value = serde_json::from_str(&result)
-            .unwrap_or_else(|_| panic!("expected JSON array, got: {result}"));
-        let arr = parsed.as_array().expect("doubled should be an array");
-        let nums: Vec<i64> = arr
-            .iter()
-            .map(|v| v.as_i64().expect("each item should be int"))
-            .collect();
-
-        assert_eq!(
-            nums,
-            vec![2, 4, 6, 8, 10],
-            "map outputs should be in input order, not finish order"
-        );
-    }
-
-    #[tokio::test]
-    async fn parallel_branch_error_aborts_super_step() {
-        if !cmd_available("bash") {
-            eprintln!("skipping: bash not available");
-            return;
-        }
-        let ws = TestWorkspace::new();
-        ws.write_script("dispatcher.sh", "#!/bin/bash\necho '{}'\n");
-        ws.write_script(
-            "worker_ok.sh",
-            "#!/bin/bash\necho '{\"results\": \"ok\"}'\n",
-        );
-        ws.write_script(
-            "worker_fail.sh",
-            "#!/bin/bash\necho 'simulated failure' >&2\nexit 1\n",
-        );
-
-        let yaml = r#"
-name: branch_error_test
-start: dispatcher
-reducers:
-  results: append
-nodes:
-  dispatcher:
-    type: script
-    script: dispatcher.sh
-    state_updates: {}
-    next: [worker_ok, worker_fail]
-  worker_ok:
-    type: script
-    script: worker_ok.sh
-    state_updates: {}
-    next: join
-  worker_fail:
-    type: script
-    script: worker_fail.sh
-    state_updates: {}
-    next: join
-  join:
-    type: end
-    output: "{{results}}"
-"#;
-        let graph: Graph = serde_yaml::from_str(yaml).unwrap();
-        let mut ctx = make_ctx();
-        let abort = create_abort_signal();
-        let result = GraphExecutor::new(graph, &ws.dir)
-            .execute(&mut ctx, abort)
-            .await;
-
-        assert!(result.is_err(), "expected branch error to propagate");
-        let err = format!("{:#}", result.unwrap_err());
-        assert!(
-            err.contains("worker_fail"),
-            "error should mention failing node: {err}"
-        );
-    }
-
-    #[tokio::test]
-    async fn multi_end_in_super_step_is_rejected() {
-        if !cmd_available("bash") {
-            eprintln!("skipping: bash not available");
-            return;
-        }
-        let ws = TestWorkspace::new();
-        ws.write_script("dispatcher.sh", "#!/bin/bash\necho '{}'\n");
-
-        let yaml = r#"
-name: multi_end_test
-start: dispatcher
-nodes:
-  dispatcher:
-    type: script
-    script: dispatcher.sh
-    state_updates: {}
-    next: [end_a, end_b]
-  end_a:
-    type: end
-    output: "from a"
-  end_b:
-    type: end
-    output: "from b"
-"#;
-        let graph: Graph = serde_yaml::from_str(yaml).unwrap();
-        let mut ctx = make_ctx();
-        let abort = create_abort_signal();
-        let result = GraphExecutor::new(graph, &ws.dir)
-            .execute(&mut ctx, abort)
-            .await;
-
-        assert!(result.is_err(), "expected multi-End to be rejected");
-        let err = format!("{:#}", result.unwrap_err());
-        assert!(
-            err.contains("multiple End targets"),
-            "error should explain multi-End cause: {err}"
-        );
-        assert!(
-            err.contains("end_a") && err.contains("end_b"),
-            "error should list both End nodes: {err}"
-        );
-    }
-}

src/graph/llm.rs

@@ -1,616 +0,0 @@
-use super::state::StateManager;
-use super::structured;
-use super::types::LlmNode;
-use crate::client::{Model, ModelType, call_chat_completions};
-use crate::config::{Input, RequestContext, Role, RoleLike};
-use crate::utils::create_abort_signal;
-use anyhow::{Context, Error, Result, anyhow, bail};
-use serde_json::Value;
-use std::collections::HashSet;
-use std::sync::Arc;
-use std::time::Duration;
-use tokio::time::timeout;
-
-const OUTPUT_KEY: &str = "output";
-
-#[derive(Debug, PartialEq, Eq)]
-pub(super) enum LlmExecutionOutcome {
-    Continue,
-    FellBack(String),
-}
-
-pub struct LlmNodeExecutor;
-
-impl LlmNodeExecutor {
-    pub(super) async fn execute(
-        node: &LlmNode,
-        state_manager: &mut StateManager,
-        parent_ctx: &mut RequestContext,
-    ) -> Result<LlmExecutionOutcome> {
-        let result = run(node, state_manager, parent_ctx).await;
-        let (output, failure_reason) = match result {
-            Ok(raw) => match &node.output_schema {
-                Some(schema) => match structured::extract(&raw, schema, parent_ctx).await {
-                    Ok(value) => (value, None),
-                    Err(e) => {
-                        warn!("llm node structured extraction failed: {e}");
-                        (
-                            Value::String(format!("LLM node structured-extraction failed: {e}")),
-                            Some(format!("structured-extraction failed: {e}")),
-                        )
-                    }
-                },
-                None => (Value::String(raw), None),
-            },
-            Err(e) => {
-                warn!("llm node failed: {e}");
-                (
-                    Value::String(format!("LLM node failed: {e}")),
-                    Some(format!("LLM call failed: {e:#}")),
-                )
-            }
-        };
-
-        apply_state_updates_with_output(node, state_manager, &output);
-        outcome_from(failure_reason.as_deref(), node.fallback.as_deref())
-    }
-}
-
-fn outcome_from(
-    failure_reason: Option<&str>,
-    fallback: Option<&str>,
-) -> Result<LlmExecutionOutcome> {
-    match (failure_reason, fallback) {
-        (None, _) => Ok(LlmExecutionOutcome::Continue),
-        (Some(_), Some(fb)) => Ok(LlmExecutionOutcome::FellBack(fb.to_string())),
-        (Some(reason), None) => bail!(
-            "LLM node failed and no fallback declared: {reason}. \
-             Add a `fallback:` route on the node to route on failure, \
-             or fix the underlying error."
-        ),
-    }
-}
-
-async fn run(
-    node: &LlmNode,
-    state_manager: &mut StateManager,
-    parent_ctx: &mut RequestContext,
-) -> Result<String> {
-    let mut instructions: Option<String> = match &node.instructions {
-        Some(s) => Some(
-            state_manager
-                .interpolate(s)
-                .context("Failed to interpolate llm node instructions")?,
-        ),
-        None => None,
-    };
-    let mut prompt = state_manager
-        .interpolate(&node.prompt)
-        .context("Failed to interpolate llm node prompt")?;
-
-    if let Some(schema) = &node.output_schema {
-        let hint = format_schema_hint(schema);
-        match instructions.as_mut() {
-            Some(s) => {
-                s.push_str("\n\n");
-                s.push_str(&hint);
-            }
-            None => {
-                prompt.push_str("\n\n");
-                prompt.push_str(&hint);
-            }
-        }
-    }
-
-    let (regular_tools, mcp_servers) = categorize_tools(node.tools.as_deref());
-    validate_tools_subset(&regular_tools, &mcp_servers, parent_ctx)?;
-
-    let role = build_inline_role(
-        node,
-        instructions.as_deref(),
-        &regular_tools,
-        &mcp_servers,
-        parent_ctx,
-    )?;
-
-    let saved_role = parent_ctx.role.clone();
-    parent_ctx.role = Some(role);
-    let result = match node.timeout {
-        Some(secs) => match timeout(
-            Duration::from_secs(secs),
-            run_with_retries(node, &prompt, parent_ctx),
-        )
-        .await
-        {
-            Ok(r) => r,
-            Err(_) => Err(anyhow!("llm node timed out after {secs}s")),
-        },
-        None => run_with_retries(node, &prompt, parent_ctx).await,
-    };
-    parent_ctx.role = saved_role;
-    result
-}
-
-async fn run_with_retries(
-    node: &LlmNode,
-    prompt: &str,
-    ctx: &mut RequestContext,
-) -> Result<String> {
-    let mut last_err: Option<Error> = None;
-    for attempt in 1..=node.max_attempts {
-        match run_chat_loop(node, prompt, ctx).await {
-            Ok(out) => return Ok(out),
-            Err(e) if is_transient(&e) && attempt < node.max_attempts => {
-                warn!("llm node attempt {attempt} failed (transient): {e}; retrying");
-                last_err = Some(e);
-            }
-            Err(e) => return Err(e),
-        }
-    }
-    Err(last_err.unwrap_or_else(|| anyhow!("llm node exhausted retries")))
-}
-
-async fn run_chat_loop(node: &LlmNode, prompt: &str, ctx: &mut RequestContext) -> Result<String> {
-    let abort = create_abort_signal();
-    let app_cfg = Arc::clone(&ctx.app.config);
-    let role_for_input = ctx.role.clone();
-    let mut input = Input::from_str(ctx, prompt, role_for_input);
-    let mut accumulated = String::new();
-
-    for turn in 0..node.max_iterations {
-        let client = input.create_client()?;
-        ctx.before_chat_completion(&input)?;
-        let (output, tool_results) =
-            call_chat_completions(&input, false, false, client.as_ref(), ctx, abort.clone())
-                .await?;
-        ctx.after_chat_completion(app_cfg.as_ref(), &input, &output, &tool_results)?;
-
-        if !output.is_empty() {
-            if !accumulated.is_empty() {
-                accumulated.push('\n');
-            }
-            accumulated.push_str(&output);
-        }
-
-        if tool_results.is_empty() {
-            return Ok(accumulated);
-        }
-
-        if turn + 1 == node.max_iterations {
-            bail!(
-                "llm node hit max_iterations ({}) before LLM concluded",
-                node.max_iterations
-            );
-        }
-
-        input = input.merge_tool_results(output, tool_results);
-    }
-
-    bail!("llm node ended without producing output")
-}
-
-fn build_inline_role(
-    node: &LlmNode,
-    instructions: Option<&str>,
-    regular_tools: &[String],
-    mcp_servers: &[String],
-    parent_ctx: &RequestContext,
-) -> Result<Role> {
-    let mut role = Role::new("llm_node", instructions.unwrap_or(""));
-
-    let model = match &node.model {
-        Some(model_id) => {
-            Model::retrieve_model(parent_ctx.app.config.as_ref(), model_id, ModelType::Chat)
-                .with_context(|| format!("Unknown model '{model_id}' on llm node"))?
-        }
-        None => parent_ctx.current_model().clone(),
-    };
-    role.set_model(model);
-
-    if let Some(t) = node.temperature {
-        role.set_temperature(Some(t));
-    }
-    if let Some(p) = node.top_p {
-        role.set_top_p(Some(p));
-    }
-
-    if node.tools.as_deref().unwrap_or_default().is_empty() {
-        role.set_enabled_tools(Some(String::new()));
-        role.set_enabled_mcp_servers(Some(String::new()));
-    } else {
-        if !regular_tools.is_empty() {
-            role.set_enabled_tools(Some(regular_tools.join(",")));
-        } else {
-            role.set_enabled_tools(Some(String::new()));
-        }
-        if !mcp_servers.is_empty() {
-            role.set_enabled_mcp_servers(Some(mcp_servers.join(",")));
-        } else {
-            role.set_enabled_mcp_servers(Some(String::new()));
-        }
-    }
-
-    Ok(role)
-}
-
-fn categorize_tools(entries: Option<&[String]>) -> (Vec<String>, Vec<String>) {
-    let mut regular = Vec::new();
-    let mut mcp = Vec::new();
-    let Some(entries) = entries else {
-        return (regular, mcp);
-    };
-
-    for e in entries {
-        if let Some(server) = e.strip_prefix("mcp:") {
-            mcp.push(server.to_string());
-        } else {
-            regular.push(e.clone());
-        }
-    }
-
-    (regular, mcp)
-}
-
-fn validate_tools_subset(
-    regular: &[String],
-    mcp_servers: &[String],
-    parent_ctx: &RequestContext,
-) -> Result<()> {
-    let agent = parent_ctx
-        .agent
-        .as_ref()
-        .ok_or_else(|| anyhow!("llm node requires an active agent"))?;
-
-    if !regular.is_empty() {
-        let known: HashSet<&str> = agent
-            .functions()
-            .declarations()
-            .iter()
-            .map(|d| d.name.as_str())
-            .collect();
-        for name in regular {
-            if !known.contains(name.as_str()) {
-                let mut avail: Vec<&str> = known.iter().copied().collect();
-                avail.sort();
-                bail!(
-                    "llm node references unknown tool '{name}'. Agent '{}' provides: {}",
-                    agent.name(),
-                    avail.join(", ")
-                );
-            }
-        }
-    }
-
-    if !mcp_servers.is_empty() {
-        let known: HashSet<&str> = agent
-            .mcp_server_names()
-            .iter()
-            .map(|s| s.as_str())
-            .collect();
-        for server in mcp_servers {
-            if !known.contains(server.as_str()) {
-                let mut avail: Vec<&str> = known.iter().copied().collect();
-                avail.sort();
-                bail!(
-                    "llm node references unknown MCP server 'mcp:{server}'. \
-                     Agent '{}' has MCP servers: [{}]",
-                    agent.name(),
-                    avail.join(", ")
-                );
-            }
-        }
-    }
-
-    Ok(())
-}
-
-fn is_transient(err: &Error) -> bool {
-    let s = format!("{err:#}");
-    s.contains("timed out")
-        || s.contains("rate limit")
-        || s.contains("429")
-        || s.contains("Connection reset")
-        || s.contains("Connection refused")
-        || s.contains("produced no output")
-}
-
-fn apply_state_updates_with_output(
-    node: &LlmNode,
-    state_manager: &mut StateManager,
-    output: &Value,
-) {
-    if node.output_schema.is_some()
-        && let Some(obj) = output.as_object()
-    {
-        for (k, v) in obj {
-            state_manager.state_mut().set(k.clone(), v.clone());
-        }
-    }
-
-    let Some(updates) = &node.state_updates else {
-        return;
-    };
-    let prev_output = state_manager.state().get(OUTPUT_KEY).cloned();
-    state_manager
-        .state_mut()
-        .set(OUTPUT_KEY.into(), output.clone());
-
-    for (key, template) in updates {
-        let value = state_manager.interpolate_lenient(template);
-        state_manager
-            .state_mut()
-            .set(key.clone(), Value::String(value));
-    }
-
-    match prev_output {
-        Some(v) => state_manager.state_mut().set(OUTPUT_KEY.into(), v),
-        None => {
-            state_manager
-                .state_mut()
-                .set(OUTPUT_KEY.into(), Value::Null);
-        }
-    }
-}
-
-fn format_schema_hint(schema: &Value) -> String {
-    let schema_json = serde_json::to_string_pretty(schema).unwrap_or_else(|_| schema.to_string());
-    format!(
-        "Respond with a JSON object that matches this schema. Output ONLY the JSON \
-         object with no surrounding prose or markdown fences.\n\nSchema:\n{schema_json}"
-    )
-}
-
-#[cfg(test)]
-mod tests {
-    use super::super::types::*;
-    use super::*;
-    use serde_json::json;
-    use std::collections::HashMap;
-
-    fn manager_with(pairs: &[(&str, Value)]) -> StateManager {
-        let mut map = HashMap::new();
-        for (k, v) in pairs {
-            map.insert((*k).into(), v.clone());
-        }
-        StateManager::new(map)
-    }
-
-    fn node_with(updates: Option<HashMap<String, String>>) -> LlmNode {
-        LlmNode {
-            instructions: Some("sys".into()),
-            prompt: "user".into(),
-            tools: None,
-            model: None,
-            temperature: None,
-            top_p: None,
-            fallback: None,
-            max_attempts: 1,
-            max_iterations: 10,
-            state_updates: updates,
-            output_schema: None,
-            timeout: None,
-        }
-    }
-
-    #[test]
-    fn state_updates_expose_output_during_evaluation() {
-        let mut u = HashMap::new();
-        u.insert("response".into(), "{{output}}".into());
-        let node = node_with(Some(u));
-        let mut state = manager_with(&[]);
-
-        apply_state_updates_with_output(&node, &mut state, &json!("the answer"));
-
-        assert_eq!(state.state().get("response"), Some(&json!("the answer")));
-    }
-
-    #[test]
-    fn state_updates_can_mix_existing_keys_with_output() {
-        let mut u = HashMap::new();
-        u.insert("summary".into(), "{{topic}}: {{output}}".into());
-        let node = node_with(Some(u));
-        let mut state = manager_with(&[("topic", json!("LOINC"))]);
-
-        apply_state_updates_with_output(&node, &mut state, &json!("abc"));
-
-        assert_eq!(state.state().get("summary"), Some(&json!("LOINC: abc")));
-    }
-
-    #[test]
-    fn output_key_is_cleared_after_state_updates() {
-        let mut u = HashMap::new();
-        u.insert("k".into(), "{{output}}".into());
-        let node = node_with(Some(u));
-        let mut state = manager_with(&[]);
-
-        apply_state_updates_with_output(&node, &mut state, &json!("anything"));
-
-        assert_eq!(state.state().get(OUTPUT_KEY), Some(&json!(null)));
-    }
-
-    #[test]
-    fn pre_existing_output_value_is_restored() {
-        let mut u = HashMap::new();
-        u.insert("greeting".into(), "{{output}}".into());
-        let node = node_with(Some(u));
-        let mut state = manager_with(&[("output", json!("preserved"))]);
-
-        apply_state_updates_with_output(&node, &mut state, &json!("new"));
-
-        assert_eq!(state.state().get("greeting"), Some(&json!("new")));
-        assert_eq!(state.state().get(OUTPUT_KEY), Some(&json!("preserved")));
-    }
-
-    #[test]
-    fn no_state_updates_is_a_noop() {
-        let node = node_with(None);
-        let mut state = manager_with(&[("k", json!("v"))]);
-
-        apply_state_updates_with_output(&node, &mut state, &json!("x"));
-
-        assert_eq!(state.state().get("k"), Some(&json!("v")));
-        assert!(state.state().get(OUTPUT_KEY).is_none());
-    }
-
-    #[test]
-    fn outcome_from_success_is_continue() {
-        assert_eq!(
-            outcome_from(None, Some("fb")).unwrap(),
-            LlmExecutionOutcome::Continue
-        );
-        assert_eq!(
-            outcome_from(None, None).unwrap(),
-            LlmExecutionOutcome::Continue
-        );
-    }
-
-    #[test]
-    fn outcome_from_failure_with_fallback_is_fell_back() {
-        assert_eq!(
-            outcome_from(Some("HTTP 404"), Some("fb")).unwrap(),
-            LlmExecutionOutcome::FellBack("fb".to_string())
-        );
-    }
-
-    #[test]
-    fn outcome_from_failure_without_fallback_propagates_error() {
-        let err = outcome_from(Some("HTTP 404"), None).unwrap_err();
-        let msg = format!("{err:#}");
-        assert!(msg.contains("no fallback declared"), "got: {msg}");
-        assert!(msg.contains("HTTP 404"), "got: {msg}");
-    }
-
-    fn node_with_schema(updates: Option<HashMap<String, String>>, schema: Value) -> LlmNode {
-        let mut n = node_with(updates);
-        n.output_schema = Some(schema);
-        n
-    }
-
-    #[test]
-    fn output_schema_auto_merges_top_level_keys() {
-        let node = node_with_schema(None, json!({"type": "object"}));
-        let mut state = manager_with(&[]);
-        let output = json!({"goal": "do X", "summary": "details"});
-
-        apply_state_updates_with_output(&node, &mut state, &output);
-
-        assert_eq!(state.state().get("goal"), Some(&json!("do X")));
-        assert_eq!(state.state().get("summary"), Some(&json!("details")));
-    }
-
-    #[test]
-    fn output_schema_preserves_nested_value_types() {
-        let node = node_with_schema(None, json!({"type": "object"}));
-        let mut state = manager_with(&[]);
-        let output = json!({
-            "tags": ["a", "b"],
-            "config": { "key": "value" },
-            "count": 42
-        });
-
-        apply_state_updates_with_output(&node, &mut state, &output);
-
-        assert_eq!(state.state().get("tags"), Some(&json!(["a", "b"])));
-        assert_eq!(state.state().get("config"), Some(&json!({"key": "value"})));
-        assert_eq!(state.state().get("count"), Some(&json!(42)));
-    }
-
-    #[test]
-    fn output_schema_explicit_state_updates_override_auto_merge() {
-        let mut u = HashMap::new();
-        u.insert("goal".into(), "renamed-{{output.goal}}".into());
-        let node = node_with_schema(Some(u), json!({"type": "object"}));
-        let mut state = manager_with(&[]);
-        let output = json!({"goal": "do X"});
-
-        apply_state_updates_with_output(&node, &mut state, &output);
-
-        assert_eq!(state.state().get("goal"), Some(&json!("renamed-do X")));
-    }
-
-    #[test]
-    fn output_schema_skips_auto_merge_for_non_object() {
-        let node = node_with_schema(None, json!({"type": "array"}));
-        let mut state = manager_with(&[]);
-        let output = json!([1, 2, 3]);
-
-        apply_state_updates_with_output(&node, &mut state, &output);
-
-        assert!(state.state().get("0").is_none());
-        assert!(state.state().get(OUTPUT_KEY).is_none());
-    }
-
-    #[test]
-    fn no_schema_does_not_auto_merge() {
-        let node = node_with(None);
-        let mut state = manager_with(&[]);
-        let output = json!({"goal": "do X"});
-
-        apply_state_updates_with_output(&node, &mut state, &output);
-
-        assert!(state.state().get("goal").is_none());
-    }
-
-    #[test]
-    fn format_schema_hint_includes_schema_and_instruction() {
-        let schema = json!({"type": "object", "properties": {"goal": {"type": "string"}}});
-
-        let hint = format_schema_hint(&schema);
-
-        assert!(hint.contains("Schema:"));
-        assert!(hint.contains("\"goal\""));
-        assert!(hint.contains("JSON"));
-        assert!(hint.contains("ONLY"));
-    }
-
-    #[test]
-    fn categorize_tools_splits_mcp_and_regular() {
-        let entries = vec![
-            "read_query".to_string(),
-            "mcp:pubmed-search".to_string(),
-            "web_search_loki".to_string(),
-            "mcp:github".to_string(),
-        ];
-
-        let (regular, mcp) = categorize_tools(Some(&entries));
-
-        assert_eq!(regular, vec!["read_query", "web_search_loki"]);
-        assert_eq!(mcp, vec!["pubmed-search", "github"]);
-    }
-
-    #[test]
-    fn categorize_tools_with_none_returns_empty() {
-        let (regular, mcp) = categorize_tools(None);
-
-        assert!(regular.is_empty());
-        assert!(mcp.is_empty());
-    }
-
-    #[test]
-    fn categorize_tools_with_empty_returns_empty() {
-        let (regular, mcp) = categorize_tools(Some(&[]));
-
-        assert!(regular.is_empty());
-        assert!(mcp.is_empty());
-    }
-
-    #[test]
-    fn is_transient_matches_expected_signatures() {
-        assert!(is_transient(&anyhow!("request timed out after 30s")));
-        assert!(is_transient(&anyhow!("rate limit reached")));
-        assert!(is_transient(&anyhow!("429 too many requests")));
-        assert!(is_transient(&anyhow!("Connection reset by peer")));
-        assert!(is_transient(&anyhow!("Connection refused")));
-        assert!(is_transient(&anyhow!("llm produced no output")));
-    }
-
-    #[test]
-    fn is_transient_rejects_non_transient_errors() {
-        assert!(!is_transient(&anyhow!("Unknown model 'foo'")));
-        assert!(!is_transient(&anyhow!(
-            "llm node references unknown tool 'bad'"
-        )));
-        assert!(!is_transient(&anyhow!("hit max_iterations")));
-        assert!(!is_transient(&anyhow!("authentication failed")));
-    }
-}

src/graph/logging.rs

@@ -1,312 +0,0 @@
-use super::state::StateManager;
-use super::types::{Node, NodeType};
-use crate::utils::dimmed_text;
-use chrono::Local;
-use indexmap::IndexMap;
-use std::cmp::Reverse;
-use std::time::Duration;
-
-fn ts() -> String {
-    Local::now().format("%H:%M:%S").to_string()
-}
-
-fn fmt_secs(elapsed: Duration) -> String {
-    let secs = elapsed.as_secs_f64();
-    if secs < 1.0 {
-        format!("{}ms", elapsed.as_millis())
-    } else {
-        format!("{secs:.2}s")
-    }
-}
-
-#[derive(Debug, Clone, Default)]
-struct NodeTiming {
-    count: usize,
-    total: Duration,
-    max: Duration,
-}
-
-impl NodeTiming {
-    fn record(&mut self, elapsed: Duration) {
-        self.count += 1;
-        self.total += elapsed;
-        if elapsed > self.max {
-            self.max = elapsed;
-        }
-    }
-}
-
-pub struct GraphLogger {
-    graph_name: String,
-    log_state_snapshots: bool,
-    silent: bool,
-    timings: IndexMap<String, NodeTiming>,
-}
-
-impl GraphLogger {
-    pub fn with_visibility(graph_name: &str, log_state_snapshots: bool, silent: bool) -> Self {
-        Self {
-            graph_name: graph_name.to_string(),
-            log_state_snapshots,
-            silent,
-            timings: IndexMap::new(),
-        }
-    }
-
-    pub fn graph_start(&self, start_node: &str, node_count: usize) {
-        info!(
-            "[graph:{}] start at '{}' ({} nodes)",
-            self.graph_name, start_node, node_count
-        );
-        if !self.silent {
-            eprintln!(
-                "{}",
-                dimmed_text(&format!(
-                    "▸ graph: {} (start: {start_node})",
-                    self.graph_name
-                ))
-            );
-        }
-    }
-
-    pub fn graph_complete(&self, end_node: &str, elapsed: Duration) {
-        info!(
-            "[graph:{}] end '{}' (elapsed {:?})",
-            self.graph_name, end_node, elapsed
-        );
-        if !self.silent {
-            eprintln!(
-                "{}",
-                dimmed_text(&format!("▸ graph done in {:.2}s", elapsed.as_secs_f64()))
-            );
-        }
-        self.log_performance_summary();
-    }
-
-    pub fn graph_error(&self, error: &anyhow::Error) {
-        error!("[graph:{}] execution failed: {error:#}", self.graph_name);
-    }
-
-    pub fn node_entry(&self, node: &Node, visit: usize) {
-        debug!(
-            "[graph:{}] entering '{}' (visit {visit})",
-            self.graph_name, node.id
-        );
-    }
-
-    pub fn silent(&self) -> bool {
-        self.silent
-    }
-
-    pub fn node_start(&self, node: &Node, in_super_step: bool) {
-        narrate_node_start(self.silent, node, in_super_step);
-    }
-
-    pub fn super_step_start(&self, branches: &[String]) {
-        if self.silent {
-            return;
-        }
-        eprintln!(
-            "{}",
-            dimmed_text(&format!(
-                "▸ {} super-step start: {}",
-                ts(),
-                branches.join(", ")
-            ))
-        );
-    }
-
-    pub fn super_step_end(&self, targets: &[String]) {
-        if self.silent {
-            return;
-        }
-        let route = if targets.is_empty() {
-            String::new()
-        } else {
-            format!(" -> {}", targets.join(", "))
-        };
-        eprintln!(
-            "{}",
-            dimmed_text(&format!("▸ {} super-step end{route}", ts()))
-        );
-    }
-
-    pub fn record_timing(&mut self, node_id: &str, elapsed: Duration) {
-        self.timings
-            .entry(node_id.to_string())
-            .or_default()
-            .record(elapsed);
-    }
-
-    pub fn routing(&self, from: &str, to: &str) {
-        debug!("[graph:{}] {from} -> {to}", self.graph_name);
-    }
-
-    pub fn validation_warning(&self, node_id: Option<&str>, message: &str) {
-        match node_id {
-            Some(id) => warn!("[graph:{}] [{id}] {message}", self.graph_name),
-            None => warn!("[graph:{}] {message}", self.graph_name),
-        }
-    }
-
-    pub fn state_snapshot(&self, node_id: &str, state: &StateManager) {
-        if !self.log_state_snapshots {
-            return;
-        }
-        let snapshot = state.snapshot();
-        let mut keys: Vec<&str> = snapshot.keys().map(String::as_str).collect();
-        keys.sort_unstable();
-
-        debug!(
-            "[graph:{}] [{node_id}] state: {} bytes, keys={:?}",
-            self.graph_name,
-            state.size_bytes(),
-            keys
-        );
-        trace!(
-            "[graph:{}] [{node_id}] full state: {:?}",
-            self.graph_name, snapshot
-        );
-    }
-
-    fn log_performance_summary(&self) {
-        if self.timings.is_empty() {
-            return;
-        }
-        let mut rows: Vec<(&String, &NodeTiming)> = self.timings.iter().collect();
-        rows.sort_by_key(|b| Reverse(b.1.total));
-
-        info!(
-            "[graph:{}] performance summary (slowest first):",
-            self.graph_name
-        );
-
-        for (node_id, t) in rows {
-            let avg = t.total / t.count.max(1) as u32;
-            info!(
-                "[graph:{}]   {node_id}: {} visit(s), total {}ms, avg {}ms, max {}ms",
-                self.graph_name,
-                t.count,
-                t.total.as_millis(),
-                avg.as_millis(),
-                t.max.as_millis(),
-            );
-        }
-    }
-}
-
-pub fn narrate_node_start(silent: bool, node: &Node, in_super_step: bool) {
-    if silent {
-        return;
-    }
-    let indent = if in_super_step { "  " } else { "" };
-    let label = node_type_label(node);
-    eprintln!(
-        "{}",
-        dimmed_text(&format!("▸ {} {indent}{} ({label}) start", ts(), node.id))
-    );
-}
-
-pub fn narrate_node_complete(
-    silent: bool,
-    node: &Node,
-    elapsed: Duration,
-    next_target: Option<&str>,
-    in_super_step: bool,
-) {
-    if silent {
-        return;
-    }
-    let indent = if in_super_step { "  " } else { "" };
-    let label = node_type_label(node);
-    let dur = fmt_secs(elapsed);
-    let route = next_target.map(|t| format!(" -> {t}")).unwrap_or_default();
-    eprintln!(
-        "{}",
-        dimmed_text(&format!(
-            "▸ {} {indent}{} ({label}) done in {dur}{route}",
-            ts(),
-            node.id
-        ))
-    );
-}
-
-pub fn narrate_node_failed(
-    silent: bool,
-    node: &Node,
-    elapsed: Duration,
-    err: &str,
-    in_super_step: bool,
-) {
-    if silent {
-        return;
-    }
-    let indent = if in_super_step { "  " } else { "" };
-    let label = node_type_label(node);
-    let dur = fmt_secs(elapsed);
-    let excerpt: String = err.chars().take(120).collect();
-    eprintln!(
-        "{}",
-        dimmed_text(&format!(
-            "▸ {} {indent}{} ({label}) FAILED in {dur} -- {excerpt}",
-            ts(),
-            node.id
-        ))
-    );
-}
-
-pub(super) fn node_type_label(node: &Node) -> &'static str {
-    match &node.node_type {
-        NodeType::Agent(_) => "agent",
-        NodeType::Script(_) => "script",
-        NodeType::Approval(_) => "approval",
-        NodeType::Input(_) => "input",
-        NodeType::Llm(_) => "llm",
-        NodeType::Rag(_) => "rag",
-        NodeType::End(_) => "end",
-        NodeType::Map(_) => "map",
-    }
-}
-
-#[cfg(test)]
-mod tests {
-    use super::*;
-
-    #[test]
-    fn records_and_aggregates_node_timings() {
-        let mut logger = GraphLogger::with_visibility("g", false, false);
-        logger.record_timing("a", Duration::from_millis(100));
-        logger.record_timing("a", Duration::from_millis(300));
-        logger.record_timing("b", Duration::from_millis(50));
-
-        let a = logger.timings.get("a").unwrap();
-        assert_eq!(a.count, 2);
-        assert_eq!(a.total, Duration::from_millis(400));
-        assert_eq!(a.max, Duration::from_millis(300));
-
-        let b = logger.timings.get("b").unwrap();
-        assert_eq!(b.count, 1);
-        assert_eq!(b.total, Duration::from_millis(50));
-    }
-
-    #[test]
-    fn node_timing_max_tracks_largest() {
-        let mut t = NodeTiming::default();
-
-        t.record(Duration::from_millis(10));
-        t.record(Duration::from_millis(80));
-        t.record(Duration::from_millis(40));
-
-        assert_eq!(t.max, Duration::from_millis(80));
-        assert_eq!(t.count, 3);
-        assert_eq!(t.total, Duration::from_millis(130));
-    }
-
-    #[test]
-    fn new_logger_has_no_timings() {
-        let logger = GraphLogger::with_visibility("g", true, false);
-
-        assert!(logger.timings.is_empty());
-        assert!(logger.log_state_snapshots);
-    }
-}

src/graph/map.rs

@@ -1,152 +0,0 @@
-use super::agent::AgentNodeExecutor;
-use super::executor::StepContext;
-use super::llm::LlmNodeExecutor;
-use super::rag::RagNodeExecutor;
-use super::state::StateManager;
-use super::types::{MapNode, NodeType};
-use crate::config::{RenderMode, RequestContext};
-use crate::graph::type_name;
-use anyhow::{Context, Result, anyhow};
-use futures_util::future::join_all;
-use serde_json::Value;
-use std::collections::HashMap;
-use std::sync::Arc;
-use tokio::sync::Semaphore;
-
-pub(super) struct MapNodeExecutor;
-
-impl MapNodeExecutor {
-    pub(super) async fn execute(
-        node: &MapNode,
-        state: &mut StateManager,
-        ctx: &mut RequestContext,
-        step_ctx: &StepContext<'_>,
-        node_id: &str,
-    ) -> Result<()> {
-        let over_value = state
-            .interpolate_raw(&node.over)
-            .with_context(|| format!("map node '{node_id}': evaluating `over` template"))?;
-
-        let items = over_value.as_array().ok_or_else(|| {
-            anyhow!(
-                "map node '{}': `over` template '{}' must resolve to an array, got {}",
-                node_id,
-                node.over,
-                type_name(&over_value)
-            )
-        })?;
-        let items = items.clone();
-
-        let branch_node = step_ctx
-            .graph
-            .get_node(&node.branch)
-            .ok_or_else(|| {
-                anyhow!(
-                    "map node '{node_id}': branch '{}' not found in graph",
-                    node.branch
-                )
-            })?
-            .clone();
-
-        let max_conc = node
-            .max_concurrency
-            .unwrap_or(step_ctx.max_concurrency)
-            .max(1);
-        let semaphore = Arc::new(Semaphore::new(max_conc));
-        let mut sub_tasks = Vec::with_capacity(items.len());
-
-        for (idx, item) in items.iter().enumerate() {
-            let item = item.clone();
-            let as_name = node.as_name.clone();
-            let branch_clone = branch_node.clone();
-            let mut sub_state = state.fork_for_branch_state();
-            let mut sub_ctx = ctx.fork_for_branch();
-            sub_ctx.render_mode = RenderMode::Silent;
-            let script_clone = step_ctx.script_executor.clone();
-            let sub_branch_id = node.branch.clone();
-            let sem = semaphore.clone();
-            let abort = step_ctx.abort_signal.clone();
-
-            sub_state.state_mut().set(as_name, item);
-
-            let task = tokio::spawn(async move {
-                let _permit = sem
-                    .acquire()
-                    .await
-                    .expect("map semaphore should not be closed");
-                if abort.aborted() {
-                    return (
-                        idx,
-                        sub_state,
-                        Err(anyhow!("map sub-branch [{idx}] aborted")),
-                    );
-                }
-                let mut state = sub_state;
-                let mut ctx = sub_ctx;
-
-                let exec_result: Result<()> = match &branch_clone.node_type {
-                    NodeType::Llm(n) => LlmNodeExecutor::execute(n, &mut state, &mut ctx)
-                        .await
-                        .map(|_| ()),
-                    NodeType::Agent(n) => AgentNodeExecutor::execute(n, &mut state, &mut ctx)
-                        .await
-                        .map(|_| ()),
-                    NodeType::Rag(n) => {
-                        RagNodeExecutor::execute(n, &sub_branch_id, &mut state, &mut ctx).await
-                    }
-                    NodeType::Script(n) => script_clone.execute(n, &mut state).await.map(|_| ()),
-                    _ => Err(anyhow!(
-                        "map branch '{}' has type that cannot run inside a map \
-                         (validator should have caught this; internal error)",
-                        branch_clone.id
-                    )),
-                };
-
-                (idx, state, exec_result)
-            });
-            sub_tasks.push(task);
-        }
-
-        let joined = join_all(sub_tasks).await;
-
-        // Collect outputs keyed by input index so order is preserved regardless of finish order.
-        let mut outputs: HashMap<usize, Value> = HashMap::new();
-        for join_result in joined {
-            let (idx, sub_state, exec_result) =
-                join_result.map_err(|e| anyhow!("map sub-branch panicked: {e}"))?;
-
-            exec_result
-                .with_context(|| format!("map node '{node_id}': sub-branch [{idx}] failed"))?;
-
-            let output_value = sub_state
-                .state()
-                .get(&node.output_key)
-                .cloned()
-                .ok_or_else(|| {
-                    anyhow!(
-                        "map node '{node_id}': sub-branch [{idx}] did not write \
-                         `output_key` '{}'",
-                        node.output_key
-                    )
-                })?;
-
-            outputs.insert(idx, output_value);
-        }
-
-        let mut collected = Vec::with_capacity(items.len());
-        for idx in 0..items.len() {
-            let value = outputs.remove(&idx).ok_or_else(|| {
-                anyhow!(
-                    "map node '{node_id}': internal error: missing result for sub-branch [{idx}]"
-                )
-            })?;
-            collected.push(value);
-        }
-
-        state
-            .state_mut()
-            .set(node.collect_into.clone(), Value::Array(collected));
-
-        Ok(())
-    }
-}

src/graph/mod.rs

@@ -1,39 +0,0 @@
-pub mod agent;
-pub mod dispatch;
-pub mod executor;
-pub mod llm;
-pub mod logging;
-pub mod map;
-pub mod parser;
-pub mod rag;
-pub mod reducer;
-pub mod script;
-pub mod staging;
-pub mod state;
-pub mod structured;
-pub mod types;
-pub mod user_interaction;
-pub mod validator;
-
-pub use dispatch::{active_agent_graph_name, run_active_agent_graph};
-pub use executor::GraphExecutor;
-pub use parser::{GraphParser, agent_has_graph};
-use serde_json::Value;
-pub use types::{Graph, NodeType};
-
-pub const GRAPH_SCHEMA_VERSION: &str = "1.0";
-
-pub const DEFAULT_MAX_LOOP_ITERATIONS: usize = 100;
-
-pub const MAX_STATE_SIZE_BYTES: usize = 32 * 1024;
-
-pub(in crate::graph) fn type_name(value: &Value) -> &'static str {
-    match value {
-        Value::Null => "null",
-        Value::Bool(_) => "bool",
-        Value::Number(_) => "number",
-        Value::String(_) => "string",
-        Value::Array(_) => "array",
-        Value::Object(_) => "object",
-    }
-}

src/graph/parser.rs

@@ -1,462 +0,0 @@
-use super::types::Graph;
-use crate::config::paths;
-use anyhow::{Context, Error, Result, anyhow, bail};
-use std::fs::read_to_string;
-use std::path::{Path, PathBuf};
-
-const SUPPORTED_VERSIONS: &[&str] = &["1.0"];
-
-pub struct GraphParser {
-    base_dir: PathBuf,
-}
-
-impl GraphParser {
-    pub fn new(base_dir: impl Into<PathBuf>) -> Self {
-        Self {
-            base_dir: base_dir.into(),
-        }
-    }
-
-    pub fn load_from_file(&self, path: impl AsRef<Path>) -> Result<Graph> {
-        let path = path.as_ref();
-        let full_path = if path.is_absolute() {
-            path.to_path_buf()
-        } else {
-            self.base_dir.join(path)
-        };
-
-        let contents = read_to_string(&full_path)
-            .with_context(|| format!("Failed to read graph file at '{}'", full_path.display()))?;
-
-        self.load_from_string(&contents)
-            .with_context(|| format!("Failed to parse graph file at '{}'", full_path.display()))
-    }
-
-    pub fn load_from_string(&self, yaml: &str) -> Result<Graph> {
-        let mut graph: Graph = serde_yaml::from_str(yaml).map_err(enhance_yaml_error)?;
-
-        validate_schema_version(&graph.version)?;
-
-        for (key, node) in &mut graph.nodes {
-            if node.id.is_empty() {
-                node.id = key.clone();
-            } else if &node.id != key {
-                bail!(
-                    "Node ID mismatch: key '{}' does not match node.id '{}'",
-                    key,
-                    node.id
-                );
-            }
-        }
-
-        validate_structure(&graph)?;
-
-        Ok(graph)
-    }
-}
-
-fn validate_schema_version(version: &str) -> Result<()> {
-    if !SUPPORTED_VERSIONS.contains(&version) {
-        bail!(
-            "Unsupported graph schema version '{}'. Supported versions: {}",
-            version,
-            SUPPORTED_VERSIONS.join(", ")
-        );
-    }
-
-    Ok(())
-}
-
-fn validate_structure(graph: &Graph) -> Result<()> {
-    if graph.name.is_empty() {
-        bail!("Graph must have a non-empty 'name' field");
-    }
-
-    if graph.nodes.is_empty() {
-        bail!("Graph '{}' has no nodes defined", graph.name);
-    }
-
-    if !graph.has_node(&graph.start) {
-        bail!(
-            "Start node '{}' not found in graph '{}'. Available nodes: {}",
-            graph.start,
-            graph.name,
-            graph.node_ids().join(", ")
-        );
-    }
-
-    Ok(())
-}
-
-fn enhance_yaml_error(error: serde_yaml::Error) -> Error {
-    let msg = error.to_string();
-
-    let hint = if msg.contains("missing field") {
-        "\n\nHint: Check that all required fields are present.\n\
-         Top-level required fields: `name`, `start`, `nodes`.\n\
-         Each node requires `type` plus that type's fields:\n\
-         - agent:    `agent`, `prompt`\n\
-         - script:   `script`\n\
-         - approval: `question`, `options`, `routes`, `on_other`\n\
-         - input:    `question`\n\
-         - llm:      `prompt`\n\
-         - rag:      `documents`\n\
-         - end:      (no required fields)"
-    } else if msg.contains("unknown field") || msg.contains("unknown variant") {
-        "\n\nHint: Check for typos in field names or `type:` values.\n\
-         Valid node types: agent, script, approval, input, llm, rag, end."
-    } else if msg.contains("invalid type") {
-        "\n\nHint: Check that field values have the correct type.\n\
-         - Strings should be quoted if they contain special characters\n\
-         - Numbers should not be quoted\n\
-         - Lists use YAML array syntax (- item1)\n\
-         - Maps use YAML object syntax (key: value)"
-    } else {
-        ""
-    };
-
-    anyhow!("YAML parsing error: {}{}", msg, hint)
-}
-
-pub fn agent_has_graph(agent_name: &str) -> bool {
-    paths::agent_graph_file(agent_name).exists()
-}
-
-#[cfg(test)]
-mod tests {
-    use super::super::GRAPH_SCHEMA_VERSION;
-    use super::super::types::NodeType;
-    use super::*;
-    use indoc::formatdoc;
-    use std::fs::File;
-    use std::io::Write;
-    use std::{env, fs, process};
-
-    fn parser() -> GraphParser {
-        GraphParser::new(env::current_dir().unwrap())
-    }
-
-    #[test]
-    fn parses_a_simple_graph() {
-        let yaml = formatdoc! {r#"
-            name: simple_graph
-            version: "1.0"
-            start: node1
-            nodes:
-              node1:
-                id: node1
-                type: agent
-                agent: test_agent
-                prompt: "Hello world"
-                next: node2
-              node2:
-                id: node2
-                type: end
-                output: done
-            "#};
-
-        let graph = parser().load_from_string(&yaml).unwrap();
-
-        assert_eq!(graph.name, "simple_graph");
-        assert_eq!(graph.start, "node1");
-        assert_eq!(graph.nodes.len(), 2);
-        assert_eq!(
-            graph.nodes.get("node1").unwrap().next_target(),
-            Some("node2")
-        );
-    }
-
-    #[test]
-    fn auto_fills_node_ids_from_keys() {
-        let yaml = formatdoc! {r#"
-            name: auto_id_graph
-            version: "1.0"
-            start: node1
-            nodes:
-              node1:
-                type: agent
-                agent: test_agent
-                prompt: Test
-                next: node2
-              node2:
-                type: end
-                output: done
-            "#};
-
-        let graph = parser().load_from_string(&yaml).unwrap();
-
-        assert_eq!(graph.nodes.get("node1").unwrap().id, "node1");
-        assert_eq!(graph.nodes.get("node2").unwrap().id, "node2");
-    }
-
-    #[test]
-    fn rejects_missing_start_node() {
-        let yaml = formatdoc! {r#"
-            name: bad_graph
-            version: "1.0"
-            start: nonexistent
-            nodes:
-              node1:
-                type: end
-            "#};
-
-        let err = parser().load_from_string(&yaml).unwrap_err().to_string();
-
-        assert!(
-            err.contains("Start node 'nonexistent' not found"),
-            "got: {err}"
-        );
-    }
-
-    #[test]
-    fn rejects_empty_graph_name() {
-        let yaml = formatdoc! {r#"
-            name: ""
-            version: "1.0"
-            start: node1
-            nodes:
-              node1:
-                type: end
-            "#};
-
-        let err = parser().load_from_string(&yaml).unwrap_err().to_string();
-
-        assert!(err.contains("non-empty 'name'"), "got: {err}");
-    }
-
-    #[test]
-    fn rejects_no_nodes() {
-        let yaml = formatdoc! {r#"
-            name: empty_graph
-            version: "1.0"
-            start: node1
-            nodes: {}
-            "#, "{}"};
-
-        let err = parser().load_from_string(&yaml).unwrap_err().to_string();
-
-        assert!(err.contains("no nodes defined"), "got: {err}");
-    }
-
-    #[test]
-    fn rejects_unsupported_version() {
-        let yaml = formatdoc! {r#"
-            name: future_graph
-            version: "2.0"
-            start: node1
-            nodes:
-              node1:
-                type: end
-            "#};
-
-        let err = parser().load_from_string(&yaml).unwrap_err().to_string();
-
-        assert!(
-            err.contains("Unsupported graph schema version"),
-            "got: {err}"
-        );
-    }
-
-    #[test]
-    fn rejects_node_id_mismatch() {
-        let yaml = formatdoc! {r#"
-            name: mismatch_graph
-            version: "1.0"
-            start: node1
-            nodes:
-              node1:
-                id: different_id
-                type: end
-            "#};
-
-        let err = parser().load_from_string(&yaml).unwrap_err().to_string();
-
-        assert!(err.contains("Node ID mismatch"), "got: {err}");
-    }
-
-    #[test]
-    fn parses_approval_node_with_routes() {
-        let yaml = formatdoc! {r#"
-            name: approval_graph
-            version: "1.0"
-            start: approval1
-            nodes:
-              approval1:
-                type: approval
-                question: "Proceed with deployment?"
-                options:
-                  - "Yes"
-                  - "No"
-                routes:
-                  "Yes": deploy
-                  "No": cancel
-                on_other: cancel
-              deploy:
-                type: end
-              cancel:
-                type: end
-            "#};
-
-        let graph = parser().load_from_string(&yaml).unwrap();
-
-        let approval = graph.nodes.get("approval1").unwrap();
-        match &approval.node_type {
-            NodeType::Approval(a) => {
-                assert_eq!(a.options.len(), 2);
-                assert_eq!(a.routes.len(), 2);
-                assert_eq!(a.routes.get("Yes").map(|s| s.as_str()), Some("deploy"));
-            }
-            _ => panic!("expected approval node"),
-        }
-    }
-
-    #[test]
-    fn parses_settings_overrides() {
-        let yaml = formatdoc! {r#"
-            name: settings_graph
-            version: "1.0"
-            start: node1
-            settings:
-              max_loop_iterations: 50
-              timeout: 300
-              log_state_snapshots: false
-            nodes:
-              node1:
-                type: end
-            "#};
-
-        let graph = parser().load_from_string(&yaml).unwrap();
-
-        assert_eq!(graph.settings.max_loop_iterations, 50);
-        assert_eq!(graph.settings.timeout, Some(300));
-        assert!(!graph.settings.log_state_snapshots);
-        assert!(graph.settings.validate_before_run);
-    }
-
-    #[test]
-    fn parses_initial_state() {
-        let yaml = formatdoc! {r#"
-            name: state_graph
-            version: "1.0"
-            start: node1
-            initial_state:
-              user_name: "Alice"
-              count: 42
-              enabled: true
-            nodes:
-              node1:
-                type: end
-            "#};
-
-        let graph = parser().load_from_string(&yaml).unwrap();
-
-        assert_eq!(graph.initial_state.len(), 3);
-        assert_eq!(graph.initial_state.get("user_name").unwrap(), "Alice");
-        assert_eq!(
-            graph.initial_state.get("count").unwrap(),
-            &serde_json::json!(42)
-        );
-        assert_eq!(
-            graph.initial_state.get("enabled").unwrap(),
-            &serde_json::json!(true)
-        );
-    }
-
-    #[test]
-    fn uses_default_version_when_absent() {
-        let yaml = formatdoc! {r#"
-            name: no_version
-            start: node1
-            nodes:
-              node1:
-                type: end
-            "#};
-
-        let graph = parser().load_from_string(&yaml).unwrap();
-
-        assert_eq!(graph.version, GRAPH_SCHEMA_VERSION);
-    }
-
-    #[test]
-    fn rejects_unknown_node_type_with_hint() {
-        let yaml = formatdoc! {r#"
-            name: bad_type
-            version: "1.0"
-            start: node1
-            nodes:
-              node1:
-                type: nonsense
-            "#};
-
-        let err = parser().load_from_string(&yaml).unwrap_err().to_string();
-
-        assert!(
-            err.contains("Valid node types") || err.contains("unknown variant"),
-            "got: {err}"
-        );
-    }
-
-    #[test]
-    fn rejects_malformed_yaml() {
-        let yaml = "name: bad\n  bad: indent\nstart: a";
-
-        let result = parser().load_from_string(yaml);
-
-        assert!(result.is_err());
-    }
-
-    #[test]
-    fn missing_required_fields_have_a_hint() {
-        let yaml = formatdoc! {r#"
-            name: missing_start
-            version: "1.0"
-            nodes:
-              node1:
-                type: end
-            "#};
-
-        let err = parser().load_from_string(&yaml).unwrap_err().to_string();
-
-        assert!(err.contains("Hint"), "got: {err}");
-    }
-
-    #[test]
-    fn load_from_file_reads_disk() {
-        let dir = env::temp_dir();
-        let path = dir.join(format!("loki_graph_parser_test_{}.yaml", process::id()));
-        let yaml = formatdoc! {r#"
-            name: disk_graph
-            version: "1.0"
-            start: only
-            nodes:
-              only:
-                type: end
-                output: ok
-            "#};
-        {
-            let mut f = File::create(&path).unwrap();
-            f.write_all(yaml.as_bytes()).unwrap();
-        }
-
-        let graph = GraphParser::new(dir).load_from_file(&path).unwrap();
-
-        assert_eq!(graph.name, "disk_graph");
-
-        let _ = fs::remove_file(&path);
-    }
-
-    #[test]
-    fn load_from_file_errors_on_missing_path() {
-        let err = parser()
-            .load_from_file("/definitely/not/a/real/path/to_any_graph.yaml")
-            .unwrap_err()
-            .to_string();
-
-        assert!(err.contains("Failed to read graph file"), "got: {err}");
-    }
-
-    #[test]
-    fn agent_has_graph_false_for_unknown_agent() {
-        assert!(!agent_has_graph("__nonexistent_agent_for_test__"));
-    }
-}

src/graph/rag.rs

@@ -1,129 +0,0 @@
-use super::state::StateManager;
-use super::types::RagNode;
-use crate::config::RequestContext;
-use crate::utils::create_abort_signal;
-use anyhow::{Context, Result, anyhow};
-use serde_json::{Map, Value};
-use std::time::Duration;
-use tokio::time::timeout;
-
-const OUTPUT_KEY: &str = "output";
-const DEFAULT_QUERY: &str = "{{initial_prompt}}";
-const DEFAULT_RAG_TIMEOUT_SECS: u64 = 120;
-
-pub struct RagNodeExecutor;
-
-impl RagNodeExecutor {
-    pub(super) async fn execute(
-        node: &RagNode,
-        node_id: &str,
-        state_manager: &mut StateManager,
-        ctx: &mut RequestContext,
-    ) -> Result<()> {
-        let query_template = node.query.as_deref().unwrap_or(DEFAULT_QUERY);
-        let query = state_manager
-            .interpolate(query_template)
-            .context("Failed to interpolate rag node query")?;
-
-        let rag = ctx
-            .agent
-            .as_ref()
-            .and_then(|a| a.graph_rag(node_id))
-            .ok_or_else(|| anyhow!("rag node '{node_id}' has no initialized knowledge base"))?;
-
-        let top_k = node.top_k.unwrap_or_else(|| rag.configured_top_k());
-        let rerank = rag.configured_reranker();
-
-        let timeout_dur = Duration::from_secs(node.timeout.unwrap_or(DEFAULT_RAG_TIMEOUT_SECS));
-        let abort = create_abort_signal();
-        let (context, sources_str, _ids) =
-            timeout(timeout_dur, rag.search(&query, top_k, rerank, abort))
-                .await
-                .with_context(|| {
-                    format!(
-                        "rag node '{node_id}' timed out after {}s",
-                        timeout_dur.as_secs()
-                    )
-                })?
-                .with_context(|| format!("rag node '{node_id}' retrieval failed"))?;
-
-        let output = build_rag_output(context, &sources_str);
-        apply_state_updates(node, state_manager, &output);
-        Ok(())
-    }
-}
-
-/// Assemble the `{{output}}` value as `{ "context": <ctx>, "sources": [...] }`.
-fn build_rag_output(context: String, sources_str: &str) -> Value {
-    let sources: Vec<Value> = sources_str
-        .lines()
-        .map(|line| line.trim().trim_start_matches("- ").trim())
-        .filter(|s| !s.is_empty())
-        .map(|s| Value::String(s.to_string()))
-        .collect();
-    let mut obj = Map::new();
-
-    obj.insert("context".into(), Value::String(context));
-    obj.insert("sources".into(), Value::Array(sources));
-
-    Value::Object(obj)
-}
-
-fn apply_state_updates(node: &RagNode, state_manager: &mut StateManager, output: &Value) {
-    let Some(updates) = &node.state_updates else {
-        return;
-    };
-    let prev_output = state_manager.state().get(OUTPUT_KEY).cloned();
-    state_manager
-        .state_mut()
-        .set(OUTPUT_KEY.into(), output.clone());
-
-    for (key, template) in updates {
-        let value = state_manager.interpolate_lenient(template);
-        state_manager
-            .state_mut()
-            .set(key.clone(), Value::String(value));
-    }
-
-    match prev_output {
-        Some(v) => state_manager.state_mut().set(OUTPUT_KEY.into(), v),
-        None => state_manager
-            .state_mut()
-            .set(OUTPUT_KEY.into(), Value::Null),
-    }
-}
-
-#[cfg(test)]
-mod tests {
-    use super::*;
-    use serde_json::json;
-
-    #[test]
-    fn build_rag_output_splits_bullet_sources_into_array() {
-        let out = build_rag_output("ctx".into(), "- a.md\n- https://x.com/spec");
-
-        assert_eq!(out["context"], json!("ctx"));
-        assert_eq!(out["sources"], json!(["a.md", "https://x.com/spec"]));
-    }
-
-    #[test]
-    fn build_rag_output_handles_empty_sources() {
-        let out = build_rag_output("ctx".into(), "");
-
-        assert_eq!(out["sources"], json!([]));
-    }
-
-    #[test]
-    fn build_rag_output_ignores_blank_lines() {
-        let out = build_rag_output("c".into(), "- a\n\n- b\n");
-
-        assert_eq!(out["sources"], json!(["a", "b"]));
-    }
-
-    #[test]
-    fn build_rag_output_tolerates_unprefixed_lines() {
-        let out = build_rag_output("c".into(), "plain/path");
-
-        assert_eq!(out["sources"], json!(["plain/path"]));
-    }
-}

src/graph/reducer.rs

@@ -1,389 +0,0 @@
-use super::types::Reducer;
-use crate::graph::type_name;
-use anyhow::{Result, bail};
-use serde_json::{Number, Value};
-
-pub fn apply(reducer: Reducer, current: Option<&Value>, incoming: Value) -> Result<Value> {
-    match reducer {
-        Reducer::Append => apply_append(current, incoming),
-        Reducer::Extend => apply_extend(current, incoming),
-        Reducer::Concat => apply_concat(current, incoming),
-        Reducer::Sum => apply_sum(current, incoming),
-        Reducer::Max => apply_max(current, incoming),
-        Reducer::Min => apply_min(current, incoming),
-        Reducer::Merge => apply_merge(current, incoming),
-        Reducer::Overwrite => Ok(incoming),
-    }
-}
-
-fn apply_append(current: Option<&Value>, incoming: Value) -> Result<Value> {
-    let mut arr = match current {
-        None => Vec::new(),
-        Some(Value::Array(a)) => a.clone(),
-        Some(other) => bail!(
-            "reducer 'append' requires an array (or absent) for the current value, got {}",
-            type_name(other)
-        ),
-    };
-    arr.push(incoming);
-
-    Ok(Value::Array(arr))
-}
-
-fn apply_extend(current: Option<&Value>, incoming: Value) -> Result<Value> {
-    let mut arr = match current {
-        None => Vec::new(),
-        Some(Value::Array(a)) => a.clone(),
-        Some(other) => bail!(
-            "reducer 'extend' requires an array (or absent) for the current value, got {}",
-            type_name(other)
-        ),
-    };
-    match incoming {
-        Value::Array(items) => arr.extend(items),
-        other => bail!(
-            "reducer 'extend' requires an array for the incoming value, got {}",
-            type_name(&other)
-        ),
-    }
-
-    Ok(Value::Array(arr))
-}
-
-fn apply_concat(current: Option<&Value>, incoming: Value) -> Result<Value> {
-    let incoming_str = match incoming {
-        Value::String(s) => s,
-        other => bail!(
-            "reducer 'concat' requires a string for the incoming value, got {}",
-            type_name(&other)
-        ),
-    };
-    let result = match current {
-        None => incoming_str,
-        Some(Value::String(c)) => {
-            if c.is_empty() {
-                incoming_str
-            } else {
-                format!("{c}\n{incoming_str}")
-            }
-        }
-        Some(other) => bail!(
-            "reducer 'concat' requires a string (or absent) for the current value, got {}",
-            type_name(other)
-        ),
-    };
-
-    Ok(Value::String(result))
-}
-
-fn apply_sum(current: Option<&Value>, incoming: Value) -> Result<Value> {
-    let i = number_or_error(&incoming, "sum", "incoming")?;
-    let c = match current {
-        None => 0.0,
-        Some(value) => number_or_error(value, "sum", "current")?,
-    };
-
-    Ok(json_number(c + i))
-}
-
-fn apply_max(current: Option<&Value>, incoming: Value) -> Result<Value> {
-    let i = number_or_error(&incoming, "max", "incoming")?;
-    match current {
-        None => Ok(json_number(i)),
-        Some(value) => {
-            let c = number_or_error(value, "max", "current")?;
-            Ok(json_number(c.max(i)))
-        }
-    }
-}
-
-fn apply_min(current: Option<&Value>, incoming: Value) -> Result<Value> {
-    let i = number_or_error(&incoming, "min", "incoming")?;
-    match current {
-        None => Ok(json_number(i)),
-        Some(value) => {
-            let c = number_or_error(value, "min", "current")?;
-            Ok(json_number(c.min(i)))
-        }
-    }
-}
-
-fn apply_merge(current: Option<&Value>, incoming: Value) -> Result<Value> {
-    let mut map = match current {
-        None => serde_json::Map::new(),
-        Some(Value::Object(m)) => m.clone(),
-        Some(other) => bail!(
-            "reducer 'merge' requires an object (or absent) for the current value, got {}",
-            type_name(other)
-        ),
-    };
-    match incoming {
-        Value::Object(items) => {
-            for (k, v) in items {
-                map.insert(k, v);
-            }
-        }
-        other => bail!(
-            "reducer 'merge' requires an object for the incoming value, got {}",
-            type_name(&other)
-        ),
-    }
-
-    Ok(Value::Object(map))
-}
-
-fn number_or_error(value: &Value, reducer_name: &str, position: &str) -> Result<f64> {
-    match value.as_f64() {
-        Some(n) => Ok(n),
-        None => bail!(
-            "reducer '{reducer_name}' requires a number for the {position} value, got {}",
-            type_name(value)
-        ),
-    }
-}
-
-// Numeric reducers compute in f64 for simplicity. Integer typing is preserved when the result is losslessly
-// representable as i64.
-fn json_number(n: f64) -> Value {
-    if n.fract() == 0.0 && n.is_finite() && n.abs() <= (i64::MAX as f64) {
-        Value::Number(Number::from(n as i64))
-    } else {
-        match Number::from_f64(n) {
-            Some(num) => Value::Number(num),
-            None => Value::Null,
-        }
-    }
-}
-
-#[cfg(test)]
-mod tests {
-    use super::*;
-    use serde_json::json;
-
-    #[test]
-    fn append_to_absent_creates_single_element_array() {
-        let result = apply(Reducer::Append, None, json!("a")).unwrap();
-
-        assert_eq!(result, json!(["a"]));
-    }
-
-    #[test]
-    fn append_pushes_onto_existing_array() {
-        let current = json!(["a", "b"]);
-        let result = apply(Reducer::Append, Some(&current), json!("c")).unwrap();
-
-        assert_eq!(result, json!(["a", "b", "c"]));
-    }
-
-    #[test]
-    fn append_errors_when_current_is_not_array() {
-        let current = json!("not an array");
-
-        let err = apply(Reducer::Append, Some(&current), json!("x"))
-            .unwrap_err()
-            .to_string();
-
-        assert!(err.contains("'append'"), "got: {err}");
-        assert!(err.contains("string"), "got: {err}");
-    }
-
-    #[test]
-    fn extend_concatenates_arrays() {
-        let current = json!([1, 2]);
-
-        let result = apply(Reducer::Extend, Some(&current), json!([3, 4])).unwrap();
-
-        assert_eq!(result, json!([1, 2, 3, 4]));
-    }
-
-    #[test]
-    fn extend_from_absent_with_array() {
-        let result = apply(Reducer::Extend, None, json!([1, 2])).unwrap();
-
-        assert_eq!(result, json!([1, 2]));
-    }
-
-    #[test]
-    fn extend_errors_when_incoming_is_not_array() {
-        let err = apply(Reducer::Extend, None, json!(42))
-            .unwrap_err()
-            .to_string();
-
-        assert!(err.contains("'extend'"), "got: {err}");
-        assert!(err.contains("number"), "got: {err}");
-        assert!(err.contains("incoming"), "got: {err}");
-    }
-
-    #[test]
-    fn concat_joins_strings_with_newline() {
-        let current = json!("first");
-
-        let result = apply(Reducer::Concat, Some(&current), json!("second")).unwrap();
-
-        assert_eq!(result, json!("first\nsecond"));
-    }
-
-    #[test]
-    fn concat_from_absent_yields_incoming() {
-        let result = apply(Reducer::Concat, None, json!("hello")).unwrap();
-
-        assert_eq!(result, json!("hello"));
-    }
-
-    #[test]
-    fn concat_skips_separator_when_current_is_empty_string() {
-        let current = json!("");
-
-        let result = apply(Reducer::Concat, Some(&current), json!("first")).unwrap();
-
-        assert_eq!(result, json!("first"));
-    }
-
-    #[test]
-    fn concat_errors_when_incoming_is_not_string() {
-        let err = apply(Reducer::Concat, None, json!(42))
-            .unwrap_err()
-            .to_string();
-
-        assert!(err.contains("'concat'"), "got: {err}");
-        assert!(err.contains("number"), "got: {err}");
-    }
-
-    #[test]
-    fn sum_adds_numbers() {
-        let current = json!(5);
-
-        let result = apply(Reducer::Sum, Some(&current), json!(7)).unwrap();
-
-        assert_eq!(result, json!(12));
-    }
-
-    #[test]
-    fn sum_starts_from_zero_when_current_absent() {
-        let result = apply(Reducer::Sum, None, json!(3.5)).unwrap();
-
-        assert_eq!(result, json!(3.5));
-    }
-
-    #[test]
-    fn sum_preserves_integer_type_for_whole_results() {
-        let current = json!(2);
-
-        let result = apply(Reducer::Sum, Some(&current), json!(3)).unwrap();
-
-        assert!(result.is_i64(), "expected integer, got {result:?}");
-        assert_eq!(result, json!(5));
-    }
-
-    #[test]
-    fn sum_uses_float_when_result_has_fractional() {
-        let current = json!(1.5);
-        let result = apply(Reducer::Sum, Some(&current), json!(2.25)).unwrap();
-
-        assert_eq!(result, json!(3.75));
-    }
-
-    #[test]
-    fn sum_errors_on_string_incoming() {
-        let err = apply(Reducer::Sum, None, json!("not a number"))
-            .unwrap_err()
-            .to_string();
-
-        assert!(err.contains("'sum'"), "got: {err}");
-        assert!(err.contains("string"), "got: {err}");
-    }
-
-    #[test]
-    fn max_returns_larger_of_two() {
-        let current = json!(5);
-        let result = apply(Reducer::Max, Some(&current), json!(3)).unwrap();
-        assert_eq!(result, json!(5));
-
-        let result = apply(Reducer::Max, Some(&current), json!(10)).unwrap();
-        assert_eq!(result, json!(10));
-    }
-
-    #[test]
-    fn max_yields_incoming_when_current_absent() {
-        let result = apply(Reducer::Max, None, json!(42)).unwrap();
-
-        assert_eq!(result, json!(42));
-    }
-
-    #[test]
-    fn min_returns_smaller_of_two() {
-        let current = json!(5);
-        let result = apply(Reducer::Min, Some(&current), json!(3)).unwrap();
-        assert_eq!(result, json!(3));
-
-        let result = apply(Reducer::Min, Some(&current), json!(10)).unwrap();
-        assert_eq!(result, json!(5));
-    }
-
-    #[test]
-    fn min_errors_on_non_numeric_current() {
-        let current = json!("oops");
-
-        let err = apply(Reducer::Min, Some(&current), json!(1))
-            .unwrap_err()
-            .to_string();
-
-        assert!(err.contains("'min'"), "got: {err}");
-        assert!(err.contains("current"), "got: {err}");
-    }
-
-    #[test]
-    fn merge_unions_objects_with_incoming_winning_collisions() {
-        let current = json!({ "a": 1, "b": 2 });
-        let incoming = json!({ "b": 99, "c": 3 });
-
-        let result = apply(Reducer::Merge, Some(&current), incoming).unwrap();
-
-        assert_eq!(result, json!({ "a": 1, "b": 99, "c": 3 }));
-    }
-
-    #[test]
-    fn merge_from_absent_yields_incoming_object() {
-        let result = apply(Reducer::Merge, None, json!({ "k": "v" })).unwrap();
-
-        assert_eq!(result, json!({ "k": "v" }));
-    }
-
-    #[test]
-    fn merge_errors_when_incoming_is_not_object() {
-        let err = apply(Reducer::Merge, None, json!([1, 2]))
-            .unwrap_err()
-            .to_string();
-
-        assert!(err.contains("'merge'"), "got: {err}");
-        assert!(err.contains("array"), "got: {err}");
-    }
-
-    #[test]
-    fn merge_errors_when_current_is_not_object() {
-        let current = json!("not object");
-
-        let err = apply(Reducer::Merge, Some(&current), json!({ "k": "v" }))
-            .unwrap_err()
-            .to_string();
-
-        assert!(err.contains("'merge'"), "got: {err}");
-        assert!(err.contains("current"), "got: {err}");
-    }
-
-    #[test]
-    fn overwrite_ignores_current_and_returns_incoming() {
-        let current = json!("old");
-
-        let result = apply(Reducer::Overwrite, Some(&current), json!("new")).unwrap();
-
-        assert_eq!(result, json!("new"));
-    }
-
-    #[test]
-    fn overwrite_works_with_absent_current() {
-        let result = apply(Reducer::Overwrite, None, json!(42)).unwrap();
-
-        assert_eq!(result, json!(42));
-    }
-}

src/graph/script.rs

@@ -1,557 +0,0 @@
-use super::state::{StateManager, StateRepresentation};
-use super::types::ScriptNode;
-use crate::config::paths;
-use crate::function::Language;
-use anyhow::{Context, Result, anyhow, bail};
-use serde_json::Value;
-use std::collections::HashMap;
-use std::env;
-use std::path::{Path, PathBuf};
-use std::process::Stdio;
-use std::time::Duration;
-use tokio::process::Command;
-use tokio::time::timeout;
-
-#[cfg(windows)]
-const PATH_SEP: &str = ";";
-#[cfg(not(windows))]
-const PATH_SEP: &str = ":";
-
-#[derive(Clone)]
-pub struct ScriptExecutor {
-    base_dir: PathBuf,
-    extra_envs: HashMap<String, String>,
-}
-
-impl ScriptExecutor {
-    pub fn new(base_dir: impl Into<PathBuf>) -> Self {
-        let base_dir = base_dir.into();
-        let extra_envs = build_default_envs(&base_dir);
-        Self {
-            base_dir,
-            extra_envs,
-        }
-    }
-
-    pub fn with_envs(mut self, envs: HashMap<String, String>) -> Self {
-        self.extra_envs.extend(envs);
-        self
-    }
-
-    pub async fn execute(
-        &self,
-        node: &ScriptNode,
-        state_manager: &mut StateManager,
-    ) -> Result<Option<String>> {
-        let script_path = self.base_dir.join(&node.script);
-        if !script_path.exists() {
-            bail!("Script file not found: '{}'", script_path.display());
-        }
-
-        let language = detect_language(&script_path)?;
-        let state_repr = state_manager.serialize_state()?;
-
-        let mut cmd = build_command(language, &script_path)?;
-        cmd.stdout(Stdio::piped());
-        cmd.stderr(Stdio::piped());
-        cmd.envs(&self.extra_envs);
-        match &state_repr {
-            StateRepresentation::Inline(json) => {
-                cmd.env("GRAPH_STATE", json);
-            }
-            StateRepresentation::File(path) => {
-                cmd.env("GRAPH_STATE_FILE", path);
-            }
-        }
-
-        let timeout_dur = Duration::from_secs(node.timeout);
-        let output = timeout(timeout_dur, cmd.output())
-            .await
-            .with_context(|| {
-                format!(
-                    "Script '{}' timed out after {}s",
-                    script_path.display(),
-                    node.timeout
-                )
-            })?
-            .with_context(|| {
-                format!(
-                    "Failed to spawn script process for '{}'",
-                    script_path.display()
-                )
-            })?;
-
-        if !output.status.success() {
-            let stderr = String::from_utf8_lossy(&output.stderr);
-            bail!(
-                "Script '{}' failed with exit code {:?}:\n{}",
-                script_path.display(),
-                output.status.code(),
-                stderr.trim()
-            );
-        }
-
-        let stdout = String::from_utf8_lossy(&output.stdout);
-        let json_output = stdout.trim();
-        if json_output.is_empty() {
-            bail!(
-                "Script '{}' produced no output (scripts must emit a single JSON object on stdout)",
-                script_path.display()
-            );
-        }
-
-        let next = state_manager
-            .merge_script_output(json_output)
-            .with_context(|| {
-                format!(
-                    "Failed to merge output from script '{}'",
-                    script_path.display()
-                )
-            })?;
-
-        apply_state_updates(node, state_manager);
-
-        Ok(next)
-    }
-}
-
-fn apply_state_updates(node: &ScriptNode, state_manager: &mut StateManager) {
-    let Some(updates) = &node.state_updates else {
-        return;
-    };
-
-    for (key, template) in updates {
-        let value = state_manager.interpolate_lenient(template);
-        state_manager
-            .state_mut()
-            .set(key.clone(), Value::String(value));
-    }
-}
-
-fn build_default_envs(agent_data_dir: &Path) -> HashMap<String, String> {
-    let mut envs = HashMap::new();
-    envs.insert(
-        "LLM_ROOT_DIR".to_string(),
-        paths::config_dir().to_string_lossy().into_owned(),
-    );
-    envs.insert(
-        "LLM_PROMPT_UTILS_FILE".to_string(),
-        paths::bash_prompt_utils_file()
-            .to_string_lossy()
-            .into_owned(),
-    );
-    envs.insert(
-        "LLM_AGENT_DATA_DIR".to_string(),
-        agent_data_dir.to_string_lossy().into_owned(),
-    );
-    envs.insert("CLICOLOR_FORCE".to_string(), "1".to_string());
-    envs.insert("FORCE_COLOR".to_string(), "1".to_string());
-
-    if let Ok(current_path) = env::var("PATH") {
-        let bin_dir = paths::functions_bin_dir();
-        envs.insert(
-            "PATH".to_string(),
-            format!("{}{}{}", bin_dir.display(), PATH_SEP, current_path),
-        );
-    }
-
-    envs
-}
-
-fn detect_language(script_path: &Path) -> Result<Language> {
-    let ext = script_path
-        .extension()
-        .and_then(|e| e.to_str())
-        .ok_or_else(|| anyhow!("Script has no file extension: '{}'", script_path.display()))?
-        .to_string();
-
-    match Language::from(&ext) {
-        Language::Unsupported => bail!(
-            "Unsupported script extension '.{}' for '{}'",
-            ext,
-            script_path.display()
-        ),
-        lang => Ok(lang),
-    }
-}
-
-fn build_command(language: Language, script_path: &Path) -> Result<Command> {
-    let (program, prefix_args) = language.direct_invoker().ok_or_else(|| {
-        anyhow!(
-            "No direct invoker available for script '{}'",
-            script_path.display()
-        )
-    })?;
-    let mut cmd = Command::new(program);
-
-    for arg in prefix_args {
-        cmd.arg(arg);
-    }
-
-    cmd.arg(script_path);
-    Ok(cmd)
-}
-
-#[cfg(test)]
-mod tests {
-    use super::super::MAX_STATE_SIZE_BYTES;
-    use super::*;
-    use crate::utils::temp_file;
-    use indoc::formatdoc;
-    use serde_json::json;
-    use std::collections::HashMap;
-    use std::env::temp_dir;
-    use std::fs;
-
-    fn cmd_available(name: &str) -> bool {
-        which::which(name).is_ok()
-    }
-
-    fn write_script(contents: &str, ext: &str) -> (PathBuf, PathBuf) {
-        let dir = temp_file("-graph-script-test-", "");
-        fs::create_dir_all(&dir).unwrap();
-        let path = dir.join(format!("script.{ext}"));
-        fs::write(&path, contents).unwrap();
-        (dir, path)
-    }
-
-    fn cleanup(dir: &Path) {
-        let _ = fs::remove_dir_all(dir);
-    }
-
-    fn node_for(script_filename: &str, timeout: u64) -> ScriptNode {
-        ScriptNode {
-            script: script_filename.into(),
-            state_updates: None,
-            fallback: None,
-            timeout,
-        }
-    }
-
-    #[tokio::test]
-    async fn bash_script_merges_json_output_into_state() {
-        if !cmd_available("bash") {
-            eprintln!("skipping: bash not available");
-            return;
-        }
-        let (dir, path) = write_script(
-            r#"#!/bin/bash
-echo '{"quality": 0.85, "issues": 3, "_next": "approve"}'
-"#,
-            "sh",
-        );
-        let mut state = StateManager::new(HashMap::new());
-        let executor = ScriptExecutor::new(&dir);
-
-        let next = executor
-            .execute(
-                &node_for(path.file_name().unwrap().to_str().unwrap(), 5),
-                &mut state,
-            )
-            .await
-            .unwrap();
-
-        assert_eq!(next.as_deref(), Some("approve"));
-        assert_eq!(state.state().get("quality"), Some(&json!(0.85)));
-        assert_eq!(state.state().get("issues"), Some(&json!(3)));
-        assert!(state.state().get("_next").is_none());
-        cleanup(&dir);
-    }
-
-    #[tokio::test]
-    async fn bash_script_can_read_state_from_env() {
-        if !cmd_available("bash") || !cmd_available("python3") {
-            eprintln!("skipping: bash or python3 not available");
-            return;
-        }
-        let (dir, path) = write_script(
-            r#"#!/bin/bash
-NAME=$(python3 -c 'import json,os; print(json.loads(os.environ["GRAPH_STATE"])["name"])')
-printf '{"greeting": "hello %s"}' "$NAME"
-"#,
-            "sh",
-        );
-        let mut initial = HashMap::new();
-        initial.insert("name".into(), json!("alice"));
-        let mut state = StateManager::new(initial);
-        let executor = ScriptExecutor::new(&dir);
-
-        let _ = executor
-            .execute(
-                &node_for(path.file_name().unwrap().to_str().unwrap(), 5),
-                &mut state,
-            )
-            .await
-            .unwrap();
-
-        assert_eq!(state.state().get("greeting"), Some(&json!("hello alice")));
-        cleanup(&dir);
-    }
-
-    #[tokio::test]
-    async fn script_without_next_returns_none() {
-        if !cmd_available("bash") {
-            return;
-        }
-        let (dir, path) = write_script(
-            r#"#!/bin/bash
-echo '{"ok": true}'
-"#,
-            "sh",
-        );
-        let mut state = StateManager::new(HashMap::new());
-        let executor = ScriptExecutor::new(&dir);
-
-        let next = executor
-            .execute(
-                &node_for(path.file_name().unwrap().to_str().unwrap(), 5),
-                &mut state,
-            )
-            .await
-            .unwrap();
-
-        assert!(next.is_none());
-        assert_eq!(state.state().get("ok"), Some(&json!(true)));
-        cleanup(&dir);
-    }
-
-    #[tokio::test]
-    async fn state_updates_apply_after_json_merge() {
-        if !cmd_available("bash") {
-            return;
-        }
-        let (dir, path) = write_script(
-            r#"#!/bin/bash
-echo '{"raw": "hello"}'
-"#,
-            "sh",
-        );
-        let mut node = node_for(path.file_name().unwrap().to_str().unwrap(), 5);
-        let mut updates = HashMap::new();
-        updates.insert("decorated".into(), "[{{raw}}]".into());
-        node.state_updates = Some(updates);
-
-        let mut state = StateManager::new(HashMap::new());
-        let executor = ScriptExecutor::new(&dir);
-        executor.execute(&node, &mut state).await.unwrap();
-
-        assert_eq!(state.state().get("raw"), Some(&json!("hello")));
-        assert_eq!(state.state().get("decorated"), Some(&json!("[hello]")));
-        cleanup(&dir);
-    }
-
-    #[tokio::test]
-    async fn missing_script_file_errors_before_spawning() {
-        let mut state = StateManager::new(HashMap::new());
-        let executor = ScriptExecutor::new(temp_dir());
-
-        let err = executor
-            .execute(&node_for("__does_not_exist__.sh", 5), &mut state)
-            .await
-            .unwrap_err()
-            .to_string();
-
-        assert!(err.contains("Script file not found"), "got: {err}");
-    }
-
-    #[tokio::test]
-    async fn empty_stdout_errors() {
-        if !cmd_available("bash") {
-            return;
-        }
-        let (dir, path) = write_script("#!/bin/bash\n", "sh");
-        let mut state = StateManager::new(HashMap::new());
-        let executor = ScriptExecutor::new(&dir);
-
-        let err = executor
-            .execute(
-                &node_for(path.file_name().unwrap().to_str().unwrap(), 5),
-                &mut state,
-            )
-            .await
-            .unwrap_err()
-            .to_string();
-
-        assert!(err.contains("produced no output"), "got: {err}");
-        cleanup(&dir);
-    }
-
-    #[tokio::test]
-    async fn non_json_output_errors() {
-        if !cmd_available("bash") {
-            return;
-        }
-        let (dir, path) = write_script(
-            &formatdoc! {r#"
-                #!/bin/bash
-                echo "not json at all"
-            "#},
-            "sh",
-        );
-        let mut state = StateManager::new(HashMap::new());
-        let executor = ScriptExecutor::new(&dir);
-
-        let err = executor
-            .execute(
-                &node_for(path.file_name().unwrap().to_str().unwrap(), 5),
-                &mut state,
-            )
-            .await
-            .unwrap_err()
-            .to_string();
-
-        assert!(err.contains("merge output"), "got: {err}");
-        cleanup(&dir);
-    }
-
-    #[tokio::test]
-    async fn non_zero_exit_errors_and_includes_stderr() {
-        if !cmd_available("bash") {
-            return;
-        }
-        let (dir, path) = write_script(
-            &formatdoc! {r#"
-                #!/bin/bash
-                echo "bad happened" >&2
-                exit 7
-            "#},
-            "sh",
-        );
-        let mut state = StateManager::new(HashMap::new());
-        let executor = ScriptExecutor::new(&dir);
-
-        let err = executor
-            .execute(
-                &node_for(path.file_name().unwrap().to_str().unwrap(), 5),
-                &mut state,
-            )
-            .await
-            .unwrap_err()
-            .to_string();
-
-        assert!(err.contains("exit code"), "got: {err}");
-        assert!(err.contains("bad happened"), "got: {err}");
-        cleanup(&dir);
-    }
-
-    #[tokio::test]
-    async fn execution_timeout_is_enforced() {
-        if !cmd_available("bash") {
-            return;
-        }
-        let (dir, path) = write_script(
-            r#"#!/bin/bash
-sleep 5
-echo '{"ok":true}'
-"#,
-            "sh",
-        );
-        let mut state = StateManager::new(HashMap::new());
-        let executor = ScriptExecutor::new(&dir);
-
-        let err = executor
-            .execute(
-                &node_for(path.file_name().unwrap().to_str().unwrap(), 1),
-                &mut state,
-            )
-            .await
-            .unwrap_err()
-            .to_string();
-
-        assert!(err.contains("timed out"), "got: {err}");
-        cleanup(&dir);
-    }
-
-    #[tokio::test]
-    async fn large_state_is_delivered_via_file_env_var() {
-        if !cmd_available("bash") || !cmd_available("python3") {
-            return;
-        }
-        let big = "x".repeat(MAX_STATE_SIZE_BYTES + 1024);
-        let mut initial = HashMap::new();
-        initial.insert("blob".into(), json!(big));
-
-        let (dir, path) = write_script(
-            r#"#!/bin/bash
-if [ -n "$GRAPH_STATE_FILE" ]; then
-    LEN=$(python3 -c 'import json,os; print(len(json.load(open(os.environ["GRAPH_STATE_FILE"]))["blob"]))')
-    printf '{"blob_len": %s, "via_file": true}' "$LEN"
-elif [ -n "$GRAPH_STATE" ]; then
-    echo '{"via_file": false}'
-fi
-"#,
-            "sh",
-        );
-
-        let mut state = StateManager::new(initial);
-        let executor = ScriptExecutor::new(&dir);
-        executor
-            .execute(
-                &node_for(path.file_name().unwrap().to_str().unwrap(), 10),
-                &mut state,
-            )
-            .await
-            .unwrap();
-
-        assert_eq!(state.state().get("via_file"), Some(&json!(true)));
-        let len = state.state().get("blob_len").unwrap().as_i64().unwrap();
-        assert_eq!(len as usize, big.len());
-        cleanup(&dir);
-    }
-
-    #[tokio::test]
-    async fn python_script_can_emit_routing_and_state() {
-        if !cmd_available("python3") {
-            eprintln!("skipping: python3 not available");
-            return;
-        }
-        let (dir, path) = write_script(
-            r#"import os, json
-state = json.loads(os.environ["GRAPH_STATE"])
-print(json.dumps({
-    "_next": "next_node",
-    "doubled": state.get("n", 0) * 2,
-}))
-"#,
-            "py",
-        );
-        let mut initial = HashMap::new();
-        initial.insert("n".into(), json!(21));
-        let mut state = StateManager::new(initial);
-
-        let executor = ScriptExecutor::new(&dir);
-        let next = executor
-            .execute(
-                &node_for(path.file_name().unwrap().to_str().unwrap(), 5),
-                &mut state,
-            )
-            .await
-            .unwrap();
-
-        assert_eq!(next.as_deref(), Some("next_node"));
-        assert_eq!(state.state().get("doubled"), Some(&json!(42)));
-        cleanup(&dir);
-    }
-
-    #[tokio::test]
-    async fn unknown_extension_is_rejected() {
-        let (dir, path) = write_script("echo hi", "xyz");
-        let mut state = StateManager::new(HashMap::new());
-        let executor = ScriptExecutor::new(&dir);
-
-        let err = executor
-            .execute(
-                &node_for(path.file_name().unwrap().to_str().unwrap(), 5),
-                &mut state,
-            )
-            .await
-            .unwrap_err()
-            .to_string();
-
-        assert!(
-            err.contains("Unsupported script extension '.xyz'"),
-            "got: {err}"
-        );
-        cleanup(&dir);
-    }
-}

src/graph/staging.rs

@@ -1,9 +0,0 @@
-use serde_json::Value;
-use std::collections::HashMap;
-
-#[derive(Debug, Clone)]
-pub struct BranchWrites {
-    pub node_id: String,
-    pub invocation_index: usize,
-    pub writes: HashMap<String, Value>,
-}

src/graph/structured.rs

@@ -1,189 +0,0 @@
-use crate::client::call_chat_completions;
-use crate::config::{Input, RequestContext, Role, RoleLike};
-use crate::utils::create_abort_signal;
-use anyhow::{Context, Result, bail};
-use serde_json::Value;
-use std::sync::Arc;
-
-const EXTRACTOR_ROLE_NAME: &str = "__structured_output__";
-
-const EXTRACTOR_ROLE_PROMPT: &str = "\
-Extract a JSON object from the user's input that strictly conforms to the provided JSON Schema.
-
-Rules:
-- Output ONLY the JSON object. No prose, no explanation, no markdown fences, no <think> tokens.
-- The first character of your response must be `{` and the last must be `}`.
-- Every key marked `required` in the schema MUST appear in the output.
-- All values MUST match the types specified in the schema.
-- If the input is already a valid JSON object matching the schema, return it unchanged.
-- If a field cannot be determined from the input, use `null` (when allowed) or your best inferred value.
-- Do NOT invent fields not present in the schema.";
-
-pub async fn extract(raw: &str, schema: &Value, parent_ctx: &mut RequestContext) -> Result<Value> {
-    if let Some(parsed) = try_parse_json(raw) {
-        return Ok(parsed);
-    }
-
-    extract_via_extractor(raw, schema, parent_ctx, false).await
-}
-
-async fn extract_via_extractor(
-    raw: &str,
-    schema: &Value,
-    parent_ctx: &mut RequestContext,
-    is_repair: bool,
-) -> Result<Value> {
-    let role = build_extractor_role()?;
-    let prompt = build_extractor_prompt(raw, schema, is_repair);
-
-    let saved_role = parent_ctx.role.clone();
-    parent_ctx.role = Some(role);
-    let result = run_one_shot(&prompt, parent_ctx).await;
-    parent_ctx.role = saved_role;
-
-    let output = result.context("Structured-output extractor LLM call failed")?;
-
-    match try_parse_json(&output) {
-        Some(value) => Ok(value),
-        None if is_repair => bail!(
-            "Structured-output extractor failed to produce valid JSON after repair retry. \
-             Last response:\n{output}"
-        ),
-        None => Box::pin(extract_via_extractor(&output, schema, parent_ctx, true)).await,
-    }
-}
-
-fn build_extractor_role() -> Result<Role> {
-    let mut role = Role::new(EXTRACTOR_ROLE_NAME, EXTRACTOR_ROLE_PROMPT);
-    role.set_enabled_tools(Some(String::new()));
-    role.set_enabled_mcp_servers(Some(String::new()));
-    Ok(role)
-}
-
-fn build_extractor_prompt(raw: &str, schema: &Value, is_repair: bool) -> String {
-    let schema_json = serde_json::to_string_pretty(schema).unwrap_or_else(|_| schema.to_string());
-    if is_repair {
-        format!(
-            "Your previous response was not valid JSON. Output ONLY a JSON object \
-             matching this schema. No prose, no fences.\n\nSchema:\n{schema_json}\n\nInput:\n{raw}"
-        )
-    } else {
-        format!("Schema:\n{schema_json}\n\nInput:\n{raw}")
-    }
-}
-
-async fn run_one_shot(prompt: &str, ctx: &mut RequestContext) -> Result<String> {
-    let abort = create_abort_signal();
-    let app_cfg = Arc::clone(&ctx.app.config);
-    let role_for_input = ctx.role.clone();
-    let input = Input::from_str(ctx, prompt, role_for_input);
-    let client = input.create_client()?;
-    ctx.before_chat_completion(&input)?;
-    let (output, tool_results) =
-        call_chat_completions(&input, false, false, client.as_ref(), ctx, abort).await?;
-    ctx.after_chat_completion(app_cfg.as_ref(), &input, &output, &tool_results)?;
-
-    Ok(output)
-}
-
-fn try_parse_json(raw: &str) -> Option<Value> {
-    let cleaned = strip_code_fences(raw.trim());
-
-    serde_json::from_str(cleaned).ok()
-}
-
-fn strip_code_fences(s: &str) -> &str {
-    let after_open = s
-        .strip_prefix("```json")
-        .or_else(|| s.strip_prefix("```"))
-        .map(str::trim_start)
-        .unwrap_or(s);
-    after_open
-        .strip_suffix("```")
-        .map(str::trim_end)
-        .unwrap_or(after_open)
-}
-
-#[cfg(test)]
-mod tests {
-    use super::*;
-    use serde_json::json;
-
-    #[test]
-    fn try_parse_json_accepts_plain_object() {
-        let v = try_parse_json(r#"{"a": 1}"#).unwrap();
-
-        assert_eq!(v, json!({"a": 1}));
-    }
-
-    #[test]
-    fn try_parse_json_strips_json_fences() {
-        let raw = "```json\n{\"a\": 1}\n```";
-
-        let v = try_parse_json(raw).unwrap();
-
-        assert_eq!(v, json!({"a": 1}));
-    }
-
-    #[test]
-    fn try_parse_json_strips_bare_fences() {
-        let raw = "```\n{\"a\": 1}\n```";
-
-        let v = try_parse_json(raw).unwrap();
-
-        assert_eq!(v, json!({"a": 1}));
-    }
-
-    #[test]
-    fn try_parse_json_tolerates_whitespace() {
-        let v = try_parse_json("   \n  {\"x\": true}\n\n").unwrap();
-
-        assert_eq!(v, json!({"x": true}));
-    }
-
-    #[test]
-    fn try_parse_json_returns_none_on_prose() {
-        assert!(try_parse_json("Here is the result: it's good").is_none());
-    }
-
-    #[test]
-    fn try_parse_json_returns_none_on_partial_json() {
-        assert!(try_parse_json("{\"a\": ").is_none());
-    }
-
-    #[test]
-    fn try_parse_json_accepts_arrays() {
-        let v = try_parse_json("[1, 2, 3]").unwrap();
-
-        assert_eq!(v, json!([1, 2, 3]));
-    }
-
-    #[test]
-    fn build_extractor_prompt_includes_schema_and_input() {
-        let schema = json!({"type": "object"});
-
-        let prompt = build_extractor_prompt("hello", &schema, false);
-
-        assert!(prompt.contains("Schema:"));
-        assert!(prompt.contains("Input:"));
-        assert!(prompt.contains("hello"));
-    }
-
-    #[test]
-    fn build_extractor_prompt_repair_includes_repair_instruction() {
-        let schema = json!({"type": "object"});
-
-        let prompt = build_extractor_prompt("oops", &schema, true);
-
-        assert!(prompt.contains("previous response"));
-        assert!(prompt.contains("oops"));
-    }
-
-    #[test]
-    fn build_extractor_role_disables_tools_and_mcp() {
-        let role = build_extractor_role().expect("builtin role must exist");
-
-        assert_eq!(role.enabled_tools().as_deref(), Some(""));
-        assert_eq!(role.enabled_mcp_servers().as_deref(), Some(""));
-    }
-}

src/graph/user_interaction.rs

@@ -1,369 +0,0 @@
-use super::state::StateManager;
-use super::types::{ApprovalNode, InputNode};
-use crate::config::RequestContext;
-use crate::function::user_interaction::{USER_FUNCTION_PREFIX, handle_user_tool};
-use anyhow::{Context, Result, anyhow, bail};
-use serde_json::{Value, json};
-use std::collections::HashMap;
-
-const CHOICE_KEY: &str = "choice";
-const INPUT_KEY: &str = "input";
-
-pub struct ApprovalNodeExecutor;
-
-impl ApprovalNodeExecutor {
-    pub async fn execute(
-        node: &ApprovalNode,
-        state_manager: &mut StateManager,
-        ctx: &mut RequestContext,
-    ) -> Result<String> {
-        let question = state_manager
-            .interpolate(&node.question)
-            .context("Failed to interpolate approval question")?;
-
-        let response = handle_user_tool(
-            ctx,
-            &format!("{USER_FUNCTION_PREFIX}ask"),
-            &json!({ "question": question, "options": node.options }),
-        )
-        .await
-        .context("user__ask failed")?;
-
-        if let Some(err) = response.get("error").and_then(Value::as_str) {
-            bail!("Approval interaction failed: {err}");
-        }
-
-        let choice = response
-            .get("answer")
-            .and_then(Value::as_str)
-            .context("Approval response missing 'answer' field")?
-            .to_string();
-
-        apply_state_updates_with_var(&node.state_updates, state_manager, CHOICE_KEY, &choice);
-
-        resolve_approval_route(node, &choice)
-    }
-}
-
-pub struct InputNodeExecutor;
-
-impl InputNodeExecutor {
-    pub async fn execute(
-        node: &InputNode,
-        node_next: Option<&str>,
-        state_manager: &mut StateManager,
-        ctx: &mut RequestContext,
-    ) -> Result<String> {
-        let question = build_input_question(node, state_manager)?;
-
-        let response = handle_user_tool(
-            ctx,
-            &format!("{USER_FUNCTION_PREFIX}input"),
-            &json!({ "question": question }),
-        )
-        .await
-        .context("user__input failed")?;
-
-        if let Some(err) = response.get("error").and_then(Value::as_str) {
-            bail!("Input interaction failed: {err}");
-        }
-
-        let raw = response
-            .get("answer")
-            .and_then(Value::as_str)
-            .context("Input response missing 'answer' field")?
-            .to_string();
-
-        let input_text = if raw.is_empty() {
-            node.default
-                .as_ref()
-                .map(|t| state_manager.interpolate_lenient(t))
-                .unwrap_or_default()
-        } else {
-            raw
-        };
-
-        if let Some(expr) = &node.validation
-            && !validate_length(&input_text, expr)?
-        {
-            bail!(
-                "Input failed validation '{}' (got {} chars)",
-                expr,
-                input_text.chars().count()
-            );
-        }
-
-        apply_state_updates_with_var(&node.state_updates, state_manager, INPUT_KEY, &input_text);
-
-        node_next
-            .map(String::from)
-            .ok_or_else(|| anyhow!("Input node has no `next` set"))
-    }
-}
-
-fn build_input_question(node: &InputNode, state_manager: &StateManager) -> Result<String> {
-    let mut question = state_manager
-        .interpolate(&node.question)
-        .context("Failed to interpolate input question")?;
-
-    if let Some(default_template) = &node.default {
-        let default = state_manager.interpolate_lenient(default_template);
-        if !default.is_empty() {
-            question = format!("{question} [default: {default}]");
-        }
-    }
-
-    Ok(question)
-}
-
-fn resolve_approval_route(node: &ApprovalNode, choice: &str) -> Result<String> {
-    if let Some(target) = node.routes.get(choice) {
-        return Ok(target.clone());
-    }
-
-    Ok(node.on_other.clone())
-}
-
-fn apply_state_updates_with_var(
-    updates: &Option<HashMap<String, String>>,
-    state_manager: &mut StateManager,
-    var_name: &str,
-    var_value: &str,
-) {
-    let Some(updates) = updates else {
-        return;
-    };
-    let prev = state_manager.state().get(var_name).cloned();
-    state_manager
-        .state_mut()
-        .set(var_name.into(), Value::String(var_value.to_string()));
-
-    for (key, template) in updates {
-        let value = state_manager.interpolate_lenient(template);
-        state_manager
-            .state_mut()
-            .set(key.clone(), Value::String(value));
-    }
-
-    match prev {
-        Some(v) => state_manager.state_mut().set(var_name.into(), v),
-        None => {
-            state_manager.state_mut().set(var_name.into(), Value::Null);
-        }
-    }
-}
-
-/// Evaluate a `len(input) OP N` expression where OP is one of `>`, `>=`,
-/// `<`, `<=`, `==`. Lengths are byte counts (matches Rust's `str::len`).
-/// Other expressions are rejected at runtime.
-fn validate_length(input: &str, expr: &str) -> Result<bool> {
-    let trimmed = expr.trim();
-    let after_len = trimmed
-        .strip_prefix("len(input)")
-        .map(str::trim)
-        .ok_or_else(|| {
-            anyhow!(
-                "Unsupported validation expression '{expr}'; only `len(input) OP N` is supported"
-            )
-        })?;
-
-    let (op, rhs_str) = if let Some(rest) = after_len.strip_prefix(">=") {
-        (">=", rest)
-    } else if let Some(rest) = after_len.strip_prefix("<=") {
-        ("<=", rest)
-    } else if let Some(rest) = after_len.strip_prefix("==") {
-        ("==", rest)
-    } else if let Some(rest) = after_len.strip_prefix('>') {
-        (">", rest)
-    } else if let Some(rest) = after_len.strip_prefix('<') {
-        ("<", rest)
-    } else {
-        bail!("No comparison operator in validation expression '{expr}'");
-    };
-
-    let rhs: usize = rhs_str
-        .trim()
-        .parse()
-        .with_context(|| format!("Invalid right-hand side in validation '{expr}'"))?;
-
-    let len = input.len();
-    Ok(match op {
-        ">=" => len >= rhs,
-        "<=" => len <= rhs,
-        "==" => len == rhs,
-        ">" => len > rhs,
-        "<" => len < rhs,
-        _ => unreachable!(),
-    })
-}
-
-#[cfg(test)]
-mod tests {
-    use super::super::types::*;
-    use super::*;
-    use serde_json::json;
-
-    fn manager_with(pairs: &[(&str, Value)]) -> StateManager {
-        let mut map = HashMap::new();
-        for (k, v) in pairs {
-            map.insert((*k).into(), v.clone());
-        }
-
-        StateManager::new(map)
-    }
-
-    fn approval(options: &[&str], routes: &[(&str, &str)], on_other: &str) -> ApprovalNode {
-        let mut r = HashMap::new();
-        for (k, v) in routes {
-            r.insert((*k).into(), (*v).into());
-        }
-
-        ApprovalNode {
-            question: "?".into(),
-            options: options.iter().map(|s| (*s).into()).collect(),
-            routes: r,
-            on_other: on_other.into(),
-            state_updates: None,
-        }
-    }
-
-    fn input(question: &str) -> InputNode {
-        InputNode {
-            question: question.into(),
-            default: None,
-            validation: None,
-            state_updates: None,
-        }
-    }
-
-    #[test]
-    fn validate_length_supports_all_comparison_operators() {
-        assert!(validate_length("hello", "len(input) > 0").unwrap());
-        assert!(!validate_length("", "len(input) > 0").unwrap());
-        assert!(validate_length("hello", "len(input) >= 5").unwrap());
-        assert!(!validate_length("hi", "len(input) >= 5").unwrap());
-        assert!(validate_length("hello", "len(input) < 10").unwrap());
-        assert!(!validate_length("hello world!", "len(input) < 10").unwrap());
-        assert!(validate_length("hi", "len(input) <= 2").unwrap());
-        assert!(!validate_length("hello", "len(input) <= 2").unwrap());
-        assert!(validate_length("hello", "len(input) == 5").unwrap());
-        assert!(!validate_length("hello", "len(input) == 3").unwrap());
-    }
-
-    #[test]
-    fn validate_length_handles_whitespace() {
-        assert!(validate_length("hi", "  len(input)   >=   1  ").unwrap());
-    }
-
-    #[test]
-    fn validate_length_rejects_unsupported_expressions() {
-        assert!(validate_length("x", "matches /[a-z]+/").is_err());
-        assert!(validate_length("x", "len(input)").is_err());
-        assert!(validate_length("x", "len(input) >").is_err());
-        assert!(validate_length("x", "len(input) >= abc").is_err());
-    }
-
-    #[test]
-    fn approval_route_lookup_returns_target_on_match() {
-        let node = approval(
-            &["yes", "no"],
-            &[("yes", "deploy"), ("no", "cancel")],
-            "clarify",
-        );
-
-        assert_eq!(resolve_approval_route(&node, "yes").unwrap(), "deploy");
-        assert_eq!(resolve_approval_route(&node, "no").unwrap(), "cancel");
-    }
-
-    #[test]
-    fn approval_route_lookup_falls_back_to_on_other_for_unknown_choice() {
-        let node = approval(
-            &["yes", "no"],
-            &[("yes", "deploy"), ("no", "cancel")],
-            "clarify",
-        );
-
-        assert_eq!(resolve_approval_route(&node, "maybe").unwrap(), "clarify");
-        assert_eq!(
-            resolve_approval_route(&node, "free-form text").unwrap(),
-            "clarify"
-        );
-    }
-
-    #[test]
-    fn state_updates_expose_choice_during_evaluation_only() {
-        let mut updates = HashMap::new();
-        updates.insert("decision".into(), "{{choice}}".into());
-        let mut state = manager_with(&[]);
-
-        apply_state_updates_with_var(&Some(updates), &mut state, CHOICE_KEY, "approve");
-
-        assert_eq!(state.state().get("decision"), Some(&json!("approve")));
-        assert_eq!(state.state().get(CHOICE_KEY), Some(&Value::Null));
-    }
-
-    #[test]
-    fn state_updates_preserve_pre_existing_var_value() {
-        let mut updates = HashMap::new();
-        updates.insert("decision".into(), "{{choice}}".into());
-        let mut state = manager_with(&[("choice", json!("preserved"))]);
-
-        apply_state_updates_with_var(&Some(updates), &mut state, CHOICE_KEY, "approve");
-
-        assert_eq!(state.state().get("decision"), Some(&json!("approve")));
-        assert_eq!(state.state().get(CHOICE_KEY), Some(&json!("preserved")));
-    }
-
-    #[test]
-    fn state_updates_for_input_use_input_key() {
-        let mut updates = HashMap::new();
-        updates.insert("api_key".into(), "{{input}}".into());
-        let mut state = manager_with(&[]);
-
-        apply_state_updates_with_var(&Some(updates), &mut state, INPUT_KEY, "sk-12345");
-
-        assert_eq!(state.state().get("api_key"), Some(&json!("sk-12345")));
-        assert_eq!(state.state().get(INPUT_KEY), Some(&Value::Null));
-    }
-
-    #[test]
-    fn input_question_appends_default_when_present() {
-        let state = manager_with(&[("name", json!("alice"))]);
-        let mut node = input("Hi, what's your name?");
-        node.default = Some("{{name}}".into());
-
-        let q = build_input_question(&node, &state).unwrap();
-
-        assert_eq!(q, "Hi, what's your name? [default: alice]");
-    }
-
-    #[test]
-    fn input_question_omits_default_when_blank_after_interpolation() {
-        let state = manager_with(&[]);
-        let mut node = input("Enter value:");
-        node.default = Some("{{missing}}".into());
-
-        let q = build_input_question(&node, &state).unwrap();
-
-        assert_eq!(q, "Enter value:");
-    }
-
-    #[test]
-    fn input_question_uses_no_default_when_field_absent() {
-        let state = manager_with(&[]);
-        let node = input("Enter value:");
-
-        let q = build_input_question(&node, &state).unwrap();
-
-        assert_eq!(q, "Enter value:");
-    }
-
-    #[test]
-    fn no_state_updates_means_var_never_appears_in_state() {
-        let mut state = manager_with(&[]);
-
-        apply_state_updates_with_var(&None, &mut state, CHOICE_KEY, "approve");
-
-        assert!(state.state().get(CHOICE_KEY).is_none());
-    }
-}

src/main.rs

@@ -2,7 +2,6 @@ mod cli;
 mod client;
 mod config;
 mod function;
-mod graph;
 mod rag;
 mod render;
 mod repl;
@@ -83,23 +82,8 @@ async fn main() -> Result<()> {
 
     let log_path = setup_logger()?;
 
-    if let Some(version) = &cli.update {
-        let version = version.clone();
-        let force = cli.force;
-        return tokio::task::spawn_blocking(move || config::run_self_update(version, force))
-            .await?;
-    }
-
     install_builtins()?;
 
-    if let Some(category) = cli.install {
-        return config::install_assets(category);
-    }
-
-    if let Some(url) = cli.install_from.as_deref() {
-        return config::install_remote(url, cli.filter, cli.install_force);
-    }
-
     if let Some(client_arg) = &cli.authenticate {
         let cfg = Config::load_with_interpolation(true).await?;
         let app_config = AppConfig::from_config(cfg)?;
@@ -327,17 +311,6 @@ async fn start_directive(
     abort_signal: AbortSignal,
 ) -> Result<()> {
     let app: Arc<AppConfig> = Arc::clone(&ctx.app.config);
-
-    if graph::active_agent_graph_name(ctx).is_some() {
-        ctx.before_chat_completion(&input)?;
-        let output =
-            graph::run_active_agent_graph(ctx, &input.text(), abort_signal.clone()).await?;
-        app.print_markdown(&output)?;
-        ctx.after_chat_completion(app.as_ref(), &input, &output, &[])?;
-        ctx.exit_session()?;
-        return Ok(());
-    }
-
     let client = input.create_client()?;
     let extract_code = !*IS_STDOUT_TERMINAL && code_mode;
     ctx.before_chat_completion(&input)?;

src/mcp/mod.rs

@@ -8,7 +8,6 @@ use crate::vault::interpolate_secrets;
 use anyhow::{Context, Result, anyhow};
 use futures_util::{StreamExt, TryStreamExt, stream};
 use http::{HeaderName, HeaderValue};
-use indexmap::IndexMap;
 use indoc::formatdoc;
 use rmcp::service::RunningService;
 use rmcp::transport::StreamableHttpClientTransport;
@@ -50,29 +49,23 @@ impl Clone for ServerCatalog {
     }
 }
 
-#[derive(Debug, Clone, Deserialize, Serialize)]
+#[derive(Debug, Clone, Deserialize)]
 pub(crate) struct McpServersConfig {
     #[serde(rename = "mcpServers")]
-    pub mcp_servers: IndexMap<String, McpServer>,
+    pub mcp_servers: HashMap<String, McpServer>,
 }
 
-#[derive(Debug, Clone, Deserialize, Serialize, PartialEq, Eq)]
+#[derive(Debug, Clone, Deserialize)]
 #[serde(deny_unknown_fields)]
 pub(crate) struct McpServer {
     #[serde(rename = "type")]
     pub transport_type: McpTransportType,
-    #[serde(skip_serializing_if = "Option::is_none")]
     pub command: Option<String>,
-    #[serde(skip_serializing_if = "Option::is_none")]
     pub args: Option<Vec<String>>,
-    #[serde(skip_serializing_if = "Option::is_none")]
-    pub env: Option<IndexMap<String, JsonField>>,
-    #[serde(skip_serializing_if = "Option::is_none")]
+    pub env: Option<HashMap<String, JsonField>>,
     pub cwd: Option<String>,
-    #[serde(skip_serializing_if = "Option::is_none")]
     pub url: Option<String>,
-    #[serde(skip_serializing_if = "Option::is_none")]
-    pub headers: Option<IndexMap<String, String>>,
+    pub headers: Option<HashMap<String, String>>,
 }
 
 impl McpServer {
@@ -118,7 +111,7 @@ impl McpServer {
     }
 }
 
-#[derive(Debug, Clone, Deserialize, Serialize, PartialEq, Eq, Hash)]
+#[derive(Debug, Clone, Deserialize, PartialEq, Eq, Hash)]
 #[serde(rename_all = "lowercase")]
 pub(crate) enum McpTransportType {
     Stdio,
@@ -126,7 +119,7 @@ pub(crate) enum McpTransportType {
     Sse,
 }
 
-#[derive(Debug, Clone, Deserialize, Serialize, PartialEq, Eq)]
+#[derive(Debug, Clone, Deserialize)]
 #[serde(untagged)]
 pub(crate) enum JsonField {
     Str(String),
@@ -359,7 +352,7 @@ pub(crate) async fn spawn_mcp_server(
 
 async fn spawn_http_mcp_server(
     url: &str,
-    headers: Option<&IndexMap<String, String>>,
+    headers: Option<&HashMap<String, String>>,
 ) -> Result<Arc<ConnectedServer>> {
     let transport = if let Some(hdrs) = headers
         && !hdrs.is_empty()
@@ -389,7 +382,7 @@ async fn spawn_http_mcp_server(
 
 async fn spawn_sse_mcp_server(
     url: &str,
-    headers: Option<&IndexMap<String, String>>,
+    headers: Option<&HashMap<String, String>>,
 ) -> Result<Arc<ConnectedServer>> {
     let sse = LegacySseTransport::connect(url, headers)
         .await
@@ -489,7 +482,7 @@ mod tests {
     }
 
     fn make_registry_with_config(server_names: &[&str]) -> McpRegistry {
-        let mut mcp_servers = IndexMap::new();
+        let mut mcp_servers = HashMap::new();
         for name in server_names {
             mcp_servers.insert(name.to_string(), stdio_server("echo"));
         }
@@ -537,7 +530,7 @@ mod tests {
 
     #[test]
     fn validate_stdio_with_headers_fails() {
-        let mut headers = IndexMap::new();
+        let mut headers = HashMap::new();
         headers.insert("Auth".into(), "Bearer tok".into());
         let spec = McpServer {
             transport_type: McpTransportType::Stdio,

src/mcp/sse_transport.rs

@@ -1,14 +1,13 @@
 use anyhow::{Context, Result, anyhow};
-use eventsource_stream::{EventStream, Eventsource};
 use fmt::{Display, Formatter};
 use futures_util::StreamExt;
-use futures_util::stream::BoxStream;
-use indexmap::IndexMap;
 use mpsc::error::SendError;
 use mpsc::{OwnedPermit, Receiver, Sender, channel};
+use reqwest::Client;
 use reqwest::header::{HeaderMap, HeaderName, HeaderValue};
-use reqwest::{Client, header};
+use reqwest_eventsource::{Event, EventSource};
 use rmcp::model::{ClientJsonRpcMessage, ServerJsonRpcMessage};
+use std::collections::HashMap;
 use std::error::Error;
 use std::fmt;
 use std::future::Future;
@@ -18,8 +17,6 @@ use tokio::sync::mpsc;
 use tokio::time::Duration;
 use url::Url;
 
-type SseEventStream = EventStream<BoxStream<'static, reqwest::Result<bytes::Bytes>>>;
-
 const CHANNEL_BUF: usize = 64;
 
 pub struct LegacySseTransport {
@@ -28,10 +25,7 @@ pub struct LegacySseTransport {
 }
 
 impl LegacySseTransport {
-    pub async fn connect(
-        sse_url: &str,
-        headers: Option<&IndexMap<String, String>>,
-    ) -> Result<Self> {
+    pub async fn connect(sse_url: &str, headers: Option<&HashMap<String, String>>) -> Result<Self> {
         let base_url =
             Url::parse(sse_url).with_context(|| format!("Invalid SSE URL: {sse_url}"))?;
 
@@ -53,15 +47,8 @@ impl LegacySseTransport {
             .build()
             .context("Failed to build HTTP client")?;
 
-        let response = client
-            .get(sse_url)
-            .header(header::ACCEPT, "text/event-stream")
-            .send()
-            .await
-            .context("Failed to open SSE connection")?
-            .error_for_status()
-            .context("SSE server returned an error status")?;
-        let mut es: SseEventStream = response.bytes_stream().boxed().eventsource();
+        let request = client.get(sse_url);
+        let mut es = EventSource::new(request).context("Failed to open SSE connection")?;
 
         let post_endpoint = wait_for_endpoint_event(&mut es, &base_url).await?;
 
@@ -96,17 +83,18 @@ impl LegacySseTransport {
     }
 }
 
-async fn wait_for_endpoint_event(es: &mut SseEventStream, base_url: &Url) -> Result<String> {
+async fn wait_for_endpoint_event(es: &mut EventSource, base_url: &Url) -> Result<String> {
     let timeout = Duration::from_secs(30);
     tokio::time::timeout(timeout, async {
         while let Some(event) = es.next().await {
             match event {
-                Ok(msg) if msg.event == "endpoint" => {
+                Ok(Event::Open) => {}
+                Ok(Event::Message(msg)) if msg.event == "endpoint" => {
                     let endpoint = msg.data.trim().to_string();
                     let resolved = resolve_endpoint(&endpoint, base_url)?;
                     return Ok(resolved);
                 }
-                Ok(_) => {}
+                Ok(Event::Message(_)) => {}
                 Err(e) => {
                     return Err(anyhow!(
                         "SSE connection error while waiting for endpoint event: {e}"
@@ -132,10 +120,10 @@ fn resolve_endpoint(endpoint: &str, base_url: &Url) -> Result<String> {
     }
 }
 
-async fn sse_reader_task(mut es: SseEventStream, tx: Sender<ServerJsonRpcMessage>) {
+async fn sse_reader_task(mut es: EventSource, tx: Sender<ServerJsonRpcMessage>) {
     while let Some(event) = es.next().await {
         match event {
-            Ok(msg) if msg.event == "message" => {
+            Ok(Event::Message(msg)) if msg.event == "message" => {
                 match serde_json::from_str::<ServerJsonRpcMessage>(&msg.data) {
                     Ok(rpc_msg) => {
                         if tx.send(rpc_msg).await.is_err() {
@@ -148,12 +136,14 @@ async fn sse_reader_task(mut es: SseEventStream, tx: Sender<ServerJsonRpcMessage
                 }
             }
             Ok(_) => {}
+            Err(reqwest_eventsource::Error::StreamEnded) => break,
             Err(e) => {
                 error!("SSE stream error: {e}");
                 break;
             }
         }
     }
+    es.close();
 }
 
 async fn post_writer_task(

src/rag/mod.rs

@@ -16,8 +16,7 @@ use parking_lot::RwLock;
 use serde::{Deserialize, Serialize};
 use serde_json::json;
 use std::{
-    collections::HashMap, env, fmt, fmt::Debug, fs, hash::Hash, path::Path, sync::Arc,
-    time::Duration,
+    collections::HashMap, env, fmt::Debug, fs, hash::Hash, path::Path, sync::Arc, time::Duration,
 };
 use tokio::time::sleep;
 
@@ -57,7 +56,7 @@ pub struct Rag {
 }
 
 impl Debug for Rag {
-    fn fmt(&self, f: &mut fmt::Formatter<'_>) -> fmt::Result {
+    fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result {
         f.debug_struct("Rag")
             .field("name", &self.name)
             .field("path", &self.path)
@@ -82,126 +81,11 @@ impl Clone for Rag {
     }
 }
 
-#[derive(Debug, Clone, Default)]
-pub struct RagInitConfig {
-    pub embedding_model: Option<String>,
-    pub chunk_size: Option<usize>,
-    pub chunk_overlap: Option<usize>,
-    pub reranker_model: Option<String>,
-    pub top_k: Option<usize>,
-    pub batch_size: Option<usize>,
-}
-
 impl Rag {
     fn create_embeddings_client(&self, model: Model) -> Result<Box<dyn Client>> {
         init_client(&self.app_config, model)
     }
 
-    pub async fn init_with_config(
-        app: &AppConfig,
-        name: &str,
-        save_path: &Path,
-        doc_paths: &[String],
-        config: &RagInitConfig,
-        abort_signal: AbortSignal,
-    ) -> Result<Self> {
-        if doc_paths.is_empty() {
-            bail!("Cannot build RAG knowledge base '{name}' with no documents");
-        }
-        println!("⚙ Initializing RAG...");
-        let data = Self::resolve_init_data(app, config)?;
-        let mut rag = Self::create(app, name, save_path, data)?;
-        let loaders = app.document_loaders.clone();
-        let (spinner, spinner_rx) = Spinner::create("");
-        abortable_run_with_spinner_rx(
-            rag.sync_documents(doc_paths, true, loaders, Some(spinner)),
-            spinner_rx,
-            abort_signal,
-        )
-        .await?;
-        if rag.save()? {
-            println!("✓ Saved RAG to '{}'.", save_path.display());
-        }
-        Ok(rag)
-    }
-
-    fn resolve_init_data(app: &AppConfig, config: &RagInitConfig) -> Result<RagData> {
-        let embedding_model_id = config
-            .embedding_model
-            .clone()
-            .or_else(|| app.rag_embedding_model.clone());
-        let embedding_model_id = match embedding_model_id {
-            Some(value) => {
-                println!("Embedding model: {value}");
-                value
-            }
-            None => {
-                if !*IS_STDOUT_TERMINAL {
-                    bail!(
-                        "RAG knowledge base needs an embedding model. Set `embedding_model` \
-                         on the rag node, or run the agent interactively once."
-                    );
-                }
-                let models = list_models(app, ModelType::Embedding);
-                if models.is_empty() {
-                    bail!("No available embedding model");
-                }
-                select_embedding_model(&models)?
-            }
-        };
-        let embedding_model =
-            Model::retrieve_model(app, &embedding_model_id, ModelType::Embedding)?;
-
-        let chunk_size = match config.chunk_size.or(app.rag_chunk_size) {
-            Some(value) => {
-                println!("Chunk size: {value}");
-                value
-            }
-            None => {
-                if !*IS_STDOUT_TERMINAL {
-                    bail!(
-                        "RAG knowledge base needs a chunk_size. Set `chunk_size` on the \
-                         rag node, or run the agent interactively once."
-                    );
-                }
-                set_chunk_size(&embedding_model)?
-            }
-        };
-        let chunk_overlap = match config.chunk_overlap.or(app.rag_chunk_overlap) {
-            Some(value) => {
-                println!("Chunk overlap: {value}");
-                value
-            }
-            None => {
-                if !*IS_STDOUT_TERMINAL {
-                    bail!(
-                        "RAG knowledge base needs a chunk_overlap. Set `chunk_overlap` on \
-                         the rag node, or run the agent interactively once."
-                    );
-                }
-                set_chunk_overlay(chunk_size / 20)?
-            }
-        };
-
-        let reranker_model = config
-            .reranker_model
-            .clone()
-            .or_else(|| app.rag_reranker_model.clone());
-        let top_k = config.top_k.unwrap_or(app.rag_top_k);
-        let batch_size = config
-            .batch_size
-            .or_else(|| embedding_model.max_batch_size());
-
-        Ok(RagData::new(
-            embedding_model.id(),
-            chunk_size,
-            chunk_overlap,
-            reranker_model,
-            top_k,
-            batch_size,
-        ))
-    }
-
     pub async fn init(
         app: &AppConfig,
         name: &str,
@@ -431,14 +315,6 @@ impl Rag {
         self.name == TEMP_RAG_NAME
     }
 
-    pub fn configured_top_k(&self) -> usize {
-        self.data.top_k
-    }
-
-    pub fn configured_reranker(&self) -> Option<&str> {
-        self.data.reranker_model.as_deref()
-    }
-
     pub async fn search(
         &self,
         text: &str,
@@ -447,7 +323,7 @@ impl Rag {
         abort_signal: AbortSignal,
     ) -> Result<(String, String, Vec<DocumentId>)> {
         let ret = abortable_run_with_spinner(
-            self.hybrid_search(text, top_k, rerank_model),
+            self.hybird_search(text, top_k, rerank_model),
             "Searching",
             abort_signal,
         )
@@ -707,7 +583,7 @@ impl Rag {
         Ok(())
     }
 
-    async fn hybrid_search(
+    async fn hybird_search(
         &self,
         query: &str,
         top_k: usize,
@@ -905,7 +781,7 @@ pub struct RagData {
 }
 
 impl Debug for RagData {
-    fn fmt(&self, f: &mut fmt::Formatter<'_>) -> fmt::Result {
+    fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result {
         f.debug_struct("RagData")
             .field("embedding_model", &self.embedding_model)
             .field("chunk_size", &self.chunk_size)
@@ -1033,7 +909,7 @@ pub type FileId = usize;
 pub struct DocumentId(usize);
 
 impl Debug for DocumentId {
-    fn fmt(&self, f: &mut fmt::Formatter<'_>) -> fmt::Result {
+    fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result {
         let (file_index, document_index) = self.split();
         f.write_fmt(format_args!("{file_index}-{document_index}"))
     }
@@ -1075,8 +951,8 @@ impl SelectOption {
     }
 }
 
-impl fmt::Display for SelectOption {
-    fn fmt(&self, f: &mut fmt::Formatter<'_>) -> fmt::Result {
+impl std::fmt::Display for SelectOption {
+    fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result {
         write!(f, "{} ({})", self.value, self.description)
     }
 }
@@ -1380,13 +1256,13 @@ mod tests {
 
     #[test]
     fn get_separators_returns_language_specific() {
-        let rs_seps = get_separators("rs");
+        let rs_seps = splitter::get_separators("rs");
         assert!(rs_seps.iter().any(|s| s.contains("fn ")));
 
-        let py_seps = get_separators("py");
+        let py_seps = splitter::get_separators("py");
         assert!(py_seps.iter().any(|s| s.contains("def ")));
 
-        let md_seps = get_separators("md");
+        let md_seps = splitter::get_separators("md");
         assert!(md_seps.iter().any(|s| s.contains("# ")));
     }
 

src/render/mod.rs

@@ -17,11 +17,7 @@ pub async fn render_stream(
     rx: UnboundedReceiver<SseEvent>,
     app: &AppConfig,
     abort_signal: AbortSignal,
-    silent: bool,
 ) -> Result<()> {
-    if silent {
-        return drain_silently(rx, &abort_signal).await;
-    }
     let ret = if *IS_STDOUT_TERMINAL && app.highlight {
         let render_options = app.render_options()?;
         let mut render = MarkdownRender::init(render_options)?;
@@ -32,22 +28,6 @@ pub async fn render_stream(
     ret.map_err(|err| err.context("Failed to reader stream"))
 }
 
-async fn drain_silently(
-    mut rx: UnboundedReceiver<SseEvent>,
-    abort_signal: &AbortSignal,
-) -> Result<()> {
-    loop {
-        if abort_signal.aborted() {
-            break;
-        }
-        match rx.recv().await {
-            Some(SseEvent::Done) | None => break,
-            Some(SseEvent::Text(_)) => {}
-        }
-    }
-    Ok(())
-}
-
 pub fn render_error(err: anyhow::Error) {
     eprintln!("{}", error_text(&pretty_error(&err)));
 }

src/repl/mod.rs

@@ -7,22 +7,20 @@ use self::highlighter::ReplHighlighter;
 use self::prompt::ReplPrompt;
 
 use crate::client::{call_chat_completions, call_chat_completions_streaming, init_client, oauth};
+use crate::config::paths;
 use crate::config::{
     AgentVariables, AppConfig, AssertState, Input, LastMessage, RequestContext, StateFlags,
     macro_execute,
 };
-use crate::config::{AssetCategory, paths};
 use crate::render::render_error;
 use crate::utils::{
     AbortSignal, abortable_run_with_spinner, create_abort_signal, dimmed_text, set_text, temp_file,
 };
 
-use crate::{config, graph, resolve_oauth_client};
+use crate::resolve_oauth_client;
 use anyhow::{Context, Result, bail};
 use crossterm::cursor::SetCursorStyle;
 use fancy_regex::Regex;
-use indoc::indoc;
-use log::warn;
 use parking_lot::RwLock;
 use reedline::CursorConfig;
 use reedline::{
@@ -33,20 +31,10 @@ use reedline::{
 use reedline::{MenuBuilder, Signal};
 use std::sync::LazyLock;
 use std::{env, process, sync::Arc};
-use tokio::task;
 
 const MENU_NAME: &str = "completion_menu";
 
-pub const DEFAULT_CONTINUATION_PROMPT: &str = indoc! {"
-    [SYSTEM REMINDER - TODO CONTINUATION]
-    You have incomplete tasks. Rules:
-    1. BEFORE marking a todo done: verify the work compiles/works. No premature completion.
-    2. If a todo is broad (e.g. \"implement X and implement Y\"): break it into specific subtasks FIRST using todo__add, then work on those.\n\
-    3. Each todo should be atomic and be \"single responsibility\" - completable in one focused action.
-    4. Continue with the next pending item now. Call tools immediately."
-};
-
-static REPL_COMMANDS: LazyLock<[ReplCommand; 42]> = LazyLock::new(|| {
+static REPL_COMMANDS: LazyLock<[ReplCommand; 39]> = LazyLock::new(|| {
     [
         ReplCommand::new(".help", "Show this help guide", AssertState::pass()),
         ReplCommand::new(".info", "Show system info", AssertState::pass()),
@@ -60,11 +48,6 @@ static REPL_COMMANDS: LazyLock<[ReplCommand; 42]> = LazyLock::new(|| {
             "Modify configuration file",
             AssertState::False(StateFlags::AGENT),
         ),
-        ReplCommand::new(
-            ".edit mcp-config",
-            "Modify the MCP servers configuration file",
-            AssertState::False(StateFlags::AGENT),
-        ),
         ReplCommand::new(".model", "Switch LLM model", AssertState::pass()),
         ReplCommand::new(
             ".prompt",
@@ -158,7 +141,7 @@ static REPL_COMMANDS: LazyLock<[ReplCommand; 42]> = LazyLock::new(|| {
         ReplCommand::new(
             ".clear todo",
             "Clear the todo list and stop auto-continuation",
-            AssertState::pass(),
+            AssertState::True(StateFlags::AGENT),
         ),
         ReplCommand::new(
             ".rag",
@@ -218,16 +201,6 @@ static REPL_COMMANDS: LazyLock<[ReplCommand; 42]> = LazyLock::new(|| {
             "View or modify the Loki vault",
             AssertState::pass(),
         ),
-        ReplCommand::new(
-            ".install",
-            "Reinstall bundled assets, or install assets from a remote git repo (.install remote <url>)",
-            AssertState::pass(),
-        ),
-        ReplCommand::new(
-            ".update",
-            "Update Loki to the latest release (or a specified version)",
-            AssertState::pass(),
-        ),
         ReplCommand::new(".exit", "Exit REPL", AssertState::pass()),
     ]
 });
@@ -514,12 +487,6 @@ pub async fn run_repl_command(
                 ),
             },
             ".session" => {
-                if let Some(name) = graph::active_agent_graph_name(ctx) {
-                    bail!(
-                        "Graph-based agent '{name}' does not support sessions. \
-                         The graph manages its own state."
-                    );
-                }
                 let app = Arc::clone(&ctx.app.config);
                 ctx.use_session(app.as_ref(), args, abort_signal.clone())
                     .await?;
@@ -531,41 +498,13 @@ pub async fn run_repl_command(
                     };
                     eprintln!("\n📢 {}", color.italic().paint("Autonaming the session."),);
                     if let Err(err) = ctx.autoname_session(app.as_ref()).await {
-                        warn!("Failed to autonaming the session: {err}");
+                        log::warn!("Failed to autonaming the session: {err}");
                     }
                     if let Some(session) = ctx.session.as_mut() {
                         session.set_autonaming(false);
                     }
                 }
             }
-            ".install" => {
-                let trimmed = args.map(str::trim).unwrap_or("");
-                let mut parts = trimmed.splitn(2, char::is_whitespace);
-                match parts.next() {
-                    Some("remote") => {
-                        let rest = parts.next().unwrap_or("").trim();
-                        config::install_remote_from_repl_args(rest)?;
-                    }
-                    Some(name) if !name.is_empty() => match AssetCategory::parse(name) {
-                        Some(category) => config::install_assets(category)?,
-                        None => println!(
-                            "Unknown asset category '{name}'. Valid categories: {}",
-                            AssetCategory::NAMES.join(", ")
-                        ),
-                    },
-                    _ => println!(
-                        "Usage: .install <{}> | .install remote <git-url>",
-                        AssetCategory::NAMES.join("|")
-                    ),
-                }
-            }
-            ".update" => {
-                if ctx.macro_flag {
-                    bail!("Cannot perform this operation because you are in a macro")
-                }
-                let version = args.map(|s| s.trim().to_string());
-                task::spawn_blocking(move || config::run_self_update(version, false)).await??;
-            }
             ".rag" => {
                 ctx.use_rag(args, abort_signal.clone()).await?;
             }
@@ -656,13 +595,8 @@ pub async fn run_repl_command(
                         let app = Arc::clone(&ctx.app.config);
                         ctx.edit_agent_config(app.as_ref())?;
                     }
-                    Some("mcp-config") => {
-                        ctx.edit_mcp_config()?;
-                    }
                     _ => {
-                        println!(
-                            r#"Usage: .edit <config|mcp-config|role|session|rag-docs|agent-config>"#
-                        )
+                        println!(r#"Usage: .edit <config|role|session|rag-docs|agent-config>"#)
                     }
                 }
             }
@@ -830,18 +764,25 @@ pub async fn run_repl_command(
                     bail!("Use '.empty session' instead");
                 }
                 Some("todo") => {
-                    let config = ctx.auto_continue_config();
-                    if !config.enabled {
-                        bail!(
-                            "Auto-continue is not enabled. Set 'auto_continue: true' in your config to enable it."
-                        );
-                    }
-                    if ctx.todo_list.is_empty() {
-                        println!("Todo list is already empty.");
-                    } else {
-                        ctx.clear_todo_list();
-                        println!("Todo list cleared.");
-                    }
+                    let cleared = match ctx.agent.as_mut() {
+                        Some(agent) => {
+                            if !agent.auto_continue_enabled() {
+                                bail!(
+                                    "The todo system is not enabled for this agent. Set 'auto_continue: true' in the agent's config.yaml to enable it."
+                                );
+                            }
+                            if ctx.todo_list.is_empty() {
+                                println!("Todo list is already empty.");
+                                false
+                            } else {
+                                ctx.clear_todo_list();
+                                println!("Todo list cleared.");
+                                true
+                            }
+                        }
+                        None => bail!("No active agent"),
+                    };
+                    let _ = cleared;
                 }
                 _ => unknown_command()?,
             },
@@ -914,18 +855,8 @@ async fn ask(
         tokio::time::sleep(std::time::Duration::from_millis(100)).await;
     }
 
-    let app = Arc::clone(&ctx.app.config);
-
-    if graph::active_agent_graph_name(ctx).is_some() {
-        ctx.before_chat_completion(&input)?;
-        let output =
-            graph::run_active_agent_graph(ctx, &input.text(), abort_signal.clone()).await?;
-        app.print_markdown(&output)?;
-        ctx.after_chat_completion(app.as_ref(), &input, &output, &[])?;
-        return Ok(());
-    }
-
     let client = input.create_client()?;
+    let app = Arc::clone(&ctx.app.config);
     ctx.before_chat_completion(&input)?;
     let (output, tool_results) = if input.stream() {
         call_chat_completions_streaming(&input, client.as_ref(), ctx, abort_signal.clone()).await?
@@ -950,22 +881,19 @@ async fn ask(
         )
         .await
     } else {
-        let do_continue = should_continue(ctx);
+        let should_continue = agent_should_continue(ctx);
 
-        if do_continue {
+        if should_continue {
             let full_prompt = {
-                let config = ctx.auto_continue_config();
                 let todo_state = ctx.todo_list.render_for_model();
                 let remaining = ctx.todo_list.incomplete_count();
                 ctx.set_last_continuation_response(output.clone());
                 ctx.increment_auto_continue_count();
+                let agent = ctx.agent.as_mut().expect("agent checked above");
                 let count = ctx.auto_continue_count;
-                let max = config.max_continues;
+                let max = agent.max_auto_continues();
 
-                let prompt = config
-                    .continuation_prompt
-                    .as_deref()
-                    .unwrap_or(DEFAULT_CONTINUATION_PROMPT);
+                let prompt = agent.continuation_prompt();
 
                 let color = if app.light_theme() {
                     nu_ansi_term::Color::LightGray
@@ -993,7 +921,7 @@ async fn ask(
                 };
                 eprintln!("\n📢 {}", color.italic().paint("Autonaming the session."),);
                 if let Err(err) = ctx.autoname_session(app.as_ref()).await {
-                    warn!("Failed to autonaming the session: {err}");
+                    log::warn!("Failed to autonaming the session: {err}");
                 }
                 if let Some(session) = ctx.session.as_mut() {
                     session.set_autonaming(false);
@@ -1006,7 +934,7 @@ async fn ask(
                 .is_some_and(|s| s.needs_compression(app.compression_threshold));
 
             if needs_compression {
-                let agent_can_continue_after_compress = should_continue(ctx);
+                let agent_can_continue_after_compress = agent_should_continue(ctx);
 
                 if let Some(session) = ctx.session.as_mut() {
                     session.set_compressing(true);
@@ -1020,7 +948,7 @@ async fn ask(
                 eprintln!("\n📢 {}", color.italic().paint("Compressing the session."),);
 
                 if let Err(err) = ctx.compress_session().await {
-                    warn!("Failed to compress the session: {err}");
+                    log::warn!("Failed to compress the session: {err}");
                 }
                 if let Some(session) = ctx.session.as_mut() {
                     session.set_compressing(false);
@@ -1028,17 +956,14 @@ async fn ask(
 
                 if agent_can_continue_after_compress {
                     let full_prompt = {
-                        let config = ctx.auto_continue_config();
                         let todo_state = ctx.todo_list.render_for_model();
                         let remaining = ctx.todo_list.incomplete_count();
                         ctx.increment_auto_continue_count();
+                        let agent = ctx.agent.as_mut().expect("agent checked above");
                         let count = ctx.auto_continue_count;
-                        let max = config.max_continues;
+                        let max = agent.max_auto_continues();
 
-                        let prompt = config
-                            .continuation_prompt
-                            .as_deref()
-                            .unwrap_or(DEFAULT_CONTINUATION_PROMPT);
+                        let prompt = agent.continuation_prompt();
 
                         let color = if app.light_theme() {
                             nu_ansi_term::Color::LightGray
@@ -1064,12 +989,10 @@ async fn ask(
     }
 }
 
-fn should_continue(ctx: &RequestContext) -> bool {
-    let config = ctx.auto_continue_config();
-    ctx.app.config.function_calling_support
-        && config.enabled
-        && ctx.auto_continue_count < config.max_continues
-        && ctx.todo_list.has_incomplete()
+fn agent_should_continue(ctx: &RequestContext) -> bool {
+    ctx.agent.as_ref().is_some_and(|agent| {
+        agent.auto_continue_enabled() && ctx.auto_continue_count < agent.max_auto_continues()
+    }) && ctx.todo_list.has_incomplete()
 }
 
 fn reset_continuation(ctx: &mut RequestContext) {
@@ -1265,8 +1188,8 @@ mod tests {
     }
 
     #[test]
-    fn repl_commands_has_42_entries() {
-        assert_eq!(REPL_COMMANDS.len(), 42);
+    fn repl_commands_has_39_entries() {
+        assert_eq!(REPL_COMMANDS.len(), 39);
     }
 
     #[test]
@@ -1388,15 +1311,13 @@ mod tests {
     }
 
     #[test]
-    fn repl_commands_clear_todo_always_available() {
+    fn repl_commands_clear_todo_requires_agent() {
         let cmd = REPL_COMMANDS
             .iter()
             .find(|c| c.name == ".clear todo")
             .unwrap();
         assert!(cmd.is_valid(StateFlags::AGENT));
-        assert!(cmd.is_valid(StateFlags::empty()));
-        assert!(cmd.is_valid(StateFlags::SESSION));
-        assert!(cmd.is_valid(StateFlags::ROLE));
+        assert!(!cmd.is_valid(StateFlags::empty()));
     }
 
     #[test]

src/utils/mod.rs

@@ -34,6 +34,7 @@ use is_terminal::IsTerminal;
 use std::borrow::Cow;
 use std::sync::LazyLock;
 use std::{cmp, env, path::PathBuf, process};
+use unicode_segmentation::UnicodeSegmentation;
 
 pub static CODE_BLOCK_RE: LazyLock<Regex> =
     LazyLock::new(|| Regex::new(r"(?ms)```\w*(.*)```").unwrap());
@@ -73,8 +74,21 @@ pub fn parse_bool(value: &str) -> Option<bool> {
 }
 
 pub fn estimate_token_length(text: &str) -> usize {
-    let weighted: usize = text.chars().map(|c| if c.is_ascii() { 1 } else { 2 }).sum();
-    weighted.div_ceil(4)
+    let words: Vec<&str> = text.unicode_words().collect();
+    let mut output: f32 = 0.0;
+    for word in words {
+        if word.is_ascii() {
+            output += 1.3;
+        } else {
+            let count = word.chars().count();
+            if count == 1 {
+                output += 1.0
+            } else {
+                output += (count as f32) * 0.5;
+            }
+        }
+    }
+    output.ceil() as usize
 }
 
 pub fn strip_think_tag(text: &str) -> Cow<'_, str> {

src/utils/path.rs

@@ -241,23 +241,23 @@ fn add_file(files: &mut IndexSet<String>, suffixes: Option<&Vec<String>>, path:
 }
 
 fn is_valid_extension(suffixes: Option<&Vec<String>>, path: &Path) -> bool {
-    let Some(suffixes) = suffixes else {
-        return true;
-    };
-    if suffixes.is_empty() {
-        return true;
-    }
-
-    let file_name = path.file_name().and_then(|v| v.to_str());
-    let extension = path.extension().and_then(|v| v.to_str());
-
-    suffixes.iter().any(|suffix| {
-        if suffix.contains('.') {
-            Some(suffix.as_str()) == file_name
-        } else {
-            Some(suffix.as_str()) == extension
+    let filename_regex = Regex::new(r"^.+\.*").unwrap();
+    if let Some(suffixes) = suffixes
+        && !suffixes.is_empty()
+    {
+        if let Ok(Some(_)) = filename_regex.find(&suffixes.join(",")) {
+            let file_name = path
+                .file_name()
+                .and_then(|v| v.to_str())
+                .expect("invalid filename")
+                .to_string();
+            return suffixes.contains(&file_name);
+        } else if let Some(extension) = path.extension().map(|v| v.to_string_lossy().to_string()) {
+            return suffixes.contains(&extension);
         }
-    })
+        return false;
+    }
+    true
 }
 
 #[cfg(test)]
@@ -352,43 +352,4 @@ mod tests {
             )
         );
     }
-
-    #[test]
-    fn test_is_valid_extension() {
-        let md_ext = vec!["md".to_string()];
-        let md_txt_ext = vec!["md".to_string(), "txt".to_string()];
-        let test_md_filename = vec!["test.md".to_string()];
-        let mixed = vec!["md".to_string(), "test.txt".to_string()];
-
-        assert!(is_valid_extension(None, Path::new("Agents.md")));
-        assert!(is_valid_extension(Some(&vec![]), Path::new("Agents.md")));
-
-        assert!(is_valid_extension(Some(&md_ext), Path::new("Agents.md")));
-        assert!(is_valid_extension(
-            Some(&md_ext),
-            Path::new("/home/atusa/code/loki.wiki/Agents.md")
-        ));
-        assert!(!is_valid_extension(Some(&md_ext), Path::new("notes.txt")));
-        assert!(!is_valid_extension(Some(&md_ext), Path::new("README")));
-
-        assert!(is_valid_extension(Some(&md_txt_ext), Path::new("a.md")));
-        assert!(is_valid_extension(Some(&md_txt_ext), Path::new("a.txt")));
-        assert!(!is_valid_extension(Some(&md_txt_ext), Path::new("a.rs")));
-
-        assert!(is_valid_extension(
-            Some(&test_md_filename),
-            Path::new("dir/test.md")
-        ));
-        assert!(!is_valid_extension(
-            Some(&test_md_filename),
-            Path::new("dir/Agents.md")
-        ));
-
-        assert!(is_valid_extension(Some(&mixed), Path::new("Agents.md")));
-        assert!(is_valid_extension(Some(&mixed), Path::new("dir/test.txt")));
-        assert!(!is_valid_extension(
-            Some(&mixed),
-            Path::new("dir/other.txt")
-        ));
-    }
 }