feat: Added new memory functions for deleting and renaming memory files, as well as new lints for memory expiration dates and staleness of memories to improve the memory system

CHANGELOG.md

@@ -1,3 +1,82 @@
+## v0.7.4 (2026-07-02)
+
+### Feat
+
+- Pin specific usql version to sbx kit
+- recursively take ownership over the copied in coyote config for the sbx
+- explicitly specify the COYOTE_CONFIG_DIR in the sbx kit
+- --tail-logs can track log rollovers and incoporates a sleep timer to minimize idle CPU cycles
+- Added support for log rolling so log files don't just blow up over time
+
+### Fix
+
+- Added back in --kit specification for the running of the sbx
+- sbx isn't copying base files in their respective directories
+- Update deprecated sbx kit config
+- Properly chown the coyote config recursively and password file in the sbx
+
+## v0.7.3 (2026-06-24)
+
+### Fix
+
+- apply bootstrapping of functions at startup to fix edge case
+
+## v0.7.2 (2026-06-19)
+
+### Fix
+
+- usql version upgrade
+
+## v0.7.1 (2026-06-19)
+
+### Fix
+
+- sbx mixins must be passed in directories, not as files and the files must be named spec.yaml per new sbx version
+
+## v0.7.0 (2026-06-18)
+
+### Feat
+
+- added configurable cache path via the COYOTE_CACHE_PATH environment variable
+- added a memory option to .set tab completions
+- Added a diagnostic .info tools subcommand to make it easier to see what tools are enabled in all contexts
+- Added additional info outputs for enabled skills and sbx directories
+- directly execute shell commands from within the REPL
+- created mixin kit for built-in functions and MCP servers
+- Added sbx mixins for the secrets providers so users can also bootstrap those as well.
+- added support for loading sbx mixins that are dynamically discovered in the users workspace and config directory
+- Added a --fresh flag to let users create a truly bare bones sandbox without bootstrapping their config
+- initial built-in sandboxing support powered by Docker sbx
+- Added the ability to auto-bootstrap workspace memory when in git repos
+- Added explicit guardrail handling for pending agents
+- auto-append memory to memory index and don't necessarily require the LLM to remember to do it after a write
+- Added an --init-memory [global|workspace] flag to easily and quickly enable memory
+- added memory global configuration settings to the output of --info and .info
+- added .set memory REPL commands to control memory injection and applied formatting
+- Create the built-in memory management tools
+- Append the memory system prompts (readonly or r/w) to the system prompt when applicable
+- Created the --no-memory CLI flag to disable memory for this invocation
+- Added the memory configuration properties and storage to the main app config, roles, sessions, and agents.
+- initial scaffolding of a memory system
+
+### Fix
+
+- rebuild the tool scope after dynamically updating the skills_enabled value in the REPL
+- properly resolve Windows-based local vault password file locations and bootstrap them into the sandbox when possible
+- auto-translation of user-prefixed Mac and Linux paths for the vault password file when running inside a sandbox
+- don't attempt to auto complete .vault list in the REPL; that's the end of the command
+- buffer tool stdout as well as stderr so that any tools that error to stdout are captured and included in the response to the model, enabling the model to see what went wrong and to reason about how to fix it.
+- auto-bootstrapped memory was accidentally putting the MEMORY.md directly in the repo root rather than .coyote/memory/MEMORY.md
+- improved the fs_patch script description and added improved error handling to it.
+- added in forgotten require_max_tokens to the fable model
+- append memory functions to non-graph based agents on init
+- when auto_continue is disabled via the .set auto_continue false command, it should strip the todo functions from the list of functions
+- use rawPredict for non-streaming Claude requests
+
+### Refactor
+
+- Migrated the .skills command completion to use StateFlags and updated the help messages
+
 ## v0.6.0 (2026-06-05)
 
 ### Feat

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "coyote-ai"
-version = "0.6.0"
+version = "0.7.4"
 edition = "2024"
 authors = ["Alex Clarke <alex.j.tusa@gmail.com>"]
 description = "An all-in-one, batteries included LLM CLI Tool"
@@ -49,7 +49,7 @@ textwrap = "0.16.0"
 ansi_colours = "1.2.2"
 eventsource-stream = "0.2.3"
 log = "0.4.28"
-log4rs = { version = "1.4.0", features = ["file_appender"] }
+log4rs = { version = "1.4.0", features = ["file_appender", "rolling_file_appender", "compound_policy", "fixed_window_roller", "size_trigger"] }
 shell-words = "1.1.0"
 sha2 = "0.10.8"
 unicode-width = "0.2.0"

README.md

@@ -59,6 +59,9 @@ Coyote requires the following tools to be installed on your system:
 * [docker](https://docs.docker.com/engine/install/)
 * [uv](https://docs.astral.sh/uv/getting-started/installation/)
     * `curl -LsSf https://astral.sh/uv/install.sh | sh`
+* [iwe](https://github.com/iwe-org/iwe) (`iwec`, for the built-in `iwe` MCP server that navigates large markdown knowledgebases)
+    * **Homebrew:** `brew tap iwe-org/iwe && brew install iwe`
+    * **Cargo:** `cargo install iwec`
 
 These tools are used to provide various functionalities within Coyote, such as document processing, JSON manipulation,
 etc., and they are used within agents and tools.
@@ -98,7 +101,7 @@ You can use the following command to run a bash script that downloads and instal
 OS (Linux/MacOS) and architecture (x86_64/arm64):
 
 ```shell
-curl -fsSL https://raw.githubusercontent.com/Dark-Alex-17/coyote/main/install_coyote.sh | bash
+curl -fsSL https://raw.githubusercontent.com/Dark-Alex-17/coyote/refs/heads/main/scripts/install_coyote.sh | bash
 ```
 
 #### Windows/Linux/MacOS (`PowerShell`)
@@ -106,7 +109,7 @@ You can use the following command to run a PowerShell script that downloads and
 for your OS (Windows/Linux/MacOS) and architecture (x86_64/arm64):
 
 ```powershell
-powershell -NoProfile -ExecutionPolicy Bypass -Command "iwr -useb https://raw.githubusercontent.com/Dark-Alex-17/coyote/main/scripts/install_coyote.ps1 | iex"
+powershell -NoProfile -ExecutionPolicy Bypass -Command "iwr -useb https://raw.githubusercontent.com/Dark-Alex-17/coyote/refs/heads/main/scripts/install_coyote.ps1 | iex"
 ```
 
 ### Manual

assets/agents/sisyphus/sbx-mixin.yaml

@@ -0,0 +1,11 @@
+schemaVersion: '1'
+kind: mixin
+name: sisyphus-ddg
+description: >
+  Allows Sisyphus to hit all domains since it utilizes the DuckDuckGo
+  MCP server. This allows the MCP server to actually perform web searches
+  on arbitrary domains and retrieve info for the agent.
+
+network:
+  allowedDomains:
+    - '*'

assets/functions/mcp.json

@@ -18,6 +18,11 @@
       "type": "stdio",
       "command": "uvx",
       "args": ["duckduckgo-mcp-server"]
+    },
+    "iwe": {
+      "type": "stdio",
+      "command": "iwec",
+      "args": ["--project", "."]
     }
   }
 }

assets/sbx-kit/spec.yaml

@@ -5,20 +5,19 @@
 #   sbx cp $HOME/.config/coyote/ testing:/home/agent/.config/
 #   sbx cp $HOME/.coyote_password testing:/home/agent/
 #   sbx run testing --kit ./sbx-kit/
-schemaVersion: "1"
-kind: agent
+schemaVersion: '1'
+kind: sandbox
 name: coyote
 displayName: Coyote
 description: >
   An all-in-one, batteries-included LLM CLI tool featuring Shell Assistant,
   CLI & REPL mode, RAG, AI tools & agents, MCP servers, skills, and macros.
 
-agent:
-  image: "docker/sandbox-templates:shell-docker"
+sandbox:
+  image: 'docker/sandbox-templates:shell-docker'
   aiFilename: COYOTE.md
-#  persistence: persistent
   entrypoint:
-    run: ["bash", "-lc", "exec /home/agent/.cargo/bin/coyote"]
+    run: ['bash', '-lc', 'exec /home/agent/.cargo/bin/coyote']
 
 network:
   # Proxy-managed LLM providers: the proxy substitutes `proxy-managed` for
@@ -51,96 +50,96 @@ network:
   serviceAuth:
     openai:
       headerName: Authorization
-      valueFormat: "Bearer %s"
+      valueFormat: 'Bearer %s'
     anthropic:
       headerName: x-api-key
-      valueFormat: "%s"
+      valueFormat: '%s'
     gemini:
       headerName: x-goog-api-key
-      valueFormat: "%s"
+      valueFormat: '%s'
     cohere:
       headerName: Authorization
-      valueFormat: "Bearer %s"
+      valueFormat: 'Bearer %s'
     groq:
       headerName: Authorization
-      valueFormat: "Bearer %s"
+      valueFormat: 'Bearer %s'
     openrouter:
       headerName: Authorization
-      valueFormat: "Bearer %s"
+      valueFormat: 'Bearer %s'
     ai21:
       headerName: Authorization
-      valueFormat: "Bearer %s"
+      valueFormat: 'Bearer %s'
     cloudflare:
       headerName: Authorization
-      valueFormat: "Bearer %s"
+      valueFormat: 'Bearer %s'
     deepinfra:
       headerName: Authorization
-      valueFormat: "Bearer %s"
+      valueFormat: 'Bearer %s'
     deepseek:
       headerName: Authorization
-      valueFormat: "Bearer %s"
+      valueFormat: 'Bearer %s'
     mistral:
       headerName: Authorization
-      valueFormat: "Bearer %s"
+      valueFormat: 'Bearer %s'
     perplexity:
       headerName: Authorization
-      valueFormat: "Bearer %s"
+      valueFormat: 'Bearer %s'
     voyageai:
       headerName: Authorization
-      valueFormat: "Bearer %s"
+      valueFormat: 'Bearer %s'
     xai:
       headerName: Authorization
-      valueFormat: "Bearer %s"
+      valueFormat: 'Bearer %s'
     jina:
       headerName: Authorization
-      valueFormat: "Bearer %s"
+      valueFormat: 'Bearer %s'
     ernie:
       headerName: Authorization
-      valueFormat: "Bearer %s"
+      valueFormat: 'Bearer %s'
     hunyuan:
       headerName: Authorization
-      valueFormat: "Bearer %s"
+      valueFormat: 'Bearer %s'
     minimax:
       headerName: Authorization
-      valueFormat: "Bearer %s"
+      valueFormat: 'Bearer %s'
     moonshot:
       headerName: Authorization
-      valueFormat: "Bearer %s"
+      valueFormat: 'Bearer %s'
     qianwen:
       headerName: Authorization
-      valueFormat: "Bearer %s"
+      valueFormat: 'Bearer %s'
     zhipuai:
       headerName: Authorization
-      valueFormat: "Bearer %s"
+      valueFormat: 'Bearer %s'
   allowedDomains:
     # Coyote release + self-update + model-registry sync
-    - "github.com:443"
-    - "api.github.com:443"
-    - "raw.githubusercontent.com:443"
-    - "objects.githubusercontent.com:443"
-    - "*.githubusercontent.com:443"
+    - 'github.com:443'
+    - 'api.github.com:443'
+    - 'raw.githubusercontent.com:443'
+    - 'objects.githubusercontent.com:443'
+    - '*.githubusercontent.com:443'
     # Coyote install paths (cargo install + uv + rustup + Python tool deps at runtime)
-    - "crates.io:443"
-    - "static.crates.io:443"
-    - "pypi.org:443"
-    - "files.pythonhosted.org:443"
-    - "astral.sh:443"
-    - "sh.rustup.rs:443"
-    - "static.rust-lang.org:443"
+    - 'crates.io:443'
+    - 'static.crates.io:443'
+    - 'pypi.org:443'
+    - 'files.pythonhosted.org:443'
+    - 'astral.sh:443'
+    - 'sh.rustup.rs:443'
+    - 'static.rust-lang.org:443'
 
     # LLM model OAuth + API endpoints
-    - "claude.ai:443"
-    - "console.anthropic.com:443"
-    - "accounts.google.com:443"
+    - 'claude.ai:443'
+    - 'console.anthropic.com:443'
+    - 'accounts.google.com:443'
     # *.googleapis.com covers oauth2 + userinfo + VertexAI regional endpoints
     # (*-aiplatform.googleapis.com). Do not narrow without re-checking VertexAI.
-    - "*.googleapis.com:443"
+    - '*.googleapis.com:443'
 
     # Bedrock and GitHub Models use signed / GitHub-PAT auth that the proxy
     # cannot rewrite. Domains are allow-listed; credentials must be injected
     # separately (see README "Extending").
-    - "*.amazonaws.com:443"
-    - "models.inference.ai.azure.com:443"
+    - '*.amazonaws.com:443'
+    - 'models.inference.ai.azure.com:443'
 
 credentials:
   sources:
@@ -211,8 +210,9 @@ credentials:
 
 environment:
   variables:
-    IS_SANDBOX: "1"
+    IS_SANDBOX: '1'
     COYOTE_LOG_LEVEL: INFO
+    COYOTE_CONFIG_DIR: /home/agent/.config/coyote
   proxyManaged:
     - OPENAI_API_KEY
     - ANTHROPIC_API_KEY
@@ -250,26 +250,37 @@ commands:
           libssl-dev \
           pandoc \
           bzip2
-      user: "1000"
+      user: '1000'
       description: Install system prerequisites (including pandoc for fetch_url_via_curl)
-    - command: "curl -LsSf https://astral.sh/uv/install.sh | sh"
-      user: "1000"
-      description: Install uv (required for Python-based custom tools)
+    - command: |
+        curl -LsSf https://astral.sh/uv/install.sh | sh
+        if [ -f "$HOME/.local/bin/uv" ]; then
+          printf '#!/bin/sh\nexec uv tool run "$@"\n' > "$HOME/.local/bin/uvx"
+          chmod +x "$HOME/.local/bin/uvx"
+        fi
+      user: '1000'
+      description: Install uv and write a uvx shell wrapper (the installer may place a macOS binary at this path on Docker-for-Mac hosts, which the Linux container cannot execute)
     - command: |
         set -euo pipefail
-        USQL_VERSION="0.19.20"
+        USQL_VERSION=0.21.4
         ARCH=$(uname -m)
         case "$ARCH" in
           x86_64) USQL_ARCH=amd64 ;;
           aarch64) USQL_ARCH=arm64 ;;
           *) echo "Unsupported arch for usql install: $ARCH" >&2; exit 1 ;;
         esac
-        curl -sSL "https://github.com/xo/usql/releases/download/v${USQL_VERSION}/usql_static-${USQL_VERSION}-linux-${USQL_ARCH}.tar.bz2" -o /tmp/usql.tar.bz2
-        sudo tar -xjf /tmp/usql.tar.bz2 -C /usr/local/bin
-        sudo chmod +x /usr/local/bin/usql
-        rm -f /tmp/usql.tar.bz2
-      user: "1000"
+        TMPDIR=$(mktemp -d)
+        trap 'rm -rf "$TMPDIR"' EXIT
+        curl -fsSL --retry 3 "https://github.com/xo/usql/releases/download/v${USQL_VERSION}/usql_static-${USQL_VERSION}-linux-${USQL_ARCH}.tar.bz2" -o "$TMPDIR/usql.tar.bz2"
+        tar -xjf "$TMPDIR/usql.tar.bz2" -C "$TMPDIR"
+        sudo install -m 0755 "$TMPDIR/usql_static" /usr/local/bin/usql
+      user: '1000'
       description: Install the usql universal SQL CLI (used by the built-in sql agent and execute_sql_code tool)
+    - command: |
+        . "$HOME/.cargo/env"
+        cargo install --locked iwec
+      user: '1000'
+      description: Install the IWE MCP server binary (iwec) used by the built-in iwe MCP server and iwe-knowledge-base skill
     - command: |
         curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | \
           sh -s -- -y \
@@ -278,16 +289,21 @@ commands:
           --target x86_64-unknown-linux-musl
         . "$HOME/.cargo/env"
         cargo install --locked coyote-ai
-      user: "1000"
+      user: '1000'
       description: Install Coyote AI CLI via Rust's Cargo
 
   startup:
-    - command: ["sh", "-c", "test -f \"$HOME/.config/coyote/config.yaml\" || coyote --info >/dev/null 2>&1 || true"]
-      user: "1000"
+    - command:
+        [
+          'sh',
+          '-c',
+          'test -f "$HOME/.config/coyote/config.yaml" || coyote --info >/dev/null 2>&1 || true',
+        ]
+      user: '1000'
       background: false
       description: Bootstrap Coyote config directory on first sandbox start
 
-memory: |
+agentContext: |
   ## Sandbox environment
 
   You are running inside a Docker sandbox launched via `sbx run coyote`. The

assets/skills/iwe-knowledge-base/SKILL.md

@@ -0,0 +1,65 @@
+---
+description: Navigate and curate markdown knowledge bases (plan repos, spec repos, companion docs) with IWE graph tools. Load when the workspace is or contains a markdown knowledge base and the task involves finding, reading, or reorganizing plans, specs, designs, or notes. Activates the iwe MCP server rooted at the current directory.
+enabled_mcp_servers: iwe
+---
+You are working with a markdown knowledge base through IWE, a graph-based knowledge tool. The `iwe` MCP server is rooted at the current working directory (`--project .`), so the knowledge base is the directory Coyote was launched in. IWE derives structure from links: a link on its own line is an *inclusion link* (parent-child hierarchy); a link inside text is an *inline reference* (cross-reference, produces backlinks). The server watches the filesystem, so external edits are picked up automatically — never ask for a restart.
+
+## When to use this (and when not)
+
+Use IWE tools when the task involves a corpus of markdown documents: plan repositories, spec/design collections, companion docs repos, meeting notes, PKM vaults.
+
+Do NOT use IWE tools for:
+
+- **Agent memory** (`.coyote/memory/`, `COYOTE.md`) — use the `memory__*` tools; they own the index conventions there.
+- **Semantic/similarity search over documents** — that is RAG's job. IWE search is fuzzy title/key matching plus structural traversal, not embeddings.
+- **Source code** — IWE only understands markdown.
+
+If unsure whether the current directory is actually a knowledge base, probe with `iwe_stats` first. Few or zero documents means this skill does not apply; unload it rather than forcing the tools.
+
+## Orientation protocol (always start here)
+
+Never guess document keys. Orient first:
+
+1. `iwe_stats` — corpus size and shape. Cheap sanity check.
+2. `iwe_find(query="<topic>")` — fuzzy search for entry points. Use `roots` behavior via structural selectors when you want top-level topics only.
+3. `iwe_tree(key="<entry>", max_depth=2)` — see the hierarchy before reading bodies.
+4. `iwe_retrieve(key="<entry>", depth=1, context=1)` — read with structure.
+
+## Reading efficiently
+
+`iwe_retrieve` is the workhorse. Control cost explicitly:
+
+- `depth` — how many levels of included children to expand. Start at 1-2; increase only if needed.
+- `context` — parent levels to include, so you know where a document sits. `context=1` is usually enough.
+- `max_tokens` — ALWAYS set a budget (e.g. 2000-4000) on large corpora; results report truncation so you can drill further deliberately.
+- `exclude` — pass keys you have already read to avoid re-retrieving known content.
+- `links` / `backlinks` — include outbound/inbound references when tracing how a topic connects.
+
+Scope searches structurally with selectors on `iwe_find`/`iwe_retrieve`/`iwe_tree`:
+
+- `in` — only sub-documents of EVERY listed key (AND)
+- `in_any` — sub-documents of at least one key (OR)
+- `not_in` — exclude subtrees (e.g. archives)
+
+Filter by frontmatter with the YAML query language: `status: draft`, `created: {$gte: "2026-01-01"}`, `tags: {$in: [urgent]}`, `reviewed: {$exists: true}`.
+
+Use `iwe_squash(key=...)` to flatten a subtree into one linear document — good for producing a full plan readout or summary input.
+
+## Writing and refactoring
+
+Write tools: `iwe_create` (new doc from title + content), `iwe_update` (replace a doc's content), `iwe_delete` (remove + clean up references). Refactor tools: `iwe_rename` (key rename with automatic link updates everywhere), `iwe_extract` (split a section into its own doc, leaving an inclusion link), `iwe_inline` (merge a referenced doc back into its parent), `iwe_normalize` (reformat all docs consistently).
+
+Rules:
+
+- **Preview destructive operations**: `iwe_rename`, `iwe_delete`, `iwe_extract`, `iwe_inline`, and `iwe_normalize` support `dry_run` — use it first, show the user what will change, then apply.
+- Never rename or delete by editing files directly; the refactor tools update every referencing document, manual edits break links.
+- When adding a document, link it from an existing parent (inclusion link on its own line) so it joins the hierarchy instead of becoming an orphan.
+- Match the corpus conventions: check an existing document's frontmatter fields before inventing your own schema.
+- Do not run `iwe_normalize` across someone's knowledge base unprompted — it rewrites every file's formatting.
+
+## Anti-patterns
+
+- Retrieving with `depth=5` and no `max_tokens` "to get everything" — you will flood the context. Iterate: shallow first, drill selectively.
+- Calling `iwe_find` repeatedly with rephrased queries when structural navigation (`iwe_tree`, selectors) would locate the document deterministically.
+- Using IWE write tools on `.coyote/memory/` files — wrong tier; that corrupts the memory index.
+- Creating documents without linking them into the hierarchy — orphans are invisible to depth-based retrieval.

models.yaml

@@ -377,6 +377,14 @@
           thinking:
             type: enabled
             budget_tokens: 16000
+    - name: claude-sonnet-5
+      max_input_tokens: 1000000
+      max_output_tokens: 128000
+      require_max_tokens: true
+      input_price: 3
+      output_price: 15
+      supports_vision: true
+      supports_function_calling: true
     - name: claude-sonnet-4-6
       max_input_tokens: 200000
       max_output_tokens: 8192
@@ -922,6 +930,14 @@
           thinking:
             type: enabled
             budget_tokens: 16000
+    - name: claude-sonnet-5
+      max_input_tokens: 1000000
+      max_output_tokens: 128000
+      require_max_tokens: true
+      input_price: 3
+      output_price: 15
+      supports_vision: true
+      supports_function_calling: true
     - name: claude-sonnet-4-6
       max_input_tokens: 200000
       max_output_tokens: 8192
@@ -1103,6 +1119,14 @@
             thinking:
               type: enabled
               budget_tokens: 16000
+    - name: us.anthropic.claude-sonnet-5
+      max_input_tokens: 1000000
+      max_output_tokens: 128000
+      require_max_tokens: true
+      input_price: 3
+      output_price: 15
+      supports_vision: true
+      supports_function_calling: true
     - name: us.anthropic.claude-sonnet-4-6
       max_input_tokens: 200000
       max_output_tokens: 8192
@@ -1785,6 +1809,14 @@
       output_price: 25
       supports_vision: true
       supports_function_calling: true
+    - name: anthropic/claude-sonnet-5
+      max_input_tokens: 1000000
+      max_output_tokens: 128000
+      require_max_tokens: true
+      input_price: 3
+      output_price: 15
+      supports_vision: true
+      supports_function_calling: true
     - name: anthropic/claude-sonnet-4.6
       max_input_tokens: 200000
       max_output_tokens: 8192

scripts/install_coyote.ps1

@@ -39,7 +39,7 @@ switch ([System.Runtime.InteropServices.RuntimeInformation]::OSArchitecture) {
 
 if (-not $BinDir) {
   if ($isWin) { $BinDir = Join-Path $env:LOCALAPPDATA 'coyote\bin' }
-  else { $home = $env:HOME; if (-not $home) { $home = (Get-Item -Path ~).FullName }; $BinDir = Join-Path $home '.local/bin' }
+  else { $userHome = $env:HOME; if (-not $userHome) { $userHome = (Get-Item -Path ~).FullName }; $BinDir = Join-Path $userHome '.local/bin' }
 }
 New-Item -ItemType Directory -Force -Path $BinDir | Out-Null
 
@@ -95,13 +95,13 @@ if ($asset.name -match '\.zip$') {
   [System.IO.Compression.ZipFile]::ExtractToDirectory($archive, $extractDir)
 } elseif ($asset.name -match '\.tar\.gz$' -or $asset.name -match '\.tgz$') {
   $tar = Get-Command tar -ErrorAction SilentlyContinue
-  if ($tar) { & $tar.FullName -xzf $archive -C $extractDir }
+  if ($tar) { & $tar.Source -xzf $archive -C $extractDir }
   else { Fail "Asset is tar archive but 'tar' is not available." }
 } else {
   try { Add-Type -AssemblyName System.IO.Compression.FileSystem; [System.IO.Compression.ZipFile]::ExtractToDirectory($archive, $extractDir) }
   catch {
     $tar = Get-Command tar -ErrorAction SilentlyContinue
-    if ($tar) { & $tar.FullName -xf $archive -C $extractDir } else { Fail "Unknown archive format; neither zip nor tar workable." }
+    if ($tar) { & $tar.Source -xf $archive -C $extractDir } else { Fail "Unknown archive format; neither zip nor tar workable." }
   }
 }
 

scripts/install_coyote.sh

@@ -133,30 +133,21 @@ else
   echo "Error: unsupported OS for this installer: $OS" >&2; exit 1
 fi
 
+DL_URLS=$(grep -oE '"browser_download_url":[[:space:]]*"[^"]+"' "$JSON" \
+  | sed -E 's/.*"browser_download_url":[[:space:]]*"//; s/"$//' \
+  || true)
+
 ASSET_NAME=""; ASSET_URL=""
 for candidate in "${ASSET_CANDIDATES[@]}"; do
-  NAME=$(grep -oE '"name":\s*"[^"]+"' "$JSON" | sed 's/"name":\s*"//; s/"$//' | grep -Fx "$candidate" || true)
-  if [[ -n "$NAME" ]]; then
-    ASSET_NAME="$NAME"
-    ASSET_URL=$(awk -v pat="$NAME" '
-      BEGIN{ FS=":"; want=0 }
-      /"name"/ {
-        line=$0;
-        gsub(/^\s+|\s+$/,"",line);
-        gsub(/"name"\s*:\s*"|"/ ,"", line);
-        want = (line==pat) ? 1 : 0;
-        next
-      }
-      want==1 && /"browser_download_url"/ {
-        u=$0;
-        gsub(/^\s+|\s+$/,"",u);
-        gsub(/.*"browser_download_url"\s*:\s*"|".*/ ,"", u);
-        print u;
-        exit
-      }
-    ' "$JSON")
-    if [[ -n "$ASSET_URL" ]]; then break; fi
-  fi
+  while IFS= read -r url; do
+    [[ -z "$url" ]] && continue
+    if [[ "$url" == */"$candidate" ]]; then
+      ASSET_NAME="$candidate"
+      ASSET_URL="$url"
+      break
+    fi
+  done <<< "$DL_URLS"
+  [[ -n "$ASSET_URL" ]] && break
 done
 
 if [[ -z "$ASSET_URL" ]]; then

src/cli/completer.rs

@@ -5,9 +5,9 @@ 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;
+use std::{env, fs};
 
 const COYOTE_CLI_NAME: &str = "coyote";
 
@@ -134,6 +134,34 @@ pub(super) fn session_completer(current: &OsStr) -> Vec<CompletionCandidate> {
         .collect()
 }
 
+pub(super) fn mcp_server_completer(current: &OsStr) -> Vec<CompletionCandidate> {
+    let cur = current.to_string_lossy();
+    let content = match fs::read_to_string(paths::mcp_config_file()) {
+        Ok(c) => c,
+        Err(_) => return vec![],
+    };
+    let json: serde_json::Value = match serde_json::from_str(&content) {
+        Ok(v) => v,
+        Err(_) => return vec![],
+    };
+    let servers = match json.get("mcpServers").and_then(|v| v.as_object()) {
+        Some(s) => s,
+        None => return vec![],
+    };
+
+    servers
+        .iter()
+        .filter(|(_, v)| {
+            v.get("type")
+                .and_then(|t| t.as_str())
+                .map(|t| t == "http" || t == "sse")
+                .unwrap_or(false)
+        })
+        .filter(|(k, _)| k.starts_with(&*cur))
+        .map(|(k, _)| CompletionCandidate::new(k))
+        .collect()
+}
+
 pub(super) fn secrets_completer(current: &OsStr) -> Vec<CompletionCandidate> {
     let cur = current.to_string_lossy();
     match load_app_config_for_completion() {

src/cli/mod.rs

@@ -1,8 +1,8 @@
 mod completer;
 
 use crate::cli::completer::{
-    ShellCompletion, agent_completer, macro_completer, model_completer, rag_completer,
-    role_completer, secrets_completer, session_completer,
+    ShellCompletion, agent_completer, macro_completer, mcp_server_completer, model_completer,
+    rag_completer, role_completer, secrets_completer, session_completer,
 };
 use crate::config::{AssetCategory, InstallFilter, MemoryScope};
 use anyhow::{Context, Result};
@@ -171,6 +171,9 @@ pub struct Cli {
     /// Authenticate with an LLM provider using OAuth (e.g., --authenticate client_name)
     #[arg(long, exclusive = true, value_name = "CLIENT_NAME")]
     pub authenticate: Option<Option<String>>,
+    /// Authenticate with an OAuth-protected remote MCP server (e.g., --auth-mcp server_name)
+    #[arg(long, exclusive = true, value_name = "SERVER_NAME", add = ArgValueCompleter::new(mcp_server_completer))]
+    pub auth_mcp: Option<String>,
     /// Generate static shell completion scripts
     #[arg(long, value_name = "SHELL", value_enum)]
     pub completions: Option<ShellCompletion>,

src/client/message.rs

@@ -133,6 +133,13 @@ impl MessageContent {
         }
     }
 
+    pub fn as_text(&self) -> Option<&str> {
+        match self {
+            MessageContent::Text(text) => Some(text),
+            _ => None,
+        }
+    }
+
     pub fn merge_prompt(&mut self, replace_fn: impl Fn(&str) -> String) {
         match self {
             MessageContent::Text(text) => *text = replace_fn(text),

src/client/oauth.rs

@@ -53,6 +53,10 @@ pub trait OAuthProvider: Send + Sync {
     fn extra_request_headers(&self) -> Vec<(&str, &str)> {
         vec![]
     }
+
+    fn fixed_redirect_uri(&self) -> Option<String> {
+        None
+    }
 }
 
 #[derive(Debug, Clone, Serialize, Deserialize)]
@@ -72,14 +76,16 @@ pub async fn run_oauth_flow(provider: &dyn OAuthProvider, client_name: &str) ->
 
     let state = Uuid::new_v4().to_string();
 
-    let redirect_uri = if provider.uses_localhost_redirect() {
+    let (redirect_uri, use_callback_listener) = if let Some(fixed) = provider.fixed_redirect_uri() {
+        (fixed, true)
+    } else if provider.uses_localhost_redirect() {
         let listener = TcpListener::bind("127.0.0.1:0")?;
         let port = listener.local_addr()?.port();
         let uri = format!("http://127.0.0.1:{port}/callback");
         drop(listener);
-        uri
+        (uri, true)
     } else {
-        provider.redirect_uri().to_string()
+        (provider.redirect_uri().to_string(), false)
     };
 
     let encoded_scopes = urlencoding::encode(provider.scopes());
@@ -112,7 +118,7 @@ pub async fn run_oauth_flow(provider: &dyn OAuthProvider, client_name: &str) ->
 
     let _ = open::that(&authorize_url);
 
-    let (code, returned_state) = if provider.uses_localhost_redirect() {
+    let (code, returned_state) = if use_callback_listener {
         listen_for_oauth_callback(&redirect_uri)?
     } else {
         let input = Text::new("Paste the authorization code:").prompt()?;

src/config/mcp_factory.rs

@@ -1,4 +1,6 @@
-use crate::mcp::{ConnectedServer, JsonField, McpServer, McpTransportType, spawn_mcp_server};
+use crate::mcp::{
+    ConnectedServer, JsonField, McpServer, McpTransportType, oauth, spawn_mcp_server,
+};
 
 use anyhow::Result;
 use parking_lot::Mutex;
@@ -99,7 +101,12 @@ impl McpFactory {
             return Ok(existing);
         }
 
-        let handle = spawn_mcp_server(spec, log_path).await?;
+        let bearer_token = if spec.is_remote() {
+            oauth::load_valid_mcp_token(name)
+        } else {
+            None
+        };
+        let handle = spawn_mcp_server(spec, log_path, bearer_token).await?;
         self.insert_active(key, &handle);
         Ok(handle)
     }
@@ -125,6 +132,7 @@ mod tests {
             cwd: None,
             url: None,
             headers: None,
+            oauth_client_id: None,
         }
     }
 
@@ -141,6 +149,7 @@ mod tests {
             cwd: None,
             url: Some(url.to_string()),
             headers,
+            oauth_client_id: None,
         }
     }
 

src/config/memory.rs

@@ -118,6 +118,14 @@ pub struct MemoryFrontmatter {
     pub description: Option<String>,
     #[serde(default, rename = "type")]
     pub kind: Option<String>,
+    #[serde(default, skip_serializing_if = "Option::is_none")]
+    pub created: Option<String>,
+    #[serde(default, skip_serializing_if = "Option::is_none")]
+    pub updated: Option<String>,
+    #[serde(default, skip_serializing_if = "Option::is_none")]
+    pub superseded_by: Option<String>,
+    #[serde(default, skip_serializing_if = "Option::is_none")]
+    pub expires: Option<String>,
 }
 
 #[derive(Debug, Clone)]
@@ -545,6 +553,7 @@ mod tests {
                 name: "test".into(),
                 description: Some("a test".into()),
                 kind: Some("user".into()),
+                ..Default::default()
             },
             body: "Hello world\nmore text".into(),
         };

src/config/mod.rs

@@ -135,6 +135,7 @@ const RAGS_DIR_NAME: &str = "rags";
 const FUNCTIONS_DIR_NAME: &str = "functions";
 const FUNCTIONS_BIN_DIR_NAME: &str = "bin";
 const AGENTS_DIR_NAME: &str = "agents";
+const REPL_HISTORY_DIR_NAME: &str = "repl-history";
 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";

src/config/paths.rs

@@ -8,6 +8,8 @@ use super::{
     SKILLS_DIR_NAME, WORKSPACE_MEMORY_DIR_NAME,
 };
 use crate::client::ProviderModels;
+use crate::config::REPL_HISTORY_DIR_NAME;
+use crate::config::session::Session;
 use crate::utils::{get_env_name, list_file_names, normalize_env_name};
 
 use anyhow::{Context, Result, anyhow, bail};
@@ -320,6 +322,20 @@ pub fn workspace_memory_dir_for(workspace_root: &Path) -> PathBuf {
         .join(MEMORY_DIR_NAME)
 }
 
+pub fn repl_history_dir() -> PathBuf {
+    cache_path().join(REPL_HISTORY_DIR_NAME)
+}
+
+pub fn repl_history_file(session: &Option<Session>) -> PathBuf {
+    let history_key = if let Some(session) = &session {
+        format!("session_{}", session.name().replace('/', "_"))
+    } else {
+        "default".to_string()
+    };
+
+    repl_history_dir().join(history_key)
+}
+
 pub fn log_config() -> Result<(LevelFilter, Option<PathBuf>)> {
     let log_level = env::var(get_env_name("log_level"))
         .ok()

src/config/prompts.rs

@@ -18,10 +18,16 @@ pub(crate) const DEFAULT_MEMORY_INSTRUCTIONS: &str = indoc! {"
         - `memory__read(name)`: Read a specific drill file's full content.
         - `memory__write(name, content, scope)`: Create or replace a drill file (scope: 'global' | 'workspace').
           The MEMORY.md index is appended automatically; do not also update the index by hand.
+          Optional `superseded_by` / `expires` (YYYY-MM-DD) mark a memory as stale for later cleanup.
+        - `memory__rename(name, new_name, scope)`: Rename a drill file. Its index entry and every
+          [[wikilink]] to it are rewritten automatically.
+        - `memory__delete(name, scope)`: Delete a drill file and its index entry. Reports any
+          [[wikilinks]] left dangling in other files.
         - `memory__edit_index(scope, content)`: Replace the entire MEMORY.md at the given scope.
           Use this to add always-on facts, reorganize, prune stale entries, or fix descriptions.
         - `memory__list()`: See all known drill files and their metadata.
-        - `memory__lint()`: Health-check memory for orphans, broken links, oversized files.
+        - `memory__lint()`: Health-check memory for orphans, broken links, oversized files,
+          stale (superseded/expired) files, and index descriptions that drifted from the files.
 
     RULES:
         - Every interaction has two outputs: your answer AND any memory updates the conversation warrants.
@@ -29,7 +35,11 @@ pub(crate) const DEFAULT_MEMORY_INSTRUCTIONS: &str = indoc! {"
         - All MEMORY.md edits MUST go through `memory__edit_index`. NEVER use `fs_write`, `fs_patch`,
           or any other generic file tool on MEMORY.md — Coyote manages its location and a stray
           MEMORY.md outside the managed path is invisible to memory.
-        - All drill files MUST go through `memory__write`. The index updates itself.
+        - All drill files MUST go through `memory__write`. The index updates itself. Renames and
+          deletions MUST go through `memory__rename` / `memory__delete` so links stay intact.
+        - When a fact becomes outdated, update it in place, delete it, or mark the old file with
+          `superseded_by`/`expires` so `memory__lint` flags it later. Never leave contradictory
+          memories side by side.
         - Use [[wikilink]] notation in memory files to reference other memories by their `name:` slug.
         - NEVER write secrets, credentials, or API keys to memory — memory is plaintext on disk.
           Use coyote's Vault for secrets.

src/config/request_context.rs

@@ -709,6 +709,10 @@ impl RequestContext {
     }
 
     pub fn extract_role(&self, app: &AppConfig) -> Result<Role> {
+        self.extract_role_impl(app, true)
+    }
+
+    fn extract_role_impl(&self, app: &AppConfig, inject_memory: bool) -> Result<Role> {
         let mut role = if let Some(session) = self.session.as_ref() {
             session.to_role()
         } else if let Some(agent) = self.agent.as_ref() {
@@ -757,34 +761,36 @@ impl RequestContext {
             }
         }
 
-        let memory_config = self.memory_config();
-        if memory_config.enabled {
-            let store = MemoryStore {
-                global_dir: paths::global_memory_dir(),
-                workspace: memory_config.workspace,
-            };
-            let with_tools = app.function_calling_support;
-            let cap = if with_tools {
-                app.memory_cap_with_tools
-                    .unwrap_or(DEFAULT_MEMORY_CAP_WITH_TOOLS)
-            } else {
-                app.memory_cap_without_tools
-                    .unwrap_or(DEFAULT_MEMORY_CAP_WITHOUT_TOOLS)
-            };
-            match memory::build_memory_section(&store, with_tools, cap) {
-                Ok(Some(section)) => {
-                    let separator = if role.is_empty_prompt() { "" } else { "\n\n" };
-                    role.append_to_prompt(separator);
-                    role.append_to_prompt(&section);
-                    role.append_to_prompt("\n\n");
-                    role.append_to_prompt(if with_tools {
-                        prompts::DEFAULT_MEMORY_INSTRUCTIONS
-                    } else {
-                        prompts::DEFAULT_MEMORY_INSTRUCTIONS_READONLY
-                    });
+        if inject_memory {
+            let memory_config = self.memory_config();
+            if memory_config.enabled {
+                let store = MemoryStore {
+                    global_dir: paths::global_memory_dir(),
+                    workspace: memory_config.workspace,
+                };
+                let with_tools = app.function_calling_support;
+                let cap = if with_tools {
+                    app.memory_cap_with_tools
+                        .unwrap_or(DEFAULT_MEMORY_CAP_WITH_TOOLS)
+                } else {
+                    app.memory_cap_without_tools
+                        .unwrap_or(DEFAULT_MEMORY_CAP_WITHOUT_TOOLS)
+                };
+                match memory::build_memory_section(&store, with_tools, cap) {
+                    Ok(Some(section)) => {
+                        let separator = if role.is_empty_prompt() { "" } else { "\n\n" };
+                        role.append_to_prompt(separator);
+                        role.append_to_prompt(&section);
+                        role.append_to_prompt("\n\n");
+                        role.append_to_prompt(if with_tools {
+                            prompts::DEFAULT_MEMORY_INSTRUCTIONS
+                        } else {
+                            prompts::DEFAULT_MEMORY_INSTRUCTIONS_READONLY
+                        });
+                    }
+                    Ok(None) => {}
+                    Err(e) => warn!("memory injection failed: {}", e),
                 }
-                Ok(None) => {}
-                Err(e) => warn!("memory injection failed: {}", e),
             }
         }
 
@@ -1276,7 +1282,7 @@ impl RequestContext {
 
     pub fn generate_prompt_context(&self, app: &AppConfig) -> HashMap<&str, String> {
         let mut output = HashMap::new();
-        let role = self.extract_role(app).unwrap_or_else(|err| {
+        let role = self.extract_role_impl(app, false).unwrap_or_else(|err| {
             warn!("failed to compute effective role for prompt rendering: {err}");
             Role::default()
         });
@@ -2334,6 +2340,17 @@ impl RequestContext {
                 }
                 _ => vec![],
             };
+        } else if cmd == ".mcp" && args.first() == Some(&"auth") && args.len() == 2 {
+            if let Some(mcp_config) = &self.app.mcp_config {
+                values = super::map_completion_values(
+                    mcp_config
+                        .mcp_servers
+                        .iter()
+                        .filter(|(_, spec)| spec.is_remote())
+                        .map(|(name, _)| name.clone())
+                        .collect(),
+                );
+            }
         } else if (cmd == ".edit" && args.first() == Some(&"skill") && args.len() == 2)
             || (cmd == ".skill" && args.first() == Some(&"load") && args.len() == 2)
         {
@@ -3681,6 +3698,7 @@ mod tests {
                         cwd: None,
                         url: None,
                         headers: None,
+                        oauth_client_id: None,
                     },
                 );
             }

src/config/session.rs

@@ -163,6 +163,14 @@ impl Session {
         self.messages.is_empty() && self.compressed_messages.is_empty()
     }
 
+    pub fn messages(&self) -> &[Message] {
+        &self.messages
+    }
+
+    pub fn compressed_messages(&self) -> &[Message] {
+        &self.compressed_messages
+    }
+
     pub fn name(&self) -> &str {
         &self.name
     }

src/config/update.rs

@@ -68,6 +68,14 @@ fn normalize_version(requested: Option<String>) -> Option<String> {
     }
 }
 
+fn preferred_update_target() -> Option<&'static str> {
+    match (env::consts::OS, env::consts::ARCH) {
+        ("linux", "x86_64") => Some("x86_64-unknown-linux-musl"),
+        ("linux", "aarch64") => Some("aarch64-unknown-linux-musl"),
+        _ => None,
+    }
+}
+
 fn is_dir_writable(dir: &Path) -> bool {
     let probe = dir.join(format!(".coyote-update-write-test-{}", process::id()));
     match OpenOptions::new().write(true).create_new(true).open(&probe) {
@@ -147,6 +155,9 @@ pub fn run_self_update(requested: Option<String>, force: bool) -> Result<()> {
     if let Some(tag) = &target_tag {
         builder.target_version_tag(tag.as_str());
     }
+    if let Some(target) = preferred_update_target() {
+        builder.target(target);
+    }
     let status = builder
         .build()
         .context("Failed to configure the self-update")?

src/function/memory.rs

@@ -3,6 +3,7 @@ use std::path::{Path, PathBuf};
 use std::{env, fs};
 
 use anyhow::{Context, Result, anyhow, bail};
+use chrono::Local;
 use indexmap::IndexMap;
 use serde_json::{Value, json};
 
@@ -97,6 +98,32 @@ pub fn memory_function_declarations() -> Vec<FunctionDeclaration> {
                             ..Default::default()
                         },
                     ),
+                    (
+                        "superseded_by".to_string(),
+                        JsonSchema {
+                            type_value: Some("string".to_string()),
+                            description: Some(
+                                "Optional `name:` slug of the memory that replaces this one. \
+                                 `memory__lint` flags superseded files for cleanup. Omitting this \
+                                 on overwrite clears any previous value."
+                                    .into(),
+                            ),
+                            ..Default::default()
+                        },
+                    ),
+                    (
+                        "expires".to_string(),
+                        JsonSchema {
+                            type_value: Some("string".to_string()),
+                            description: Some(
+                                "Optional ISO date (YYYY-MM-DD) after which this memory is stale. \
+                                 `memory__lint` flags expired files. Omitting this on overwrite \
+                                 clears any previous value."
+                                    .into(),
+                            ),
+                            ..Default::default()
+                        },
+                    ),
                 ])),
                 required: Some(vec![
                     "name".to_string(),
@@ -164,6 +191,90 @@ pub fn memory_function_declarations() -> Vec<FunctionDeclaration> {
             },
             agent: false,
         },
+        FunctionDeclaration {
+            name: format!("{MEMORY_FUNCTION_PREFIX}rename"),
+            description:
+                "Rename a memory file. Its MEMORY.md index entry and every [[wikilink]] to it in \
+                 other memory files are rewritten automatically."
+                    .to_string(),
+            parameters: JsonSchema {
+                type_value: Some("object".to_string()),
+                properties: Some(IndexMap::from([
+                    (
+                        "name".to_string(),
+                        JsonSchema {
+                            type_value: Some("string".to_string()),
+                            description: Some("Current `name:` slug of the memory file".into()),
+                            ..Default::default()
+                        },
+                    ),
+                    (
+                        "new_name".to_string(),
+                        JsonSchema {
+                            type_value: Some("string".to_string()),
+                            description: Some(
+                                "New kebab-case slug for the file (no extension)".into(),
+                            ),
+                            ..Default::default()
+                        },
+                    ),
+                    (
+                        "scope".to_string(),
+                        JsonSchema {
+                            type_value: Some("string".to_string()),
+                            description: Some(
+                                "Scope of the file: 'global' (user-level) or 'workspace' (project-level)"
+                                    .into(),
+                            ),
+                            ..Default::default()
+                        },
+                    ),
+                ])),
+                required: Some(vec![
+                    "name".to_string(),
+                    "new_name".to_string(),
+                    "scope".to_string(),
+                ]),
+                ..Default::default()
+            },
+            agent: false,
+        },
+        FunctionDeclaration {
+            name: format!("{MEMORY_FUNCTION_PREFIX}delete"),
+            description:
+                "Delete a memory file and remove its MEMORY.md index entry. Reports any \
+                 [[wikilinks]] in other memory files left dangling by the deletion."
+                    .to_string(),
+            parameters: JsonSchema {
+                type_value: Some("object".to_string()),
+                properties: Some(IndexMap::from([
+                    (
+                        "name".to_string(),
+                        JsonSchema {
+                            type_value: Some("string".to_string()),
+                            description: Some(
+                                "The `name:` slug of the memory file to delete".into(),
+                            ),
+                            ..Default::default()
+                        },
+                    ),
+                    (
+                        "scope".to_string(),
+                        JsonSchema {
+                            type_value: Some("string".to_string()),
+                            description: Some(
+                                "Scope of the file: 'global' (user-level) or 'workspace' (project-level)"
+                                    .into(),
+                            ),
+                            ..Default::default()
+                        },
+                    ),
+                ])),
+                required: Some(vec!["name".to_string(), "scope".to_string()]),
+                ..Default::default()
+            },
+            agent: false,
+        },
     ]
 }
 
@@ -214,47 +325,13 @@ pub fn handle_memory_tool(ctx: &mut RequestContext, cmd_name: &str, args: &Value
                 "workspace": store.workspace.as_ref().map(workspace_label),
             }))
         }
-        "write" => {
-            let name = arg_str(args, "name")?;
-            let description = arg_str(args, "description")?;
-            let content = arg_str(args, "content")?;
-            let scope = arg_str(args, "scope")?;
-            let kind = args.get("type").and_then(Value::as_str).map(String::from);
-
-            let target_dir = match scope.as_str() {
-                "global" => paths::global_memory_dir(),
-                "workspace" => workspace_write_dir(&store, &cwd)?,
-                other => bail!("unknown scope '{}': use 'global' or 'workspace'", other),
-            };
-            let file = MemoryFile {
-                path: target_dir.join(format!("{name}.md")),
-                frontmatter: MemoryFrontmatter {
-                    name: name.clone(),
-                    description: Some(description.clone()),
-                    kind,
-                },
-                body: content,
-            };
-            file.save()?;
-
-            let index_path = target_dir.join("MEMORY.md");
-            let index_updated = ensure_index_entry(&index_path, &name, &description)?;
-
-            Ok(json!({
-                "status": "ok",
-                "path": file.path.display().to_string(),
-                "index_path": index_path.display().to_string(),
-                "index_updated": index_updated,
-            }))
-        }
+        "write" => write_memory(&store, &cwd, args),
+        "rename" => rename_memory(&store, &cwd, args),
+        "delete" => delete_memory(&store, &cwd, args),
         "edit_index" => {
             let scope = arg_str(args, "scope")?;
             let content = arg_str(args, "content")?;
-            let target_dir = match scope.as_str() {
-                "global" => paths::global_memory_dir(),
-                "workspace" => workspace_write_dir(&store, &cwd)?,
-                other => bail!("unknown scope '{}': use 'global' or 'workspace'", other),
-            };
+            let target_dir = scope_dir(&store, &cwd, &scope)?;
             let index_path = write_memory_index(&target_dir, &content)?;
 
             Ok(json!({
@@ -267,19 +344,229 @@ pub fn handle_memory_tool(ctx: &mut RequestContext, cmd_name: &str, args: &Value
     }
 }
 
+fn write_memory(store: &MemoryStore, cwd: &Path, args: &Value) -> Result<Value> {
+    let name = arg_str(args, "name")?;
+    let description = arg_str(args, "description")?;
+    let content = arg_str(args, "content")?;
+    let scope = arg_str(args, "scope")?;
+    let kind = args.get("type").and_then(Value::as_str).map(String::from);
+    let superseded_by = args
+        .get("superseded_by")
+        .and_then(Value::as_str)
+        .map(String::from);
+    let expires = args
+        .get("expires")
+        .and_then(Value::as_str)
+        .map(String::from);
+
+    let target_dir = scope_dir(store, cwd, &scope)?;
+    let path = target_dir.join(format!("{name}.md"));
+    let previous = if path.exists() {
+        MemoryFile::load(&path).ok()
+    } else {
+        None
+    };
+    let today = today_string();
+    let created = previous
+        .as_ref()
+        .and_then(|p| p.frontmatter.created.clone())
+        .unwrap_or_else(|| today.clone());
+
+    let file = MemoryFile {
+        path,
+        frontmatter: MemoryFrontmatter {
+            name: name.clone(),
+            description: Some(description.clone()),
+            kind,
+            created: Some(created),
+            updated: Some(today),
+            superseded_by,
+            expires,
+        },
+        body: content,
+    };
+    file.save()?;
+
+    let index_path = target_dir.join("MEMORY.md");
+    let index_updated = ensure_index_entry(&index_path, &name, &description)?;
+
+    Ok(json!({
+        "status": "ok",
+        "path": file.path.display().to_string(),
+        "index_path": index_path.display().to_string(),
+        "index_updated": index_updated,
+        "replaced": previous.is_some(),
+        "previous_description": previous.and_then(|p| p.frontmatter.description),
+    }))
+}
+
+fn rename_memory(store: &MemoryStore, cwd: &Path, args: &Value) -> Result<Value> {
+    let name = arg_str(args, "name")?;
+    let new_name = arg_str(args, "new_name")?;
+    let scope = arg_str(args, "scope")?;
+    if new_name.is_empty()
+        || !new_name
+            .chars()
+            .all(|c| c.is_alphanumeric() || c == '-' || c == '_')
+    {
+        bail!(
+            "invalid new_name '{}': use a kebab-case slug (alphanumeric, hyphens, underscores)",
+            new_name
+        );
+    }
+
+    if name == new_name {
+        bail!("new_name matches the current name");
+    }
+
+    let target_dir = scope_dir(store, cwd, &scope)?;
+    let files = store.list_files()?;
+    let file = files
+        .iter()
+        .find(|f| f.path.starts_with(&target_dir) && f.frontmatter.name == name)
+        .ok_or_else(|| anyhow!("memory file '{}' not found in scope '{}'", name, scope))?
+        .clone();
+
+    if target_dir.join(format!("{new_name}.md")).exists()
+        || files
+            .iter()
+            .any(|f| f.path.starts_with(&target_dir) && f.frontmatter.name == new_name)
+    {
+        bail!(
+            "memory file '{}' already exists in scope '{}'",
+            new_name,
+            scope
+        );
+    }
+
+    let needle = format!("[[{name}]]");
+    let replacement = format!("[[{new_name}]]");
+
+    let mut renamed = file.clone();
+    renamed.path = target_dir.join(format!("{new_name}.md"));
+    renamed.frontmatter.name = new_name.clone();
+    renamed.frontmatter.updated = Some(today_string());
+    renamed.body = renamed.body.replace(&needle, &replacement);
+    renamed.save()?;
+    fs::remove_file(&file.path).with_context(|| format!("remove {}", file.path.display()))?;
+
+    let mut rewritten = Vec::new();
+    for f in &files {
+        if f.path == file.path || !f.body.contains(&needle) {
+            continue;
+        }
+        let mut updated = f.clone();
+        updated.body = updated.body.replace(&needle, &replacement);
+        updated.save()?;
+        rewritten.push(f.frontmatter.name.clone());
+    }
+
+    // Own-scope index: rewrite the wikilink, drop any leftover references to the
+    // old name, and guarantee the new name is present.
+    let index_path = target_dir.join("MEMORY.md");
+    if let Ok(existing) = fs::read_to_string(&index_path)
+        && existing.contains(&needle)
+    {
+        fs::write(&index_path, existing.replace(&needle, &replacement))?;
+    }
+
+    remove_index_entry(&index_path, &name)?;
+    let description = renamed.frontmatter.description.clone().unwrap_or_default();
+    ensure_index_entry(&index_path, &new_name, &description)?;
+
+    // Other indexes (other scope's MEMORY.md, lite COYOTE.md): rewrite wikilinks only.
+    for other_index in other_index_paths(store, &target_dir) {
+        if let Ok(existing) = fs::read_to_string(&other_index)
+            && existing.contains(&needle)
+        {
+            fs::write(&other_index, existing.replace(&needle, &replacement))?;
+        }
+    }
+
+    Ok(json!({
+        "status": "ok",
+        "old_path": file.path.display().to_string(),
+        "new_path": renamed.path.display().to_string(),
+        "rewritten_references": rewritten,
+    }))
+}
+
+fn delete_memory(store: &MemoryStore, cwd: &Path, args: &Value) -> Result<Value> {
+    let name = arg_str(args, "name")?;
+    let scope = arg_str(args, "scope")?;
+    let target_dir = scope_dir(store, cwd, &scope)?;
+    let files = store.list_files()?;
+    let file = files
+        .iter()
+        .find(|f| f.path.starts_with(&target_dir) && f.frontmatter.name == name)
+        .ok_or_else(|| anyhow!("memory file '{}' not found in scope '{}'", name, scope))?;
+    let deleted_path = file.path.clone();
+    fs::remove_file(&deleted_path).with_context(|| format!("delete {}", deleted_path.display()))?;
+
+    let index_path = target_dir.join("MEMORY.md");
+    let index_updated = remove_index_entry(&index_path, &name)?;
+
+    let dangling: Vec<String> = files
+        .iter()
+        .filter(|f| f.path != deleted_path && extract_wikilinks(&f.body).iter().any(|l| l == &name))
+        .map(|f| f.frontmatter.name.clone())
+        .collect();
+
+    Ok(json!({
+        "status": "ok",
+        "deleted_path": deleted_path.display().to_string(),
+        "index_updated": index_updated,
+        "dangling_references": dangling,
+    }))
+}
+
+fn scope_dir(store: &MemoryStore, cwd: &Path, scope: &str) -> Result<PathBuf> {
+    match scope {
+        "global" => Ok(paths::global_memory_dir()),
+        "workspace" => workspace_write_dir(store, cwd),
+        other => bail!("unknown scope '{}': use 'global' or 'workspace'", other),
+    }
+}
+
+fn today_string() -> String {
+    Local::now().format("%Y-%m-%d").to_string()
+}
+
+fn other_index_paths(store: &MemoryStore, own_dir: &Path) -> Vec<PathBuf> {
+    let mut out = Vec::new();
+    let global_index = store.global_dir.join("MEMORY.md");
+    if store.global_dir.as_path() != own_dir && global_index.exists() {
+        out.push(global_index);
+    }
+
+    match &store.workspace {
+        Some(WorkspaceMemory::Structured { dir, .. }) => {
+            let index = dir.join("MEMORY.md");
+            if dir.as_path() != own_dir && index.exists() {
+                out.push(index);
+            }
+        }
+        Some(WorkspaceMemory::Lite { file, .. }) if file.exists() => {
+            out.push(file.clone());
+        }
+        _ => {}
+    }
+
+    out
+}
+
 fn write_memory_index(target_dir: &Path, content: &str) -> Result<PathBuf> {
     fs::create_dir_all(target_dir)?;
     let index_path = target_dir.join("MEMORY.md");
+
     fs::write(&index_path, content)?;
+
     Ok(index_path)
 }
 
 fn ensure_index_entry(index_path: &Path, name: &str, description: &str) -> Result<bool> {
     let existing = fs::read_to_string(index_path).unwrap_or_default();
-    let already_referenced =
-        existing.contains(&format!("[[{name}]]")) || existing.contains(&format!("{name}.md"));
-
-    if already_referenced {
+    if index_references(&existing, name) {
         return Ok(false);
     }
 
@@ -297,6 +584,40 @@ fn ensure_index_entry(index_path: &Path, name: &str, description: &str) -> Resul
     }
 
     fs::write(index_path, new_content)?;
+
+    Ok(true)
+}
+
+fn line_references(line: &str, name: &str) -> bool {
+    let file_name = format!("{name}.md");
+    line.split(|c: char| !(c.is_alphanumeric() || c == '-' || c == '_' || c == '.'))
+        .any(|token| token == file_name || token.trim_matches('.') == name)
+}
+
+fn index_references(index: &str, name: &str) -> bool {
+    index.lines().any(|line| line_references(line, name))
+}
+
+fn remove_index_entry(index_path: &Path, name: &str) -> Result<bool> {
+    let Ok(existing) = fs::read_to_string(index_path) else {
+        return Ok(false);
+    };
+    let kept: Vec<&str> = existing
+        .lines()
+        .filter(|line| !line_references(line, name))
+        .collect();
+    let mut new_content = kept.join("\n");
+
+    if existing.ends_with('\n') && !new_content.is_empty() {
+        new_content.push('\n');
+    }
+
+    if new_content == existing {
+        return Ok(false);
+    }
+
+    fs::write(index_path, new_content)?;
+
     Ok(true)
 }
 
@@ -350,9 +671,11 @@ fn workspace_label(w: &WorkspaceMemory) -> Value {
 fn lint_memory(store: &MemoryStore) -> Result<Value> {
     let files = store.list_files()?;
     let names: HashSet<&str> = files.iter().map(|f| f.frontmatter.name.as_str()).collect();
+    let today = today_string();
 
     let mut oversized = Vec::new();
     let mut broken_links = Vec::new();
+    let mut stale = Vec::new();
     for f in &files {
         if f.char_len() > PER_FILE_SOFT_CAP {
             oversized.push(json!({"name": &f.frontmatter.name, "chars": f.char_len()}));
@@ -362,16 +685,54 @@ fn lint_memory(store: &MemoryStore) -> Result<Value> {
                 broken_links.push(json!({"from": &f.frontmatter.name, "to": link}));
             }
         }
+        if let Some(target) = &f.frontmatter.superseded_by {
+            stale.push(json!({
+                "name": &f.frontmatter.name,
+                "reason": "superseded",
+                "superseded_by": target,
+                "target_exists": names.contains(target.as_str()),
+            }));
+        }
+
+        if let Some(expires) = &f.frontmatter.expires
+            && expires.as_str() < today.as_str()
+        {
+            stale.push(json!({
+                "name": &f.frontmatter.name,
+                "reason": "expired",
+                "expires": expires,
+            }));
+        }
     }
 
-    let index_content = store
-        .load_global_index()?
-        .or_else(|| store.load_workspace_index().ok().flatten())
+    let global_index = store.load_global_index()?.unwrap_or_default();
+    let workspace_index = store
+        .load_workspace_index()
+        .ok()
+        .flatten()
         .unwrap_or_default();
     let mut orphans = Vec::new();
+    let mut description_drift = Vec::new();
+
     for f in &files {
-        if !index_content.contains(&f.frontmatter.name) {
+        let index = if f.path.starts_with(&store.global_dir) {
+            &global_index
+        } else {
+            &workspace_index
+        };
+
+        if !index_references(index, &f.frontmatter.name) {
             orphans.push(f.frontmatter.name.clone());
+        } else if let (Some(index_desc), Some(file_desc)) = (
+            index_description(index, &f.frontmatter.name),
+            f.frontmatter.description.as_deref(),
+        ) && index_desc != file_desc
+        {
+            description_drift.push(json!({
+                "name": &f.frontmatter.name,
+                "index_description": index_desc,
+                "file_description": file_desc,
+            }));
         }
     }
 
@@ -380,13 +741,26 @@ fn lint_memory(store: &MemoryStore) -> Result<Value> {
         "oversized": oversized,
         "broken_wikilinks": broken_links,
         "orphans": orphans,
+        "stale": stale,
+        "description_drift": description_drift,
     }))
 }
 
+fn index_description(index: &str, name: &str) -> Option<String> {
+    let marker = format!("[[{name}]]");
+    index.lines().find_map(|line| {
+        let pos = line.find(&marker)?;
+        let rest = line[pos + marker.len()..].trim_start();
+        let desc = rest.strip_prefix(':')?.trim();
+        (!desc.is_empty()).then(|| desc.to_string())
+    })
+}
+
 fn extract_wikilinks(body: &str) -> Vec<String> {
     let mut out = Vec::new();
     let bytes = body.as_bytes();
     let mut i = 0;
+
     while i + 1 < bytes.len() {
         if bytes[i] == b'['
             && bytes[i + 1] == b'['
@@ -676,4 +1050,305 @@ mod tests {
 
         let _ = fs::remove_dir_all(&root);
     }
+
+    #[test]
+    fn line_references_requires_exact_token_match() {
+        assert!(line_references("- [[auth]]: description", "auth"));
+        assert!(line_references("- auth.md is here", "auth"));
+        assert!(line_references("- referenced", "referenced"));
+        assert!(line_references("see auth.", "auth"));
+        assert!(!line_references("- [[auth-flow]]: description", "auth"));
+        assert!(!line_references("- oauth.md legacy", "auth"));
+        assert!(!line_references("- preauth notes", "auth"));
+    }
+
+    #[test]
+    fn remove_index_entry_drops_only_matching_lines() {
+        let root = temp_root("index_remove");
+        let index = root.join("MEMORY.md");
+        fs::write(
+            &index,
+            "# Memory Index\n\n- [[keep]]: stays\n- [[gone]]: removed\n",
+        )
+        .unwrap();
+
+        assert!(remove_index_entry(&index, "gone").unwrap());
+        let content = fs::read_to_string(&index).unwrap();
+        assert!(content.contains("[[keep]]"));
+        assert!(!content.contains("[[gone]]"));
+
+        assert!(!remove_index_entry(&index, "gone").unwrap());
+
+        let _ = fs::remove_dir_all(&root);
+    }
+
+    #[test]
+    fn lint_checks_orphans_against_own_scope_index() {
+        let root = temp_root("lint_scopes");
+        let global = root.join("global");
+        fs::create_dir_all(&global).unwrap();
+        fs::write(global.join("MEMORY.md"), "- [[global-note]]: g\n").unwrap();
+        fs::write(
+            global.join("global-note.md"),
+            "---\nname: global-note\n---\ng\n",
+        )
+        .unwrap();
+
+        let workspace = root.join("ws");
+        let structured = workspace.join(".coyote").join("memory");
+        fs::create_dir_all(&structured).unwrap();
+        fs::write(structured.join("MEMORY.md"), "- [[ws-note]]: w\n").unwrap();
+        fs::write(
+            structured.join("ws-note.md"),
+            "---\nname: ws-note\n---\nw\n",
+        )
+        .unwrap();
+
+        let store = MemoryStore {
+            global_dir: global,
+            workspace: discover_workspace_memory(&workspace),
+        };
+
+        let report = lint_memory(&store).unwrap();
+        assert!(
+            report["orphans"].as_array().unwrap().is_empty(),
+            "expected no orphans, got: {report}"
+        );
+
+        let _ = fs::remove_dir_all(&root);
+    }
+
+    #[test]
+    fn lint_flags_stale_and_description_drift() {
+        let root = temp_root("lint_stale");
+        let workspace = root.join("ws");
+        let structured = workspace.join(".coyote").join("memory");
+        fs::create_dir_all(&structured).unwrap();
+        fs::write(
+            structured.join("MEMORY.md"),
+            "- [[old-plan]]: old\n- [[bygone]]: e\n- [[drifted]]: index says this\n",
+        )
+        .unwrap();
+        fs::write(
+            structured.join("old-plan.md"),
+            "---\nname: old-plan\nsuperseded_by: new-plan\n---\nx\n",
+        )
+        .unwrap();
+        fs::write(
+            structured.join("bygone.md"),
+            "---\nname: bygone\nexpires: 2000-01-01\n---\nx\n",
+        )
+        .unwrap();
+        fs::write(
+            structured.join("drifted.md"),
+            "---\nname: drifted\ndescription: file says that\n---\nx\n",
+        )
+        .unwrap();
+
+        let store = MemoryStore {
+            global_dir: root.join("nonexistent_global"),
+            workspace: discover_workspace_memory(&workspace),
+        };
+
+        let report = lint_memory(&store).unwrap();
+        let stale = report["stale"].as_array().unwrap();
+        let reasons: Vec<(&str, &str)> = stale
+            .iter()
+            .map(|v| (v["name"].as_str().unwrap(), v["reason"].as_str().unwrap()))
+            .collect();
+        assert!(reasons.contains(&("old-plan", "superseded")));
+        assert!(reasons.contains(&("bygone", "expired")));
+        let superseded = stale.iter().find(|v| v["name"] == "old-plan").unwrap();
+        assert_eq!(superseded["target_exists"], false);
+
+        let drift = report["description_drift"].as_array().unwrap();
+        assert_eq!(drift.len(), 1);
+        assert_eq!(drift[0]["name"], "drifted");
+
+        let _ = fs::remove_dir_all(&root);
+    }
+
+    #[test]
+    fn delete_memory_removes_file_index_entry_and_reports_dangling() {
+        let root = temp_root("delete");
+        let workspace = root.join("ws");
+        let structured = workspace.join(".coyote").join("memory");
+        fs::create_dir_all(&structured).unwrap();
+        fs::write(
+            structured.join("MEMORY.md"),
+            "# Memory Index\n\n- [[doomed]]: bye\n- [[linker]]: links\n",
+        )
+        .unwrap();
+        fs::write(
+            structured.join("doomed.md"),
+            "---\nname: doomed\n---\nbye\n",
+        )
+        .unwrap();
+        fs::write(
+            structured.join("linker.md"),
+            "---\nname: linker\n---\nsee [[doomed]]\n",
+        )
+        .unwrap();
+
+        let store = MemoryStore {
+            global_dir: root.join("g"),
+            workspace: discover_workspace_memory(&workspace),
+        };
+
+        let args = json!({"name": "doomed", "scope": "workspace"});
+        let result = delete_memory(&store, &workspace, &args).unwrap();
+
+        assert_eq!(result["status"], "ok");
+        assert_eq!(result["index_updated"], true);
+        assert!(!structured.join("doomed.md").exists());
+        let index = fs::read_to_string(structured.join("MEMORY.md")).unwrap();
+        assert!(!index.contains("doomed"));
+        assert!(index.contains("[[linker]]"));
+        assert_eq!(
+            result["dangling_references"].as_array().unwrap(),
+            &vec![json!("linker")]
+        );
+
+        let _ = fs::remove_dir_all(&root);
+    }
+
+    #[test]
+    fn rename_memory_moves_file_and_rewrites_references() {
+        let root = temp_root("rename");
+        let workspace = root.join("ws");
+        let structured = workspace.join(".coyote").join("memory");
+        fs::create_dir_all(&structured).unwrap();
+        fs::write(
+            structured.join("MEMORY.md"),
+            "# Memory Index\n\n- [[old-name]]: the plan\n- [[linker]]: links\n",
+        )
+        .unwrap();
+        fs::write(
+            structured.join("old-name.md"),
+            "---\nname: old-name\ndescription: the plan\n---\nself link [[old-name]]\n",
+        )
+        .unwrap();
+        fs::write(
+            structured.join("linker.md"),
+            "---\nname: linker\n---\nsee [[old-name]] and [[old-name-extended]]\n",
+        )
+        .unwrap();
+
+        let store = MemoryStore {
+            global_dir: root.join("g"),
+            workspace: discover_workspace_memory(&workspace),
+        };
+
+        let args = json!({"name": "old-name", "new_name": "new-name", "scope": "workspace"});
+        let result = rename_memory(&store, &workspace, &args).unwrap();
+
+        assert_eq!(result["status"], "ok");
+        assert!(!structured.join("old-name.md").exists());
+        let renamed = MemoryFile::load(&structured.join("new-name.md")).unwrap();
+        assert_eq!(renamed.frontmatter.name, "new-name");
+        assert!(renamed.body.contains("[[new-name]]"));
+
+        let linker = fs::read_to_string(structured.join("linker.md")).unwrap();
+        assert!(linker.contains("[[new-name]]"));
+        assert!(
+            linker.contains("[[old-name-extended]]"),
+            "unrelated links must be untouched: {linker}"
+        );
+
+        let index = fs::read_to_string(structured.join("MEMORY.md")).unwrap();
+        assert!(index.contains("- [[new-name]]: the plan"));
+        assert!(!index.contains("[[old-name]]"));
+        assert!(index.contains("[[linker]]"));
+
+        assert_eq!(
+            result["rewritten_references"].as_array().unwrap(),
+            &vec![json!("linker")]
+        );
+
+        let _ = fs::remove_dir_all(&root);
+    }
+
+    #[test]
+    fn rename_memory_rejects_collisions_and_bad_slugs() {
+        let root = temp_root("rename_guard");
+        let workspace = root.join("ws");
+        let structured = workspace.join(".coyote").join("memory");
+        fs::create_dir_all(&structured).unwrap();
+        fs::write(structured.join("MEMORY.md"), "- [[a]]: a\n- [[b]]: b\n").unwrap();
+        fs::write(structured.join("a.md"), "---\nname: a\n---\nx\n").unwrap();
+        fs::write(structured.join("b.md"), "---\nname: b\n---\nx\n").unwrap();
+
+        let store = MemoryStore {
+            global_dir: root.join("g"),
+            workspace: discover_workspace_memory(&workspace),
+        };
+
+        let collision = json!({"name": "a", "new_name": "b", "scope": "workspace"});
+        let err = rename_memory(&store, &workspace, &collision).unwrap_err();
+        assert!(err.to_string().contains("already exists"));
+
+        let bad_slug = json!({"name": "a", "new_name": "bad name!", "scope": "workspace"});
+        let err = rename_memory(&store, &workspace, &bad_slug).unwrap_err();
+        assert!(err.to_string().contains("invalid new_name"));
+
+        let _ = fs::remove_dir_all(&root);
+    }
+
+    #[test]
+    fn write_memory_stamps_timestamps_and_reports_replacement() {
+        let root = temp_root("write_stamps");
+        let workspace = root.join("ws");
+        let structured = workspace.join(".coyote").join("memory");
+        fs::create_dir_all(&structured).unwrap();
+        fs::write(structured.join("MEMORY.md"), "# Memory Index\n").unwrap();
+
+        let store = MemoryStore {
+            global_dir: root.join("g"),
+            workspace: discover_workspace_memory(&workspace),
+        };
+
+        let first = json!({
+            "name": "fact",
+            "description": "first version",
+            "content": "body v1",
+            "scope": "workspace",
+            "expires": "2099-01-01",
+        });
+        let before = today_string();
+        let result = write_memory(&store, &workspace, &first).unwrap();
+        let after = today_string();
+        assert_eq!(result["replaced"], false);
+        assert_eq!(result["previous_description"], Value::Null);
+
+        let saved = MemoryFile::load(&structured.join("fact.md")).unwrap();
+        let created = saved.frontmatter.created.clone().expect("created stamped");
+        assert!(
+            created == before || created == after,
+            "created '{created}' should be stamped with today's date"
+        );
+        assert_eq!(saved.frontmatter.updated, Some(created.clone()));
+        assert_eq!(saved.frontmatter.expires.as_deref(), Some("2099-01-01"));
+        assert_eq!(saved.frontmatter.superseded_by, None);
+
+        let second = json!({
+            "name": "fact",
+            "description": "second version",
+            "content": "body v2",
+            "scope": "workspace",
+        });
+        let result = write_memory(&store, &workspace, &second).unwrap();
+        assert_eq!(result["replaced"], true);
+        assert_eq!(result["previous_description"], "first version");
+
+        let saved = MemoryFile::load(&structured.join("fact.md")).unwrap();
+        assert_eq!(
+            saved.frontmatter.created,
+            Some(created),
+            "creation date must be preserved across overwrites"
+        );
+        assert!(saved.frontmatter.updated.is_some());
+        assert_eq!(saved.frontmatter.expires, None);
+
+        let _ = fs::remove_dir_all(&root);
+    }
 }

src/main.rs

@@ -28,18 +28,22 @@ use crate::config::{
     install_builtins, list_agents, load_env_file, macro_execute, sync_models,
 };
 use crate::function::supervisor::{GuardrailAction, check_pending_agents_guardrail};
+use crate::mcp::McpServersConfig;
 use crate::render::{prompt_theme, render_error};
 use crate::repl::Repl;
 use crate::utils::*;
-use crate::vault::Vault;
-use anyhow::{Result, anyhow, bail};
+use crate::vault::{Vault, interpolate_secrets};
+use anyhow::{Context, Result, anyhow, bail};
 use clap::{CommandFactory, Parser};
 use clap_complete::CompleteEnv;
 use client::ClientConfig;
 use inquire::{Select, Text, set_global_render_config};
 use log::{LevelFilter, warn};
 use log4rs::append::console::ConsoleAppender;
-use log4rs::append::file::FileAppender;
+use log4rs::append::rolling_file::RollingFileAppender;
+use log4rs::append::rolling_file::policy::compound::CompoundPolicy;
+use log4rs::append::rolling_file::policy::compound::roll::fixed_window::FixedWindowRoller;
+use log4rs::append::rolling_file::policy::compound::trigger::size::SizeTrigger;
 use log4rs::config::{Appender, Logger, Root};
 use log4rs::encode::pattern::PatternEncoder;
 use oauth::OAuthProvider;
@@ -117,6 +121,49 @@ async fn main() -> Result<()> {
         return Ok(());
     }
 
+    if let Some(server_name) = &cli.auth_mcp {
+        let cfg = Config::load_with_interpolation(true).await?;
+        let app_config = AppConfig::from_config(cfg)?;
+        let vault = Vault::init(&app_config)?;
+        let mcp_path = paths::mcp_config_file();
+        if !mcp_path.exists() {
+            bail!(
+                "No MCP configuration file found at '{}'",
+                mcp_path.display()
+            );
+        }
+
+        let raw = tokio::fs::read_to_string(&mcp_path)
+            .await
+            .with_context(|| format!("Failed to read MCP config at '{}'", mcp_path.display()))?;
+
+        let (content, missing) = interpolate_secrets(&raw, &vault)?;
+        if !missing.is_empty() {
+            bail!(
+                "MCP config references vault secrets that are missing: {:?}",
+                missing
+            );
+        }
+
+        let mcp_config: McpServersConfig =
+            serde_json::from_str(&content).context("Failed to parse MCP config file")?;
+        let spec = mcp_config
+            .mcp_servers
+            .get(server_name.as_str())
+            .ok_or_else(|| anyhow!("MCP server '{server_name}' not found in mcp.json"))?;
+        if !spec.is_remote() {
+            bail!(
+                "MCP server '{server_name}' is a stdio server; OAuth is only supported for http/sse servers"
+            );
+        }
+
+        let url = spec.url.as_deref().expect("validated: remote spec has url");
+        mcp::oauth::run_mcp_oauth_flow(server_name, url, spec.oauth_client_id.as_deref()).await?;
+        println!("Authentication saved. '{server_name}' is now available for use.");
+
+        return Ok(());
+    }
+
     if vault_flags {
         let cfg = Config::load_with_interpolation(true).await?;
         let app_config = AppConfig::from_config(cfg)?;
@@ -137,7 +184,10 @@ async fn main() -> Result<()> {
         )
         .await?,
     );
-    let ctx = RequestContext::bootstrap(app_state, working_mode, info_flag)?;
+    let mut ctx = RequestContext::bootstrap(app_state, working_mode, info_flag)?;
+    let app_config = Arc::clone(&ctx.app.config);
+    ctx.bootstrap_tools(&app_config, start_mcp_servers, abort_signal.clone())
+        .await?;
 
     {
         let app = &*ctx.app.config;
@@ -582,7 +632,20 @@ fn setup_logger() -> Result<Option<PathBuf>> {
         }
         Some(path) => {
             ensure_parent_exists(&path)?;
-            let file_appender = FileAppender::builder().encoder(encoder.clone()).build(path);
+
+            let archive_pattern = path
+                .with_extension("archived.{}.log")
+                .to_string_lossy()
+                .into_owned();
+            let trigger = SizeTrigger::new(10 * 1024 * 1024);
+            let roller = FixedWindowRoller::builder()
+                .build(&archive_pattern, 5)
+                .unwrap();
+            let policy = CompoundPolicy::new(Box::new(trigger), Box::new(roller));
+
+            let file_appender = RollingFileAppender::builder()
+                .encoder(encoder.clone())
+                .build(path, Box::new(policy));
 
             match file_appender {
                 Ok(appender) => {
@@ -605,7 +668,7 @@ fn setup_logger() -> Result<Option<PathBuf>> {
 fn init_file_logger(
     log_level: LevelFilter,
     log_filter: Option<String>,
-    file_appender: FileAppender,
+    file_appender: RollingFileAppender,
 ) -> log4rs::Config {
     let root_log_level = if log_filter.is_some() {
         LevelFilter::Off

src/mcp/mod.rs

@@ -1,3 +1,4 @@
+pub(crate) mod oauth;
 mod sse_transport;
 
 use crate::config::AppConfig;
@@ -73,6 +74,8 @@ pub(crate) struct McpServer {
     pub url: Option<String>,
     #[serde(skip_serializing_if = "Option::is_none")]
     pub headers: Option<IndexMap<String, String>>,
+    #[serde(skip_serializing_if = "Option::is_none")]
+    pub oauth_client_id: Option<String>,
 }
 
 impl McpServer {
@@ -107,10 +110,10 @@ impl McpServer {
                     "MCP server '{name}' is missing a \"command\" field (required for stdio transport)"
                 ));
             }
-            if self.url.is_some() || self.headers.is_some() {
+            if self.url.is_some() || self.headers.is_some() || self.oauth_client_id.is_some() {
                 return Err(anyhow!(
                     "MCP server '{name}' has type \"stdio\" but also specifies remote fields \
-                     (url/headers). Remove the remote fields or change the type to \"http\" or \"sse\"."
+                     (url/headers/oauth_client_id). Remove the remote fields or change the type to \"http\" or \"sse\"."
                 ));
             }
         }
@@ -237,7 +240,7 @@ impl McpRegistry {
 
         debug!("Starting selected MCP servers: {:?}", ids_to_start);
 
-        let results: Vec<(String, Arc<_>, ServerCatalog)> = stream::iter(
+        let results: Vec<Option<(String, Arc<ConnectedServer>, ServerCatalog)>> = stream::iter(
             ids_to_start
                 .into_iter()
                 .map(|id| async { self.start_server(id).await }),
@@ -246,7 +249,7 @@ impl McpRegistry {
         .try_collect()
         .await?;
 
-        for (id, server, catalog) in results {
+        for (id, server, catalog) in results.into_iter().flatten() {
             self.servers.insert(id.clone(), server);
             self.catalogs.insert(id, catalog);
         }
@@ -257,14 +260,30 @@ impl McpRegistry {
     async fn start_server(
         &self,
         id: String,
-    ) -> Result<(String, Arc<ConnectedServer>, ServerCatalog)> {
+    ) -> Result<Option<(String, Arc<ConnectedServer>, ServerCatalog)>> {
         let spec = self
             .config
             .as_ref()
             .and_then(|c| c.mcp_servers.get(&id))
             .with_context(|| format!("MCP server not found in config: {id}"))?;
 
-        let service = spawn_mcp_server(spec, self.log_path.as_deref()).await?;
+        let bearer_token = if spec.is_remote() {
+            oauth::load_valid_mcp_token(&id)
+        } else {
+            None
+        };
+
+        let service = match spawn_mcp_server(spec, self.log_path.as_deref(), bearer_token).await {
+            Ok(s) => s,
+            Err(e) if is_auth_required_error(&e) => {
+                warn!(
+                    "MCP server '{id}' requires OAuth authentication. \
+                     Run `.mcp auth {id}` in the REPL to authenticate, then restart Coyote."
+                );
+                return Ok(None);
+            }
+            Err(e) => return Err(e),
+        };
 
         let tools = service.list_tools(None).await?;
         debug!("Available tools for MCP server {id}: {tools:?}");
@@ -289,7 +308,7 @@ impl McpRegistry {
 
         info!("Started MCP server: {id}");
 
-        Ok((id.to_string(), service, catalog))
+        Ok(Some((id.to_string(), service, catalog)))
     }
 
     fn resolve_server_ids(&self, enabled_mcp_servers: Option<Vec<String>>) -> Vec<String> {
@@ -337,15 +356,18 @@ impl McpRegistry {
 pub(crate) async fn spawn_mcp_server(
     spec: &McpServer,
     log_path: Option<&Path>,
+    bearer_token: Option<String>,
 ) -> Result<Arc<ConnectedServer>> {
     match spec.transport_type {
         McpTransportType::Http => {
             let url = spec.url.as_deref().expect("validated: http spec has url");
-            spawn_http_mcp_server(url, spec.headers.as_ref()).await
+            let headers = merge_bearer_token(spec.headers.as_ref(), bearer_token);
+            spawn_http_mcp_server(url, headers.as_ref()).await
         }
         McpTransportType::Sse => {
             let url = spec.url.as_deref().expect("validated: sse spec has url");
-            spawn_sse_mcp_server(url, spec.headers.as_ref()).await
+            let headers = merge_bearer_token(spec.headers.as_ref(), bearer_token);
+            spawn_sse_mcp_server(url, headers.as_ref()).await
         }
         McpTransportType::Stdio => {
             let command = spec
@@ -357,6 +379,30 @@ pub(crate) async fn spawn_mcp_server(
     }
 }
 
+fn merge_bearer_token(
+    headers: Option<&IndexMap<String, String>>,
+    bearer_token: Option<String>,
+) -> Option<IndexMap<String, String>> {
+    match (headers, bearer_token) {
+        (None, None) => None,
+        (Some(h), None) => Some(h.clone()),
+        (None, Some(token)) => {
+            let mut m = IndexMap::new();
+            m.insert("Authorization".to_string(), format!("Bearer {token}"));
+            Some(m)
+        }
+        (Some(h), Some(token)) => {
+            let mut m = h.clone();
+            m.insert("Authorization".to_string(), format!("Bearer {token}"));
+            Some(m)
+        }
+    }
+}
+
+fn is_auth_required_error(e: &anyhow::Error) -> bool {
+    e.to_string().contains("Auth required")
+}
+
 async fn spawn_http_mcp_server(
     url: &str,
     headers: Option<&IndexMap<String, String>>,
@@ -433,8 +479,12 @@ async fn spawn_stdio_mcp_server(
         let log_file = OpenOptions::new()
             .create(true)
             .append(true)
-            .open(log_path)?;
-        let (transport, _) = TokioChildProcess::builder(cmd).stderr(log_file).spawn()?;
+            .open(log_path)
+            .with_context(|| format!("Failed to open MCP log file at '{}'", log_path.display()))?;
+        let (transport, _) = TokioChildProcess::builder(cmd)
+            .stderr(log_file)
+            .spawn()
+            .with_context(|| format!("Failed to spawn MCP server: {command}"))?;
         transport
     } else {
         TokioChildProcess::new(cmd)?
@@ -461,6 +511,7 @@ mod tests {
             cwd: None,
             url: None,
             headers: None,
+            oauth_client_id: None,
         }
     }
 
@@ -473,6 +524,7 @@ mod tests {
             cwd: None,
             url: Some(url.to_string()),
             headers: None,
+            oauth_client_id: None,
         }
     }
 
@@ -485,6 +537,7 @@ mod tests {
             cwd: None,
             url: Some(url.to_string()),
             headers: None,
+            oauth_client_id: None,
         }
     }
 
@@ -502,6 +555,7 @@ mod tests {
     #[test]
     fn validate_stdio_with_command_succeeds() {
         let spec = stdio_server("npx");
+
         assert!(spec.validate("test").is_ok());
     }
 
@@ -515,8 +569,11 @@ mod tests {
             cwd: None,
             url: None,
             headers: None,
+            oauth_client_id: None,
         };
+
         let err = spec.validate("test").unwrap_err();
+
         assert!(err.to_string().contains("missing a \"command\" field"));
     }
 
@@ -530,8 +587,11 @@ mod tests {
             cwd: None,
             url: Some("http://localhost".into()),
             headers: None,
+            oauth_client_id: None,
         };
+
         let err = spec.validate("test").unwrap_err();
+
         assert!(err.to_string().contains("remote fields"));
     }
 
@@ -547,14 +607,18 @@ mod tests {
             cwd: None,
             url: None,
             headers: Some(headers),
+            oauth_client_id: None,
         };
+
         let err = spec.validate("test").unwrap_err();
+
         assert!(err.to_string().contains("remote fields"));
     }
 
     #[test]
     fn validate_http_with_url_succeeds() {
         let spec = http_server("http://localhost:8080");
+
         assert!(spec.validate("test").is_ok());
     }
 
@@ -568,8 +632,11 @@ mod tests {
             cwd: None,
             url: None,
             headers: None,
+            oauth_client_id: None,
         };
+
         let err = spec.validate("test").unwrap_err();
+
         assert!(err.to_string().contains("missing a \"url\" field"));
     }
 
@@ -583,8 +650,11 @@ mod tests {
             cwd: None,
             url: Some("http://localhost".into()),
             headers: None,
+            oauth_client_id: None,
         };
+
         let err = spec.validate("test").unwrap_err();
+
         assert!(err.to_string().contains("stdio fields"));
     }
 
@@ -598,8 +668,11 @@ mod tests {
             cwd: None,
             url: Some("http://localhost".into()),
             headers: None,
+            oauth_client_id: None,
         };
+
         let err = spec.validate("test").unwrap_err();
+
         assert!(err.to_string().contains("stdio fields"));
     }
 
@@ -613,14 +686,18 @@ mod tests {
             cwd: Some("/tmp".into()),
             url: Some("http://localhost".into()),
             headers: None,
+            oauth_client_id: None,
         };
+
         let err = spec.validate("test").unwrap_err();
+
         assert!(err.to_string().contains("stdio fields"));
     }
 
     #[test]
     fn validate_sse_with_url_succeeds() {
         let spec = sse_server("http://sse.example.com");
+
         assert!(spec.validate("test").is_ok());
     }
 
@@ -634,8 +711,11 @@ mod tests {
             cwd: None,
             url: None,
             headers: None,
+            oauth_client_id: None,
         };
+
         let err = spec.validate("test").unwrap_err();
+
         assert!(err.to_string().contains("missing a \"url\" field"));
     }
 
@@ -661,9 +741,13 @@ mod tests {
                 }
             }
         }"#;
+
         let config: McpServersConfig = serde_json::from_str(json).unwrap();
+
         assert!(config.mcp_servers.contains_key("my-server"));
+
         let spec = &config.mcp_servers["my-server"];
+
         assert_eq!(spec.transport_type, McpTransportType::Stdio);
         assert_eq!(spec.command.as_deref(), Some("npx"));
         assert_eq!(
@@ -684,7 +768,9 @@ mod tests {
             }
         }"#;
         let config: McpServersConfig = serde_json::from_str(json).unwrap();
+
         let spec = &config.mcp_servers["remote"];
+
         assert_eq!(spec.transport_type, McpTransportType::Http);
         assert_eq!(spec.url.as_deref(), Some("http://localhost:8080/mcp"));
         assert_eq!(
@@ -709,7 +795,9 @@ mod tests {
             }
         }"#;
         let config: McpServersConfig = serde_json::from_str(json).unwrap();
+
         let env = config.mcp_servers["s"].env.as_ref().unwrap();
+
         assert!(matches!(env["STR_VAR"], JsonField::Str(ref s) if s == "hello"));
         assert!(matches!(env["BOOL_VAR"], JsonField::Bool(true)));
         assert!(matches!(env["INT_VAR"], JsonField::Int(42)));
@@ -723,7 +811,9 @@ mod tests {
                 "remote-api": { "type": "http", "url": "http://api.example.com" }
             }
         }"#;
+
         let config: McpServersConfig = serde_json::from_str(json).unwrap();
+
         assert_eq!(config.mcp_servers.len(), 2);
         assert!(config.mcp_servers.contains_key("github"));
         assert!(config.mcp_servers.contains_key("remote-api"));
@@ -732,7 +822,9 @@ mod tests {
     #[test]
     fn deserialize_empty_servers_map() {
         let json = r#"{ "mcpServers": {} }"#;
+
         let config: McpServersConfig = serde_json::from_str(json).unwrap();
+
         assert!(config.mcp_servers.is_empty());
     }
 
@@ -747,77 +839,96 @@ mod tests {
                 }
             }
         }"#;
+
         let config: McpServersConfig = serde_json::from_str(json).unwrap();
+
         assert_eq!(config.mcp_servers["s"].cwd.as_deref(), Some("/tmp/work"));
     }
 
     #[test]
     fn resolve_all_returns_all_configured_servers() {
         let registry = make_registry_with_config(&["github", "slack", "jira"]);
+
         let mut ids = registry.resolve_server_ids(Some(vec!["all".to_string()]));
         ids.sort();
+
         assert_eq!(ids, vec!["github", "jira", "slack"]);
     }
 
     #[test]
     fn resolve_comma_separated_returns_matching_servers() {
         let registry = make_registry_with_config(&["github", "slack", "jira"]);
+
         let mut ids =
             registry.resolve_server_ids(Some(vec!["github".to_string(), "jira".to_string()]));
         ids.sort();
+
         assert_eq!(ids, vec!["github", "jira"]);
     }
 
     #[test]
     fn resolve_single_server_name() {
         let registry = make_registry_with_config(&["github", "slack"]);
+
         let ids = registry.resolve_server_ids(Some(vec!["slack".to_string()]));
+
         assert_eq!(ids, vec!["slack"]);
     }
 
     #[test]
     fn resolve_none_returns_empty() {
         let registry = make_registry_with_config(&["github"]);
+
         let ids = registry.resolve_server_ids(None);
+
         assert!(ids.is_empty());
     }
 
     #[test]
     fn resolve_no_config_returns_empty() {
         let registry = McpRegistry::default();
+
         let ids = registry.resolve_server_ids(Some(vec!["all".to_string()]));
+
         assert!(ids.is_empty());
     }
 
     #[test]
     fn resolve_nonexistent_server_filtered_out() {
         let registry = make_registry_with_config(&["github"]);
+
         let ids = registry
             .resolve_server_ids(Some(vec!["github".to_string(), "nonexistent".to_string()]));
+
         assert_eq!(ids, vec!["github"]);
     }
 
     #[test]
     fn resolve_all_nonexistent_returns_empty() {
         let registry = make_registry_with_config(&["github"]);
+
         let ids = registry.resolve_server_ids(Some(vec!["foo".to_string(), "bar".to_string()]));
+
         assert!(ids.is_empty());
     }
 
     #[test]
     fn resolve_trims_whitespace() {
         let registry = make_registry_with_config(&["github", "slack"]);
+
         let mut ids = registry.resolve_server_ids(Some(vec![
             "  github  ".to_string(),
             "  slack  ".to_string(),
         ]));
         ids.sort();
+
         assert_eq!(ids, vec!["github", "slack"]);
     }
 
     #[test]
     fn registry_default_is_empty() {
         let registry = McpRegistry::default();
+
         assert!(registry.is_empty());
         assert!(registry.list_started_servers().is_empty());
         assert!(registry.mcp_config().is_none());
@@ -827,6 +938,7 @@ mod tests {
     #[test]
     fn registry_with_config_reports_config() {
         let registry = make_registry_with_config(&["github"]);
+
         assert!(registry.mcp_config().is_some());
         assert!(
             registry
@@ -843,4 +955,53 @@ mod tests {
         assert_eq!(MCP_SEARCH_META_FUNCTION_NAME_PREFIX, "mcp_search");
         assert_eq!(MCP_DESCRIBE_META_FUNCTION_NAME_PREFIX, "mcp_describe");
     }
+
+    #[test]
+    fn merge_bearer_token_both_none_returns_none() {
+        assert!(merge_bearer_token(None, None).is_none());
+    }
+
+    #[test]
+    fn merge_bearer_token_headers_only_passes_through() {
+        let mut h = IndexMap::new();
+        h.insert("X-Key".to_string(), "val".to_string());
+
+        let result = merge_bearer_token(Some(&h), None).unwrap();
+
+        assert_eq!(result["X-Key"], "val");
+        assert!(!result.contains_key("Authorization"));
+    }
+
+    #[test]
+    fn merge_bearer_token_token_only_injects_bearer() {
+        let result = merge_bearer_token(None, Some("tok123".to_string())).unwrap();
+
+        assert_eq!(result["Authorization"], "Bearer tok123");
+    }
+
+    #[test]
+    fn merge_bearer_token_both_merges_and_overrides_authorization() {
+        let mut h = IndexMap::new();
+        h.insert("Authorization".to_string(), "old".to_string());
+        h.insert("X-Custom".to_string(), "keep".to_string());
+
+        let result = merge_bearer_token(Some(&h), Some("newtoken".to_string())).unwrap();
+
+        assert_eq!(result["Authorization"], "Bearer newtoken");
+        assert_eq!(result["X-Custom"], "keep");
+    }
+
+    #[test]
+    fn is_auth_required_error_matches_rmcp_message() {
+        let e = anyhow!("Auth required, when send initialize request");
+
+        assert!(is_auth_required_error(&e));
+    }
+
+    #[test]
+    fn is_auth_required_error_does_not_match_unrelated() {
+        let e = anyhow!("Connection refused");
+
+        assert!(!is_auth_required_error(&e));
+    }
 }

src/mcp/oauth.rs

@@ -0,0 +1,329 @@
+use crate::client::oauth::{OAuthProvider, TokenRequestFormat, load_oauth_tokens, run_oauth_flow};
+use crate::config::paths;
+use anyhow::{Context, Result, anyhow};
+use chrono::Utc;
+use inquire::Text;
+use log::warn;
+use reqwest::Client;
+use serde::{Deserialize, Serialize};
+use std::fs;
+use std::net::TcpListener;
+use url::Url;
+
+#[derive(Debug, Deserialize)]
+struct ProtectedResourceMetadata {
+    #[serde(default)]
+    authorization_servers: Vec<String>,
+}
+
+#[derive(Debug, Deserialize)]
+struct OAuthServerMetadata {
+    authorization_endpoint: String,
+    token_endpoint: String,
+    #[serde(default)]
+    scopes_supported: Vec<String>,
+    registration_endpoint: Option<String>,
+}
+
+#[derive(Serialize, Deserialize)]
+struct McpRegistration {
+    client_id: String,
+}
+
+struct McpOAuthProvider {
+    client_id: String,
+    authorize_url: String,
+    token_url: String,
+    scopes: String,
+    fixed_redirect: String,
+}
+
+impl OAuthProvider for McpOAuthProvider {
+    fn provider_name(&self) -> &str {
+        "MCP"
+    }
+
+    fn client_id(&self) -> &str {
+        &self.client_id
+    }
+
+    fn authorize_url(&self) -> &str {
+        &self.authorize_url
+    }
+
+    fn token_url(&self) -> &str {
+        &self.token_url
+    }
+
+    fn redirect_uri(&self) -> &str {
+        ""
+    }
+
+    fn scopes(&self) -> &str {
+        &self.scopes
+    }
+
+    fn token_request_format(&self) -> TokenRequestFormat {
+        TokenRequestFormat::FormUrlEncoded
+    }
+
+    fn uses_localhost_redirect(&self) -> bool {
+        false
+    }
+
+    fn fixed_redirect_uri(&self) -> Option<String> {
+        Some(self.fixed_redirect.clone())
+    }
+}
+
+pub async fn run_mcp_oauth_flow(
+    server_name: &str,
+    server_url: &str,
+    configured_client_id: Option<&str>,
+) -> Result<()> {
+    let metadata = discover_oauth_metadata(server_url).await?;
+
+    let listener = TcpListener::bind("127.0.0.1:0")?;
+    let port = listener.local_addr()?.port();
+    drop(listener);
+    let redirect_uri = format!("http://127.0.0.1:{port}/callback");
+
+    let client_id = if let Some(id) = configured_client_id {
+        id.to_string()
+    } else if let Some(cached) = load_registered_client_id(server_name) {
+        cached
+    } else if let Some(reg_endpoint) = &metadata.registration_endpoint {
+        match register_client(reg_endpoint, &redirect_uri).await {
+            Ok(id) => {
+                let _ = save_registered_client_id(server_name, &id);
+                id
+            }
+            Err(e) => {
+                warn!("Dynamic client registration failed: {e}. Falling back to manual entry.");
+                Text::new("Enter the OAuth client ID for this MCP server:")
+                    .prompt()
+                    .context("Failed to read client ID")?
+            }
+        }
+    } else {
+        Text::new("Enter the OAuth client ID for this MCP server:")
+            .prompt()
+            .context("Failed to read client ID")?
+    };
+
+    let provider = McpOAuthProvider {
+        client_id,
+        authorize_url: metadata.authorization_endpoint,
+        token_url: metadata.token_endpoint,
+        scopes: metadata.scopes_supported.join(" "),
+        fixed_redirect: redirect_uri,
+    };
+
+    run_oauth_flow(&provider, &mcp_token_key(server_name)).await
+}
+
+pub fn load_valid_mcp_token(server_name: &str) -> Option<String> {
+    let tokens = load_oauth_tokens(&mcp_token_key(server_name))?;
+    if Utc::now().timestamp() < tokens.expires_at {
+        Some(tokens.access_token)
+    } else {
+        None
+    }
+}
+
+fn mcp_token_key(server_name: &str) -> String {
+    format!("mcp_{server_name}")
+}
+
+fn load_registered_client_id(server_name: &str) -> Option<String> {
+    let path = paths::oauth_tokens_path().join(format!("mcp_{server_name}_registration.json"));
+    let content = fs::read_to_string(path).ok()?;
+    let reg: McpRegistration = serde_json::from_str(&content).ok()?;
+
+    Some(reg.client_id)
+}
+
+fn save_registered_client_id(server_name: &str, client_id: &str) -> Result<()> {
+    let dir = paths::oauth_tokens_path();
+    fs::create_dir_all(&dir)?;
+
+    let path = dir.join(format!("mcp_{server_name}_registration.json"));
+    let reg = McpRegistration {
+        client_id: client_id.to_string(),
+    };
+
+    fs::write(path, serde_json::to_string_pretty(&reg)?)?;
+
+    Ok(())
+}
+
+async fn register_client(endpoint: &str, redirect_uri: &str) -> Result<String> {
+    let body = serde_json::json!({
+        "client_name": "Coyote",
+        "redirect_uris": [redirect_uri],
+        "grant_types": ["authorization_code", "refresh_token"],
+        "response_types": ["code"],
+        "token_endpoint_auth_method": "none"
+    });
+
+    let response: serde_json::Value = Client::new()
+        .post(endpoint)
+        .json(&body)
+        .send()
+        .await
+        .context("Failed to reach registration endpoint")?
+        .json()
+        .await
+        .context("Failed to parse registration response")?;
+
+    response["client_id"]
+        .as_str()
+        .ok_or_else(|| anyhow!("Missing client_id in registration response: {response}"))
+        .map(|s| s.to_string())
+}
+
+async fn discover_oauth_metadata(server_url: &str) -> Result<OAuthServerMetadata> {
+    let base = extract_base_url(server_url)?;
+    let client = Client::new();
+
+    // RFC 9728: try protected resource metadata first; it points to the auth server
+    let pr_url = format!("{base}/.well-known/oauth-protected-resource");
+    if let Ok(resp) = client.get(&pr_url).send().await
+        && resp.status().is_success()
+        && let Ok(pr) = resp.json::<ProtectedResourceMetadata>().await
+        && let Some(auth_server) = pr.authorization_servers.first()
+    {
+        let as_url = format!("{auth_server}/.well-known/oauth-authorization-server");
+        if let Ok(resp) = client.get(&as_url).send().await
+            && resp.status().is_success()
+            && let Ok(meta) = resp.json::<OAuthServerMetadata>().await
+        {
+            return Ok(meta);
+        }
+    }
+
+    let as_url = format!("{base}/.well-known/oauth-authorization-server");
+    let resp = client
+        .get(&as_url)
+        .send()
+        .await
+        .with_context(|| format!("Failed to reach {as_url}"))?;
+
+    if resp.status().is_success() {
+        return resp
+            .json::<OAuthServerMetadata>()
+            .await
+            .with_context(|| format!("Failed to parse OAuth metadata from {as_url}"));
+    }
+
+    Err(anyhow!(
+        "Could not discover OAuth metadata for '{server_url}'.\n\
+         Tried:\n  {pr_url}\n  {as_url}\n\
+         Ensure the server supports MCP OAuth discovery, or consult its documentation."
+    ))
+}
+
+fn extract_base_url(url: &str) -> Result<String> {
+    let parsed = Url::parse(url).with_context(|| format!("Invalid URL: {url}"))?;
+    let scheme = parsed.scheme();
+    let host = parsed
+        .host_str()
+        .ok_or_else(|| anyhow!("No host in URL: {url}"))?;
+    let port = parsed.port().map(|p| format!(":{p}")).unwrap_or_default();
+
+    Ok(format!("{scheme}://{host}{port}"))
+}
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+    use crate::utils::get_env_name;
+    use serial_test::serial;
+    use std::{
+        env, fs,
+        time::{self, SystemTime},
+    };
+
+    fn with_temp_cache<F: FnOnce()>(f: F) {
+        let unique = SystemTime::now()
+            .duration_since(time::UNIX_EPOCH)
+            .unwrap()
+            .as_nanos();
+        let root = env::temp_dir().join(format!("coyote-mcp-oauth-test-{unique}"));
+        fs::create_dir_all(&root).unwrap();
+        let env_key = get_env_name("cache_dir");
+        let prev = env::var_os(&env_key);
+        unsafe {
+            env::set_var(&env_key, &root);
+        }
+        f();
+        unsafe {
+            match prev {
+                Some(v) => env::set_var(&env_key, v),
+                None => env::remove_var(&env_key),
+            }
+        }
+        let _ = fs::remove_dir_all(&root);
+    }
+
+    #[test]
+    fn extract_base_url_strips_path_and_query() {
+        let result = extract_base_url("https://mcp.notion.com/mcp?foo=bar").unwrap();
+
+        assert_eq!(result, "https://mcp.notion.com");
+    }
+
+    #[test]
+    fn extract_base_url_preserves_explicit_port() {
+        let result = extract_base_url("http://localhost:8080/mcp").unwrap();
+
+        assert_eq!(result, "http://localhost:8080");
+    }
+
+    #[test]
+    fn extract_base_url_standard_port_omitted() {
+        let result = extract_base_url("https://example.com/mcp/v1").unwrap();
+
+        assert_eq!(result, "https://example.com");
+    }
+
+    #[test]
+    fn extract_base_url_rejects_invalid_url() {
+        assert!(extract_base_url("not-a-url").is_err());
+    }
+
+    #[test]
+    #[serial]
+    fn registered_client_id_roundtrip() {
+        with_temp_cache(|| {
+            save_registered_client_id("notion", "client-xyz-123").unwrap();
+
+            let loaded = load_registered_client_id("notion");
+
+            assert_eq!(loaded, Some("client-xyz-123".to_string()));
+        });
+    }
+
+    #[test]
+    #[serial]
+    fn load_registered_client_id_returns_none_for_missing() {
+        with_temp_cache(|| {
+            let loaded = load_registered_client_id("no-such-server");
+
+            assert!(loaded.is_none());
+        });
+    }
+
+    #[test]
+    #[serial]
+    fn registered_client_id_second_save_overwrites_first() {
+        with_temp_cache(|| {
+            save_registered_client_id("github", "first-id").unwrap();
+            save_registered_client_id("github", "second-id").unwrap();
+
+            let loaded = load_registered_client_id("github");
+
+            assert_eq!(loaded, Some("second-id".to_string()));
+        });
+    }
+}

src/repl/mod.rs

@@ -6,7 +6,10 @@ use self::completer::ReplCompleter;
 use self::highlighter::ReplHighlighter;
 use self::prompt::ReplPrompt;
 
-use crate::client::{call_chat_completions, call_chat_completions_streaming, init_client, oauth};
+use crate::client::{
+    Message, MessageRole, call_chat_completions, call_chat_completions_streaming, init_client,
+    oauth,
+};
 use crate::config::{
     AgentVariables, AppConfig, AssertState, Input, LastMessage, RequestContext, StateFlags,
     macro_execute,
@@ -20,7 +23,7 @@ use crate::utils::{
 };
 
 use crate::sandbox::SANDBOX_ENV_FLAG;
-use crate::{config, graph, resolve_oauth_client};
+use crate::{config, graph, mcp, resolve_oauth_client};
 use anyhow::{Context, Result, bail};
 use crossterm::cursor::SetCursorStyle;
 use fancy_regex::Regex;
@@ -29,9 +32,9 @@ use log::warn;
 use parking_lot::RwLock;
 use reedline::CursorConfig;
 use reedline::{
-    ColumnarMenu, EditCommand, EditMode, Emacs, KeyCode, KeyModifiers, Keybindings, Reedline,
-    ReedlineEvent, ReedlineMenu, ValidationResult, Validator, Vi, default_emacs_keybindings,
-    default_vi_insert_keybindings, default_vi_normal_keybindings,
+    ColumnarMenu, EditCommand, EditMode, Emacs, FileBackedHistory, KeyCode, KeyModifiers,
+    Keybindings, Reedline, ReedlineEvent, ReedlineMenu, ValidationResult, Validator, Vi,
+    default_emacs_keybindings, default_vi_insert_keybindings, default_vi_normal_keybindings,
 };
 use reedline::{MenuBuilder, Signal};
 use std::sync::LazyLock;
@@ -49,7 +52,7 @@ pub const DEFAULT_CONTINUATION_PROMPT: &str = indoc! {"
     4. Continue with the next pending item now. Call tools immediately."
 };
 
-static REPL_COMMANDS: LazyLock<[ReplCommand; 49]> = LazyLock::new(|| {
+static REPL_COMMANDS: LazyLock<[ReplCommand; 50]> = LazyLock::new(|| {
     [
         ReplCommand::new(".help", "Show this help guide", AssertState::pass()),
         ReplCommand::new(".info", "Show system info", AssertState::pass()),
@@ -63,6 +66,11 @@ static REPL_COMMANDS: LazyLock<[ReplCommand; 49]> = LazyLock::new(|| {
             "Authenticate the current model client via OAuth (if configured)",
             AssertState::pass(),
         ),
+        ReplCommand::new(
+            ".mcp auth",
+            "Authenticate with an MCP server via OAuth",
+            AssertState::pass(),
+        ),
         ReplCommand::new(
             ".edit config",
             "Modify configuration file",
@@ -313,6 +321,58 @@ Type ".help" for additional help.
             }
         }
 
+        {
+            let (messages_snapshot, compressed_count) = {
+                let ctx = self.ctx.read();
+                if let Some(session) = &ctx.session {
+                    let msgs: Vec<Message> = session
+                        .messages()
+                        .iter()
+                        .filter(|m| !m.role.is_system())
+                        .cloned()
+                        .collect();
+                    let compressed = session.compressed_messages().len();
+                    (msgs, compressed)
+                } else {
+                    (vec![], 0)
+                }
+            };
+
+            if !messages_snapshot.is_empty() || compressed_count > 0 {
+                let app = Arc::clone(&self.ctx.read().app.config);
+                if compressed_count > 0 {
+                    println!(
+                        "{}",
+                        dimmed_text(&format!(
+                            "({compressed_count} earlier messages not shown; compressed for context)"
+                        ))
+                    );
+                    println!();
+                }
+
+                for message in &messages_snapshot {
+                    match message.role {
+                        MessageRole::User => {
+                            if let Some(text) = message.content.as_text() {
+                                println!("{}", dimmed_text("You:"));
+                                println!("{text}");
+                                println!();
+                            }
+                        }
+                        MessageRole::Assistant => {
+                            if let Some(text) = message.content.as_text() {
+                                app.print_markdown(text)?;
+                                println!();
+                            }
+                        }
+                        _ => {}
+                    }
+                }
+                println!("{}", dimmed_text("─── ↑ previous conversation ↑ ───"));
+                println!();
+            }
+        }
+
         loop {
             if self.abort_signal.aborted_ctrld() {
                 break;
@@ -388,6 +448,14 @@ Type ".help" for additional help.
             editor = editor.with_buffer_editor(command, temp_file);
         }
 
+        if app.save_shell_history {
+            let ctx = ctx.read();
+            let history_path = paths::repl_history_file(&ctx.session);
+            if let Ok(history) = FileBackedHistory::with_file(1000, history_path) {
+                editor = editor.with_history(Box::new(history));
+            }
+        }
+
         Ok(editor)
     }
 
@@ -541,6 +609,53 @@ pub async fn run_repl_command(
                 let (client_name, provider) = resolve_oauth_client(Some(client.name()), &clients)?;
                 oauth::run_oauth_flow(&*provider, &client_name).await?;
             }
+            ".mcp" => match args {
+                Some(args) => {
+                    let mut parts = args.splitn(2, char::is_whitespace);
+                    let sub = parts.next().unwrap_or("").trim();
+                    let rest = parts.next().map(str::trim).unwrap_or("");
+                    match sub {
+                        "auth" => {
+                            if rest.is_empty() {
+                                println!("Usage: .mcp auth <server_name>");
+                            } else {
+                                let server_name = rest;
+                                let server_spec = ctx
+                                    .app
+                                    .mcp_config
+                                    .as_ref()
+                                    .and_then(|c| c.mcp_servers.get(server_name))
+                                    .cloned();
+                                match server_spec {
+                                    None => {
+                                        bail!("MCP server '{}' not found in mcp.json.", server_name)
+                                    }
+                                    Some(spec) if !spec.is_remote() => bail!(
+                                        "MCP server '{}' uses stdio transport; \
+                                         OAuth is only supported for http/sse servers.",
+                                        server_name
+                                    ),
+                                    Some(spec) => {
+                                        let url = spec
+                                            .url
+                                            .as_deref()
+                                            .expect("validated: remote spec has url");
+                                        let client_id = spec.oauth_client_id.as_deref();
+                                        mcp::oauth::run_mcp_oauth_flow(server_name, url, client_id)
+                                            .await?;
+                                        println!(
+                                            "Authentication saved. \
+                                             Restart Coyote to connect to '{server_name}'."
+                                        );
+                                    }
+                                }
+                            }
+                        }
+                        _ => unknown_command()?,
+                    }
+                }
+                None => println!("Usage: .mcp auth <server_name>"),
+            },
             ".prompt" => match args {
                 Some(text) => {
                     let app = Arc::clone(&ctx.app.config);
@@ -632,6 +747,46 @@ pub async fn run_repl_command(
                         session.set_autonaming(false);
                     }
                 }
+                if let Some(session) = &ctx.session {
+                    let messages_snapshot: Vec<Message> = session
+                        .messages()
+                        .iter()
+                        .filter(|m| !m.role.is_system())
+                        .cloned()
+                        .collect();
+                    let compressed_count = session.compressed_messages().len();
+                    if !messages_snapshot.is_empty() || compressed_count > 0 {
+                        if compressed_count > 0 {
+                            println!(
+                                "{}",
+                                dimmed_text(&format!(
+                                    "({compressed_count} earlier messages not shown — compressed for context)"
+                                ))
+                            );
+                            println!();
+                        }
+                        for message in &messages_snapshot {
+                            match message.role {
+                                MessageRole::User => {
+                                    if let Some(text) = message.content.as_text() {
+                                        println!("{}", dimmed_text("You:"));
+                                        println!("{text}");
+                                        println!();
+                                    }
+                                }
+                                MessageRole::Assistant => {
+                                    if let Some(text) = message.content.as_text() {
+                                        app.print_markdown(text)?;
+                                        println!();
+                                    }
+                                }
+                                _ => {}
+                            }
+                        }
+                        println!("{}", dimmed_text("─── ↑ previous conversation ↑ ───"));
+                        println!();
+                    }
+                }
             }
             ".install" => {
                 let trimmed = args.map(str::trim).unwrap_or("");
@@ -1415,8 +1570,8 @@ mod tests {
     }
 
     #[test]
-    fn repl_commands_has_49_entries() {
-        assert_eq!(REPL_COMMANDS.len(), 49);
+    fn repl_commands_has_50_entries() {
+        assert_eq!(REPL_COMMANDS.len(), 50);
     }
 
     #[test]

src/sandbox/mod.rs

@@ -316,6 +316,7 @@ fn sandbox_exists(name: &str) -> Result<bool> {
 fn create_sandbox(name: &str, kit_path: &Path, mixins: &[DiscoveredMixin]) -> Result<()> {
     info!("Creating sandbox '{name}'");
     let args = build_create_args(name, kit_path, mixins)?;
+    debug!("sbx {}", args.join(" "));
     let status = Command::new(SBX_BINARY)
         .args(&args)
         .stdin(Stdio::inherit())
@@ -342,6 +343,8 @@ fn build_create_args(
 
     let mut args = vec![
         "create".to_string(),
+        "--name".to_string(),
+        name.to_string(),
         "--kit".to_string(),
         kit_str.to_string(),
     ];
@@ -357,8 +360,6 @@ fn build_create_args(
     }
 
     args.push(SANDBOX_AGENT.to_string());
-    args.push("--name".to_string());
-    args.push(name.to_string());
     args.push(".".to_string());
 
     Ok(args)
@@ -369,10 +370,17 @@ fn copy_host_files(name: &str) -> Result<()> {
     let home_dir = dirs::home_dir().context("Could not determine home directory")?;
 
     if config_dir.exists() {
-        ensure_sandbox_dir(name, "/home/agent/.config")?;
-        let src = format!("{}/", config_dir.display());
-        let dest = format!("{name}:/home/agent/.config/");
-        sbx_cp(&src, &dest)?;
+        let sandbox_config_dir = "/home/agent/.config/coyote";
+        ensure_sandbox_dir(name, sandbox_config_dir)?;
+        let dest = format!("{name}:{sandbox_config_dir}/");
+        for entry in fs::read_dir(&config_dir)
+            .with_context(|| format!("Failed to read {}", config_dir.display()))?
+        {
+            let entry = entry?;
+            let path = entry.path();
+            sbx_cp(&path.display().to_string(), &dest)?;
+        }
+        chown_agent_recursive(name, sandbox_config_dir)?;
     } else {
         debug!(
             "Skipping config copy: {} does not exist",
@@ -390,6 +398,7 @@ fn copy_host_files(name: &str) -> Result<()> {
             }
             let dest = format!("{name}:{dest_path}");
             sbx_cp(&password_file.display().to_string(), &dest)?;
+            chown_agent_recursive(name, &dest_path)?;
         }
         Some(password_file) => {
             debug!(
@@ -505,8 +514,9 @@ fn exec_run(name: &str, kit_path: &Path) -> Result<()> {
     let kit_str = kit_path
         .to_str()
         .ok_or_else(|| anyhow!("Kit path is not valid UTF-8: {}", kit_path.display()))?;
+    debug!("sbx run --name {name} --kit {kit_str}");
     let status = Command::new(SBX_BINARY)
-        .args(["run", name, "--kit", kit_str])
+        .args(["run", "--name", name, "--kit", kit_str])
         .stdin(Stdio::inherit())
         .stdout(Stdio::inherit())
         .stderr(Stdio::inherit())
@@ -520,6 +530,27 @@ fn exec_run(name: &str, kit_path: &Path) -> Result<()> {
     Ok(())
 }
 
+fn chown_agent_recursive(sandbox: &str, path: &str) -> Result<()> {
+    let path_q = shell_words::quote(path);
+    let cmd = format!("sudo chown -R agent:agent {path_q}");
+
+    debug!("sbx exec {sandbox}: {cmd}");
+
+    let status = Command::new(SBX_BINARY)
+        .args(["exec", sandbox, "sh", "-c", &cmd])
+        .stdin(Stdio::inherit())
+        .stdout(Stdio::inherit())
+        .stderr(Stdio::inherit())
+        .status()
+        .context("Failed to spawn `sbx exec` to chown copied files")?;
+
+    if !status.success() {
+        bail!("Chowning '{path}' in sandbox failed: sbx exec exited with {status}");
+    }
+
+    Ok(())
+}
+
 #[cfg(test)]
 mod tests {
     use super::*;
@@ -621,6 +652,8 @@ mod tests {
             args,
             vec![
                 "create".to_string(),
+                "--name".to_string(),
+                "my-box".to_string(),
                 "--kit".to_string(),
                 "/cache/sbx-kit".to_string(),
                 "--kit".to_string(),
@@ -628,8 +661,6 @@ mod tests {
                 "--kit".to_string(),
                 dir_b.display().to_string(),
                 "coyote".to_string(),
-                "--name".to_string(),
-                "my-box".to_string(),
                 ".".to_string(),
             ]
         );
@@ -646,11 +677,11 @@ mod tests {
             args,
             vec![
                 "create".to_string(),
+                "--name".to_string(),
+                "box".to_string(),
                 "--kit".to_string(),
                 "/cache/sbx-kit".to_string(),
                 "coyote".to_string(),
-                "--name".to_string(),
-                "box".to_string(),
                 ".".to_string(),
             ]
         );

src/utils/logs.rs

@@ -1,9 +1,11 @@
 use crate::config::paths;
 use colored::Colorize;
 use fancy_regex::Regex;
-use std::fs::File;
+use std::fs::{self, File};
 use std::io::{BufRead, BufReader, Seek, SeekFrom};
 use std::process;
+use std::time::Duration;
+use tokio::time::sleep;
 
 pub async fn tail_logs(no_color: bool) {
     let re = Regex::new(r"^(?P<timestamp>\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2}\.\d{3})\s+<(?P<opid>[^\s>]+)>\s+\[(?P<level>[A-Z]+)\]\s+(?P<logger>[^:]+):(?P<line>\d+)\s+-\s+(?P<message>.*)$").unwrap();
@@ -16,20 +18,43 @@ pub async fn tail_logs(no_color: bool) {
         process::exit(1);
     };
 
-    let mut lines = reader.lines();
+    let mut line_buf = String::new();
 
     loop {
-        if let Some(Ok(line)) = lines.next() {
-            if no_color {
-                println!("{line}");
-            } else {
-                let colored_line = colorize_log_line(&line, &re);
-                println!("{colored_line}");
+        match reader.read_line(&mut line_buf) {
+            Ok(0) => {
+                if file_was_rotated(&file_path, &mut reader) {
+                    let file = File::open(&file_path).expect("Cannot open file");
+                    reader = BufReader::new(file);
+                }
+                sleep(Duration::from_millis(100)).await;
+            }
+            Ok(_) => {
+                let line = line_buf.trim_end();
+                if no_color {
+                    println!("{line}");
+                } else {
+                    let colored_line = colorize_log_line(line, &re);
+                    println!("{colored_line}");
+                }
+                line_buf.clear();
+            }
+            Err(_) => {
+                line_buf.clear();
+                sleep(Duration::from_millis(100)).await;
             }
         }
     }
 }
 
+fn file_was_rotated(path: &std::path::Path, reader: &mut BufReader<File>) -> bool {
+    let current_pos = reader.stream_position().unwrap_or(0);
+    match fs::metadata(path) {
+        Ok(metadata) => metadata.len() < current_pos,
+        Err(_) => true,
+    }
+}
+
 fn colorize_log_line(line: &str, re: &Regex) -> String {
     if let Some(caps) = re.captures(line).expect("Failed to capture log line") {
         let level = &caps["level"];