feat: Added todo__clear function to the todo system and updated REPL commands to have a .clear todo as well for significant changes in agent direction

assets/agents/.shared/utils.sh

@@ -2,68 +2,6 @@
 # Shared Agent Utilities - Minimal, focused helper functions
 set -euo pipefail
 
-#############################
-## CONTEXT FILE MANAGEMENT ##
-#############################
-
-get_context_file() {
-  local project_dir="${LLM_AGENT_VAR_PROJECT_DIR:-.}"
-  echo "${project_dir}/.loki-context"
-}
-
-# Initialize context file for a new task
-# Usage: init_context "Task description"
-init_context() {
-  local task="$1"
-  local project_dir="${LLM_AGENT_VAR_PROJECT_DIR:-.}"
-  local context_file
-  context_file=$(get_context_file)
-  
-  cat > "${context_file}" <<EOF
-## Project: ${project_dir}
-## Task: ${task}
-## Started: $(date -Iseconds)
-
-### Prior Findings
-
-EOF
-}
-
-# Append findings to the context file
-# Usage: append_context "agent_name" "finding summary
-append_context() {
-  local agent="$1"
-  local finding="$2"
-  local context_file
-  context_file=$(get_context_file)
-
-  if [[ -f "${context_file}" ]]; then
-    {
-      echo ""
-      echo "[${agent}]:"
-      echo "${finding}"
-    } >> "${context_file}"
-  fi
-}
-
-# Read the current context (returns empty string if no context)
-# Usage: context=$(read_context)
-read_context() {
-  local context_file
-  context_file=$(get_context_file)
-  
-  if [[ -f "${context_file}" ]]; then
-    cat "${context_file}"
-  fi
-}
-
-# Clear the context file
-clear_context() {
-  local context_file
-  context_file=$(get_context_file)
-  rm -f "${context_file}"
-}
-
 #######################
 ## PROJECT DETECTION ##
 #######################
@@ -279,9 +217,9 @@ _detect_with_llm() {
   evidence=$(_gather_project_evidence "${dir}")
   local prompt
   prompt=$(cat <<-EOF
-		
+
 		Analyze this project directory and determine the project type, primary language, and the correct shell commands to build, test, and check (lint/typecheck) it.
-		
+
 		EOF
 	)
   prompt+=$'\n'"${evidence}"$'\n'
@@ -348,77 +286,11 @@ detect_project() {
   echo '{"type":"unknown","build":"","test":"","check":""}'
 }
 
-######################
-## AGENT INVOCATION ##
-######################
-
-# Invoke a subagent with optional context injection
-# Usage: invoke_agent <agent_name> <prompt> [extra_args...]
-invoke_agent() {
-  local agent="$1"
-  local prompt="$2"
-  shift 2
-
-  local context
-  context=$(read_context)
-
-  local full_prompt
-  if [[ -n "${context}" ]]; then
-    full_prompt="## Orchestrator Context
-
-The orchestrator (sisyphus) has gathered this context from prior work:
-
-<context>
-${context}
-</context>
-
-## Your Task
-
-${prompt}"
-  else
-    full_prompt="${prompt}"
-  fi
-
-  env AUTO_CONFIRM=true loki --agent "${agent}" "$@" "${full_prompt}" 2>&1
-}
-
-# Invoke a subagent and capture a summary of its findings
-# Usage: result=$(invoke_agent_with_summary "explore" "find auth patterns")
-invoke_agent_with_summary() {
-  local agent="$1"
-  local prompt="$2"
-  shift 2
-
-  local output
-  output=$(invoke_agent "${agent}" "${prompt}" "$@")
-
-  local summary=""
-
-  if echo "${output}" | grep -q "FINDINGS:"; then
-    summary=$(echo "${output}" | sed -n '/FINDINGS:/,/^[A-Z_]*COMPLETE/p' | grep "^- " | sed 's/^- /  - /')
-  elif echo "${output}" | grep -q "CODER_COMPLETE:"; then
-    summary=$(echo "${output}" | grep "CODER_COMPLETE:" | sed 's/CODER_COMPLETE: *//')
-  elif echo "${output}" | grep -q "ORACLE_COMPLETE"; then
-    summary=$(echo "${output}" | sed -n '/^## Recommendation/,/^## /{/^## Recommendation/d;/^## /d;p}' | sed '/^$/d' | head -10)
-  fi
-
-  # Failsafe: extract up to 5 meaningful lines if no markers found
-  if [[ -z "${summary}" ]]; then
-    summary=$(echo "${output}" | grep -v "^$" | grep -v "^#" | grep -v "^\-\-\-" | tail -10 | head -5)
-  fi
-
-  if [[ -n "${summary}" ]]; then
-    append_context "${agent}" "${summary}"
-  fi
-
-  echo "${output}"
-}
-
 ###########################
 ## FILE SEARCH UTILITIES ##
 ###########################
 
-search_files() {
+_search_files() {
   local pattern="$1"
   local dir="${2:-.}"
   

assets/agents/code-reviewer/config.yaml

@@ -122,3 +122,6 @@ instructions: |
   - Project: {{project_dir}}
   - CWD: {{__cwd__}}
   - Shell: {{__shell__}}
+  
+  ## Available Tools:
+  {{__tools__}}

assets/agents/coder/config.yaml

@@ -29,11 +29,30 @@ instructions: |
   ## Your Mission
 
   Given an implementation task:
-  1. Understand what to build (from context provided)
-  2. Study existing patterns (read 1-2 similar files)
+  1. Check for orchestrator context first (see below)
+  2. Fill gaps only. Read files NOT already covered in context
   3. Write the code (using tools, NOT chat output)
   4. Verify it compiles/builds
-  5. Signal completion
+  5. Signal completion with a summary
+
+  ## Using Orchestrator Context (IMPORTANT)
+
+  When spawned by sisyphus, your prompt will often contain a `<context>` block
+  with prior findings: file paths, code patterns, and conventions discovered by
+  explore agents.
+
+  **If context is provided:**
+  1. Use it as your primary reference. Don't re-read files already summarized
+  2. Follow the code patterns shown. Snippets in context ARE the style guide
+  3. Read the referenced files ONLY IF you need more detail (e.g. full function
+     signature, import list, or adjacent code not included in the snippet)
+  4. If context includes a "Conventions" section, follow it exactly
+
+  **If context is NOT provided or is too vague to act on:**
+  Fall back to self-exploration: grep for similar files, read 1-2 examples,
+  match their style.
+
+  **Never ignore provided context.** It represents work already done upstream.
 
   ## Todo System
 
@@ -82,12 +101,13 @@ instructions: |
 
   ## Completion Signal
 
-  End with:
+  When done, end your response with a summary so the parent agent knows what happened:
+
   ```
-  CODER_COMPLETE: [summary of what was implemented]
+  CODER_COMPLETE: [summary of what was implemented, which files were created/modified, and build status]
   ```
 
-  Or if failed:
+  Or if something went wrong:
   ```
   CODER_FAILED: [what went wrong]
   ```
@@ -104,4 +124,6 @@ instructions: |
   - Project: {{project_dir}}
   - CWD: {{__cwd__}}
   - Shell: {{__shell__}}
-
+  
+  ## Available tools:
+  {{__tools__}}

assets/agents/explore/config.yaml

@@ -8,12 +8,13 @@ variables:
     description: Project directory to explore
     default: '.'
 
+mcp_servers:
+  - ddg-search
 global_tools:
   - fs_read.sh
   - fs_grep.sh
   - fs_glob.sh
   - fs_ls.sh
-  - web_search_loki.sh
 
 instructions: |
   You are a codebase explorer. Your job: Search, find, report. Nothing else.
@@ -67,6 +68,9 @@ instructions: |
   ## Context
   - Project: {{project_dir}}
   - CWD: {{__cwd__}}
+  
+  ## Available Tools:
+  {{__tools__}}
 
 conversation_starters:
   - 'Find how authentication is implemented'

assets/agents/explore/tools.sh

@@ -60,7 +60,7 @@ search_files() {
   echo "" >> "$LLM_OUTPUT"
   
   local results
-  results=$(search_files "${pattern}" "${project_dir}")
+  results=$(_search_files "${pattern}" "${project_dir}")
   
   if [[ -n "${results}" ]]; then
     echo "${results}" >> "$LLM_OUTPUT"

assets/agents/file-reviewer/config.yaml

@@ -108,3 +108,6 @@ instructions: |
   ## Context
   - Project: {{project_dir}}
   - CWD: {{__cwd__}}
+  
+  ## Available Tools:
+  {{__tools__}}

assets/agents/oracle/config.yaml

@@ -8,12 +8,13 @@ variables:
     description: Project directory for context
     default: '.'
 
+mcp_servers:
+  - ddg-search
 global_tools:
   - fs_read.sh
   - fs_grep.sh
   - fs_glob.sh
   - fs_ls.sh
-  - web_search_loki.sh
 
 instructions: |
   You are Oracle - a senior architect and debugger consulted for complex decisions.
@@ -74,6 +75,9 @@ instructions: |
   ## Context
   - Project: {{project_dir}}
   - CWD: {{__cwd__}}
+  
+  ## Available Tools:
+  {{__tools__}}
 
 conversation_starters:
   - 'Review this architecture design'

assets/agents/sisyphus/config.yaml

@@ -12,7 +12,7 @@ can_spawn_agents: true
 max_concurrent_agents: 4
 max_agent_depth: 3
 inject_spawn_instructions: true
-summarization_threshold: 4000
+summarization_threshold: 8000
 
 variables:
   - name: project_dir
@@ -22,12 +22,13 @@ variables:
     description: Auto-confirm command execution
     default: '1'
 
+mcp_servers:
+  - ddg-search
 global_tools:
   - fs_read.sh
   - fs_grep.sh
   - fs_glob.sh
   - fs_ls.sh
-  - web_search_loki.sh
   - execute_command.sh
 
 instructions: |
@@ -69,6 +70,45 @@ instructions: |
   | coder | Write/edit files, implement features | Creates/modifies files, runs builds |
   | oracle | Architecture decisions, complex debugging | Advisory, high-quality reasoning |
 
+  ## Coder Delegation Format (MANDATORY)
+
+  When spawning the `coder` agent, your prompt MUST include these sections.
+  The coder has NOT seen the codebase. Your prompt IS its entire context.
+
+  ### Template:
+
+  ```
+  ## Goal
+  [1-2 sentences: what to build/modify and where]
+
+  ## Reference Files
+  [Files that explore found, with what each demonstrates]
+  - `path/to/file.ext` - what pattern this file shows
+  - `path/to/other.ext` - what convention this file shows
+
+  ## Code Patterns to Follow
+  [Paste ACTUAL code snippets from explore results, not descriptions]
+  <code>
+  // From path/to/file.ext - this is the pattern to follow:
+  [actual code explore found, 5-20 lines]
+  </code>
+
+  ## Conventions
+  [Naming, imports, error handling, file organization]
+  - Convention 1
+  - Convention 2
+
+  ## Constraints
+  [What NOT to do, scope boundaries]
+  - Do NOT modify X
+  - Only touch files in Y/
+  ```
+
+  **CRITICAL**: Include actual code snippets, not just file paths.
+  If explore returned code patterns, paste them into the coder prompt.
+  Vague prompts like "follow existing patterns" waste coder's tokens on
+  re-exploration that you already did.
+
   ## Workflow Examples
 
   ### Example 1: Implementation task (explore -> coder, parallel exploration)
@@ -80,12 +120,12 @@ instructions: |
   2. todo__add --task "Explore existing API patterns"
   3. todo__add --task "Implement profile endpoint"
   4. todo__add --task "Verify with build/test"
-  5. agent__spawn --agent explore --prompt "Find existing API endpoint patterns, route structures, and controller conventions"
-  6. agent__spawn --agent explore --prompt "Find existing data models and database query patterns"
+  5. agent__spawn --agent explore --prompt "Find existing API endpoint patterns, route structures, and controller conventions. Include code snippets."
+  6. agent__spawn --agent explore --prompt "Find existing data models and database query patterns. Include code snippets."
   7. agent__collect --id <id1>
   8. agent__collect --id <id2>
   9. todo__done --id 1
-  10. agent__spawn --agent coder --prompt "Create user profiles endpoint following existing patterns. [Include context from explore results]"
+  10. agent__spawn --agent coder --prompt "<structured prompt using Coder Delegation Format above, including code snippets from explore results>"
   11. agent__collect --id <coder_id>
   12. todo__done --id 2
   13. run_build
@@ -134,7 +174,6 @@ instructions: |
 
   ## When to Do It Yourself
 
-  - Single-file reads/writes
   - Simple command execution
   - Trivial changes (typos, renames)
   - Quick file searches

docs/AGENTS.md

@@ -467,11 +467,12 @@ inject_todo_instructions: true   # Include the default todo instructions into pr
 
 ### How It Works
 
-1. When `inject_todo_instructions` is enabled, agents receive instructions on using four built-in tools:
+1. When `inject_todo_instructions` is enabled, agents receive instructions on using five built-in tools:
     - `todo__init`: Initialize a todo list with a goal
     - `todo__add`: Add a task to the list
     - `todo__done`: Mark a task complete
     - `todo__list`: View current todo state
+    - `todo__clear`: Clear the entire todo list and reset the goal
    
    These instructions are a reasonable default that detail how to use Loki's To-Do System. If you wish, 
    you can disable the injection of the default instructions and specify your own instructions for how 

docs/REPL.md

@@ -120,13 +120,14 @@ For more information on sessions and how to use them in Loki, refer to the [sess
 Loki lets you build OpenAI GPT-style agents. The following commands let you interact with and manage your agents in 
 Loki:
 
-| Command              | Description                                                |
-|----------------------|------------------------------------------------------------|
-| `.agent`             | Use an agent                                               |
-| `.starter`           | Display and use conversation starters for the active agent |
-| `.edit agent-config` | Open the agent configuration in your preferred text editor |
-| `.info agent`        | Display information about the active agent                 |
-| `.exit agent`        | Leave the active agent                                     |
+| Command              | Description                                                                                   |
+|----------------------|-----------------------------------------------------------------------------------------------|
+| `.agent`             | Use an agent                                                                                  |
+| `.starter`           | Display and use conversation starters for the active agent                                    |
+| `.clear todo`        | Clear the todo list and stop auto-continuation (requires `auto_continue: true` on the agent)  |
+| `.edit agent-config` | Open the agent configuration in your preferred text editor                                    |
+| `.info agent`        | Display information about the active agent                                                    |
+| `.exit agent`        | Leave the active agent                                                                        |
 
 ![agent](./images/agents/sql.gif)
 

docs/TODO-SYSTEM.md

@@ -117,6 +117,22 @@ Display the current todo list with status of each item.
 
 **Returns:** The full todo list with goal, progress, and item statuses
 
+### `todo__clear`
+Clear the entire todo list and reset the goal. Use when the current task has been canceled or invalidated.
+
+**Parameters:** None
+
+**Returns:** Confirmation that the todo list was cleared
+
+### REPL Command: `.clear todo`
+You can also clear the todo list manually from the REPL by typing `.clear todo`. This is useful when:
+- You gave a custom response that changes or cancels the current task
+- The agent is stuck in auto-continuation with stale todos
+- You want to start fresh without leaving and re-entering the agent
+
+**Note:** This command is only available when an agent with `auto_continue: true` is active. If the todo
+system isn't enabled for the current agent, the command will display an error message.
+
 ## Auto-Continuation
 When `auto_continue` is enabled, Loki automatically sends a continuation prompt if:
 

src/client/claude.rs

@@ -11,6 +11,7 @@ use serde::Deserialize;
 use serde_json::{Value, json};
 
 const API_BASE: &str = "https://api.anthropic.com/v1";
+const CLAUDE_CODE_PREFIX: &str = "You are Claude Code, Anthropic's official CLI for Claude.";
 
 #[derive(Debug, Clone, Deserialize)]
 pub struct ClaudeConfig {
@@ -84,7 +85,7 @@ async fn prepare_chat_completions(
         let ready = oauth::prepare_oauth_access_token(client, &provider, self_.name()).await?;
         if !ready {
             bail!(
-                "OAuth configured but no tokens found for '{}'. Run: loki --authenticate {}",
+                "OAuth configured but no tokens found for '{}'. Run: 'loki --authenticate {}' or '.authenticate' in the REPL",
                 self_.name(),
                 self_.name()
             );
@@ -94,6 +95,7 @@ async fn prepare_chat_completions(
         for (key, value) in provider.extra_request_headers() {
             request_data.header(key, value);
         }
+        inject_oauth_system_prompt(&mut request_data.body);
     } else if let Ok(api_key) = self_.get_api_key() {
         request_data.header("x-api-key", api_key);
     } else {
@@ -107,6 +109,43 @@ async fn prepare_chat_completions(
     Ok(request_data)
 }
 
+/// Anthropic requires OAuth-authenticated requests to include a Claude Code
+/// system prompt prefix in order to consider a request body as "valid".
+///
+/// This behavior was discovered 2026-03-17.
+///
+/// So this function injects the Claude Code system prompt into the request
+/// body to make it a valid request.
+fn inject_oauth_system_prompt(body: &mut Value) {
+    let prefix_block = json!({
+        "type": "text",
+        "text": CLAUDE_CODE_PREFIX,
+    });
+
+    match body.get("system") {
+        Some(Value::String(existing)) => {
+            let existing_block = json!({
+                "type": "text",
+                "text": existing,
+            });
+            body["system"] = json!([prefix_block, existing_block]);
+        }
+        Some(Value::Array(_)) => {
+            if let Some(arr) = body["system"].as_array_mut() {
+                let already_injected = arr
+                    .iter()
+                    .any(|block| block["text"].as_str() == Some(CLAUDE_CODE_PREFIX));
+                if !already_injected {
+                    arr.insert(0, prefix_block);
+                }
+            }
+        }
+        _ => {
+            body["system"] = json!([prefix_block]);
+        }
+    }
+}
+
 pub async fn claude_chat_completions(
     builder: RequestBuilder,
     _model: &Model,

src/client/gemini.rs

@@ -111,7 +111,7 @@ async fn prepare_chat_completions(
         let ready = oauth::prepare_oauth_access_token(client, &provider, self_.name()).await?;
         if !ready {
             bail!(
-                "OAuth configured but no tokens found for '{}'. Run: loki --authenticate {}",
+                "OAuth configured but no tokens found for '{}'. Run: 'loki --authenticate {}' or '.authenticate' in the REPL",
                 self_.name(),
                 self_.name()
             );
@@ -181,7 +181,7 @@ async fn prepare_embeddings(
         let ready = oauth::prepare_oauth_access_token(client, &provider, self_.name()).await?;
         if !ready {
             bail!(
-                "OAuth configured but no tokens found for '{}'. Run: loki --authenticate {}",
+                "OAuth configured but no tokens found for '{}'. Run: 'loki --authenticate {}' or '.authenticate' in the REPL",
                 self_.name(),
                 self_.name()
             );

src/client/model.rs

@@ -177,6 +177,10 @@ impl Model {
         self.data.max_output_tokens
     }
 
+    pub fn supports_function_calling(&self) -> bool {
+        self.data.supports_function_calling
+    }
+
     pub fn no_stream(&self) -> bool {
         self.data.no_stream
     }

src/config/agent.rs

@@ -476,6 +476,11 @@ impl Agent {
         self.todo_list.mark_done(id)
     }
 
+    pub fn clear_todo_list(&mut self) {
+        self.todo_list.clear();
+        self.reset_continuation();
+    }
+
     pub fn continuation_prompt(&self) -> String {
         self.config.continuation_prompt.clone().unwrap_or_else(|| {
             formatdoc! {"

src/config/input.rs

@@ -239,12 +239,17 @@ impl Input {
         patch_messages(&mut messages, model);
         model.guard_max_input_tokens(&messages)?;
         let (temperature, top_p) = (self.role().temperature(), self.role().top_p());
-        let functions = self.config.read().select_functions(self.role());
-        if let Some(vec) = &functions {
-            for def in vec {
-                debug!("Function definition: {:?}", def.name);
+        let functions = if model.supports_function_calling() {
+            let fns = self.config.read().select_functions(self.role());
+            if let Some(vec) = &fns {
+                for def in vec {
+                    debug!("Function definition: {:?}", def.name);
+                }
             }
-        }
+            fns
+        } else {
+            None
+        };
         Ok(ChatCompletionsData {
             messages,
             temperature,

src/config/mod.rs

@@ -1842,6 +1842,12 @@ impl Config {
             bail!("Already in an agent, please run '.exit agent' first to exit the current agent.");
         }
         let agent = Agent::init(config, agent_name, abort_signal.clone()).await?;
+        if !agent.model().supports_function_calling() {
+            eprintln!(
+                "Warning: The model '{}' does not support function calling. Agent tools (including todo, spawning, and user interaction) will not be available.",
+                agent.model().id()
+            );
+        }
         let session = session_name.map(|v| v.to_string()).or_else(|| {
             if config.read().macro_flag {
                 None

src/config/prompts.rs

@@ -7,10 +7,12 @@ pub(in crate::config) const DEFAULT_TODO_INSTRUCTIONS: &str = indoc! {"
         - `todo__add`: Add individual tasks. Add all planned steps before starting work.
         - `todo__done`: Mark a task done by id. Call this immediately after completing each step.
         - `todo__list`: Show the current todo list.
+        - `todo__clear`: Clear the entire todo list and reset the goal. Use when the user cancels or changes direction.
 
     RULES:
         - Always create a todo list before starting work.
         - Mark each task done as soon as you finish it; do not batch.
+        - If the user cancels the current task or changes direction, call `todo__clear` immediately.
         - If you stop with incomplete tasks, the system will automatically prompt you to continue."
 };
 

src/config/todo.rs

@@ -67,6 +67,11 @@ impl TodoList {
         self.todos.is_empty()
     }
 
+    pub fn clear(&mut self) {
+        self.goal.clear();
+        self.todos.clear();
+    }
+
     pub fn render_for_model(&self) -> String {
         let mut lines = Vec::new();
         if !self.goal.is_empty() {
@@ -149,6 +154,21 @@ mod tests {
         assert!(rendered.contains("○ 2. Map"));
     }
 
+    #[test]
+    fn test_clear() {
+        let mut list = TodoList::new("Some goal");
+        list.add("Task 1");
+        list.add("Task 2");
+        list.mark_done(1);
+        assert!(!list.is_empty());
+
+        list.clear();
+        assert!(list.is_empty());
+        assert!(list.goal.is_empty());
+        assert_eq!(list.todos.len(), 0);
+        assert!(!list.has_incomplete());
+    }
+
     #[test]
     fn test_serialization_roundtrip() {
         let mut list = TodoList::new("Roundtrip");

src/function/todo.rs

@@ -76,6 +76,16 @@ pub fn todo_function_declarations() -> Vec<FunctionDeclaration> {
             },
             agent: false,
         },
+        FunctionDeclaration {
+            name: format!("{TODO_FUNCTION_PREFIX}clear"),
+            description: "Clear the entire todo list and reset the goal. Use when the current task has been canceled or invalidated.".to_string(),
+            parameters: JsonSchema {
+                type_value: Some("object".to_string()),
+                properties: Some(IndexMap::new()),
+                ..Default::default()
+            },
+            agent: false,
+        },
     ]
 }
 
@@ -156,6 +166,17 @@ pub fn handle_todo_tool(config: &GlobalConfig, cmd_name: &str, args: &Value) ->
                 None => bail!("No active agent"),
             }
         }
+        "clear" => {
+            let mut cfg = config.write();
+            let agent = cfg.agent.as_mut();
+            match agent {
+                Some(agent) => {
+                    agent.clear_todo_list();
+                    Ok(json!({"status": "ok", "message": "Todo list cleared"}))
+                }
+                None => bail!("No active agent"),
+            }
+        }
         _ => bail!("Unknown todo action: {action}"),
     }
 }

src/function/user_interaction.rs

@@ -181,7 +181,7 @@ fn handle_direct_input(args: &Value) -> Result<Value> {
         .and_then(Value::as_str)
         .ok_or_else(|| anyhow!("'question' is required"))?;
 
-    let answer = Text::new(question).prompt()?;
+    let answer = Text::new(&format!("{question}\nYour answer: ")).prompt()?;
 
     Ok(json!({ "answer": answer }))
 }

src/repl/mod.rs

@@ -33,7 +33,7 @@ use std::{env, mem, process};
 
 const MENU_NAME: &str = "completion_menu";
 
-static REPL_COMMANDS: LazyLock<[ReplCommand; 38]> = LazyLock::new(|| {
+static REPL_COMMANDS: LazyLock<[ReplCommand; 39]> = LazyLock::new(|| {
     [
         ReplCommand::new(".help", "Show this help guide", AssertState::pass()),
         ReplCommand::new(".info", "Show system info", AssertState::pass()),
@@ -137,6 +137,11 @@ static REPL_COMMANDS: LazyLock<[ReplCommand; 38]> = LazyLock::new(|| {
             "Leave agent",
             AssertState::True(StateFlags::AGENT),
         ),
+        ReplCommand::new(
+            ".clear todo",
+            "Clear the todo list and stop auto-continuation",
+            AssertState::True(StateFlags::AGENT),
+        ),
         ReplCommand::new(
             ".rag",
             "Initialize or access RAG",
@@ -804,6 +809,25 @@ pub async fn run_repl_command(
                 Some("messages") => {
                     bail!("Use '.empty session' instead");
                 }
+                Some("todo") => {
+                    let mut cfg = config.write();
+                    match cfg.agent.as_mut() {
+                        Some(agent) => {
+                            if !agent.auto_continue_enabled() {
+                                bail!(
+                                    "The todo system is not enabled for this agent. Set 'auto_continue: true' in the agent's config.yaml to enable it."
+                                );
+                            }
+                            if agent.todo_list().is_empty() {
+                                println!("Todo list is already empty.");
+                            } else {
+                                agent.clear_todo_list();
+                                println!("Todo list cleared.");
+                            }
+                        }
+                        None => bail!("No active agent"),
+                    }
+                }
                 _ => unknown_command()?,
             },
             ".vault" => match split_first_arg(args) {