Bump version to 0.3.1

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

.gitignore

@@ -1,27 +1,14 @@
 # Claude Code
 .claude/settings.local.json
+.mcp.json
 
 # Local environment (secrets)
 .env
 
-# App specific
+# App specific (root-level; story-kit subdirectory patterns live in .story_kit/.gitignore)
 store.json
 .story_kit_port
 
-# Bot config (contains credentials)
-.story_kit/bot.toml
-
-# Matrix SDK state store
-.story_kit/matrix_store/
-.story_kit/matrix_device_id
-
-# Agent worktrees and merge workspace (managed by the server, not tracked in git)
-.story_kit/worktrees/
-.story_kit/merge_workspace/
-
-# Coverage reports (generated by cargo-llvm-cov, not tracked in git)
-.story_kit/coverage/
-
 # Rust stuff
 target
 
@@ -39,6 +26,7 @@ frontend/node_modules
 frontend/dist
 frontend/dist-ssr
 frontend/test-results
+frontend/serve
 frontend/*.local
 server/target
 

.mcp.json

@@ -1,8 +0,0 @@
-{
-  "mcpServers": {
-    "story-kit": {
-      "type": "http",
-      "url": "http://localhost:3001/mcp"
-    }
-  }
-}

.story_kit/.gitignore

@@ -0,0 +1,19 @@
+# Bot config (contains credentials)
+bot.toml
+
+# Matrix SDK state store
+matrix_store/
+matrix_device_id
+matrix_history.json
+
+# Agent worktrees and merge workspace (managed by the server, not tracked in git)
+worktrees/
+merge_workspace/
+
+# Intermediate pipeline stages (transient, not committed per spike 92)
+work/2_current/
+work/3_qa/
+work/4_merge/
+
+# Coverage reports (generated by cargo-llvm-cov, not tracked in git)
+coverage/

.story_kit/problems.md

@@ -0,0 +1,7 @@
+# Problems
+
+Recurring issues observed during pipeline operation. Review periodically and create stories for systemic problems.
+
+## 2026-03-18: Agent committed directly to master instead of worktree
+
+Commit `5f4591f` ("fix: update should_commit_stage test to match 5_done") was made directly on master by an agent (likely mergemaster). Agents should only commit to their feature branch or merge-queue branch, never to master directly. The commit content was correct but the target branch was wrong. Suspect the agent ran `git commit` in the project root instead of the merge worktree directory.

.story_kit/project.toml

@@ -220,7 +220,7 @@ role = "Merges completed coder work into master, runs quality gates, archives st
 model = "opus"
 max_turns = 30
 max_budget_usd = 5.00
-prompt = """You are the mergemaster agent for story {{story_id}}. Your job is to merge the completed coder work into master using the merge_agent_work MCP tool.
+prompt = """You are the mergemaster agent for story {{story_id}}. Your job is to merge the completed coder work into master.
 
 Read CLAUDE.md first, then .story_kit/README.md to understand the dev process.
 
@@ -229,20 +229,43 @@ Read CLAUDE.md first, then .story_kit/README.md to understand the dev process.
 2. Review the result: check success, had_conflicts, conflicts_resolved, gates_passed, and gate_output
 3. If merge succeeded and gates passed: report success to the human
 4. If conflicts were auto-resolved (conflicts_resolved=true) and gates passed: report success, noting which conflicts were resolved
-5. If conflicts could not be auto-resolved: call report_merge_failure(story_id='{{story_id}}', reason='<conflict details>') and report to the human. Master is untouched.
+5. If conflicts could not be auto-resolved: **resolve them yourself** in the merge worktree (see below)
-6. If merge failed for any other reason: call report_merge_failure(story_id='{{story_id}}', reason='<details>') and report to the human.
+6. If merge failed for any other reason: call report_merge_failure(story_id='{{story_id}}', reason='<details>') and report to the human
-7. If gates failed after merge: attempt to fix minor issues (see below), then re-trigger merge_agent_work. After 2 fix attempts, call report_merge_failure and stop.
+7. If gates failed after merge: attempt to fix the issues yourself in the merge worktree, then re-trigger merge_agent_work. After 3 fix attempts, call report_merge_failure and stop.
 
-## How Conflict Resolution Works
+## Resolving Complex Conflicts Yourself
-The merge pipeline uses a temporary merge-queue branch and worktree to isolate merges from master. Simple additive conflicts (both branches adding code at the same location) are resolved automatically by keeping both additions. Complex conflicts (modifying the same lines differently) are reported without touching master.
 
-## Fixing Minor Gate Failures
+When the auto-resolver fails, you have access to the merge worktree at `.story_kit/merge_workspace/`. Go in there and resolve the conflicts manually:
-If quality gates fail (cargo clippy, cargo test, npm run build, npm test), attempt to fix minor issues yourself before reporting to the human.
 
-**Fix yourself (up to 2 attempts total):**
+1. Run `git diff --name-only --diff-filter=U` in the merge worktree to list conflicted files
+2. **Build context before touching code.** Run `git log --oneline master...HEAD` on the feature branch to see its commits. Then run `git log --oneline --since="$(git log -1 --format=%ci <feature-branch-base-commit>)" master` to see what landed on master since the branch was created. Read the story files in `.story_kit/work/` for any recently merged stories that touch the same files — this tells you WHY master changed and what must be preserved.
+3. Read each conflicted file and understand both sides of the conflict
+4. **Understand intent, not just syntax.** The feature branch may be behind master — master's version of shared infrastructure is almost always correct. The feature branch's contribution is the NEW functionality it adds. Your job is to integrate the new into master's structure, not pick one side.
+5. Resolve by integrating the feature's new functionality into master's code structure
+5. Stage resolved files with `git add`
+6. Run `cargo check` (and `npm run build` if frontend changed) to verify compilation
+7. If it compiles, commit and re-trigger merge_agent_work
+
+### Common conflict patterns in this project:
+
+**Story file rename/rename conflicts:** Both branches moved the story .md file to different pipeline directories. Resolution: `git rm` both sides — story files in `work/2_current/`, `work/3_qa/`, `work/4_merge/` are gitignored and don't need to be committed.
+
+**bot.rs tokio::select! conflicts:** Master has a `tokio::select!` loop in `handle_message()` that handles permission forwarding (story 275). Feature branches created before story 275 have a simpler direct `provider.chat_stream().await` call. Resolution: KEEP master's tokio::select! loop. Integrate only the feature's new logic (e.g. typing indicators, new callbacks) into the existing loop structure. Do NOT replace the loop with the old direct call.
+
+**Duplicate functions/imports:** The auto-resolver keeps both sides, producing duplicates. Resolution: keep one copy (prefer master's version), delete the duplicate.
+
+**Formatting-only conflicts:** Both sides reformatted the same code differently. Resolution: pick either side (prefer master).
+
+## Fixing Gate Failures
+
+If quality gates fail (cargo clippy, cargo test, npm run build, npm test), attempt to fix issues yourself in the merge worktree.
+
+**Fix yourself (up to 3 attempts total):**
 - Syntax errors (missing semicolons, brackets, commas)
+- Duplicate definitions from merge artifacts
 - Simple type annotation errors
 - Unused import warnings flagged by clippy
+- Mismatched braces from bad conflict resolution
 - Trivial formatting issues that block compilation or linting
 
 **Report to human without attempting a fix:**
@@ -250,17 +273,14 @@ If quality gates fail (cargo clippy, cargo test, npm run build, npm test), attem
 - Missing function implementations
 - Architectural changes required
 - Non-trivial refactoring needed
-- Anything requiring understanding of broader system context
 
-**Max retry limit:** If gates still fail after 2 fix attempts, call report_merge_failure to record the failure, then stop immediately and report the full gate output to the human. Do not retry further.
+**Max retry limit:** If gates still fail after 3 fix attempts, call report_merge_failure to record the failure, then stop immediately and report the full gate output to the human.
 
 ## CRITICAL Rules
 - NEVER manually move story files between pipeline stages (e.g. from 4_merge/ to 5_done/)
 - NEVER call accept_story — only merge_agent_work can move stories to done after a successful merge
-- When merge fails, ALWAYS call report_merge_failure to record the failure — do NOT improvise with file moves
+- When merge fails after exhausting your fix attempts, ALWAYS call report_merge_failure
-- Only use MCP tools (merge_agent_work, report_merge_failure) to drive the merge process
-- Only attempt fixes that are clearly minor and low-risk
 - Report conflict resolution outcomes clearly
 - Report gate failures with full output so the human can act if needed
 - The server automatically runs acceptance gates when your process exits"""
-system_prompt = "You are the mergemaster agent. Your primary responsibility is to trigger the merge_agent_work MCP tool and report the results. CRITICAL: Never manually move story files or call accept_story. When merge fails, call report_merge_failure to record the failure. For minor gate failures (syntax errors, unused imports, missing semicolons), attempt to fix them yourself — but stop after 2 attempts, call report_merge_failure, and report to the human. For complex failures or unresolvable conflicts, call report_merge_failure and report clearly so the human can act. The merge pipeline automatically resolves simple additive conflicts."
+system_prompt = "You are the mergemaster agent. Your primary job is to merge feature branches to master. First try the merge_agent_work MCP tool. If the auto-resolver fails on complex conflicts, resolve them yourself in the merge worktree — you are an opus-class agent capable of understanding both sides of a conflict and producing correct merged code. Common patterns: keep master's tokio::select! permission loop in bot.rs, discard story file rename conflicts (gitignored), remove duplicate definitions. After resolving, verify compilation before re-triggering merge. CRITICAL: Never manually move story files or call accept_story. After 3 failed fix attempts, call report_merge_failure and stop."

.story_kit/work/1_upcoming/260_refactor_upgrade_libsqlite3_sys.md

@@ -0,0 +1,24 @@
+---
+name: "Upgrade libsqlite3-sys"
+---
+
+# Refactor 260: Upgrade libsqlite3-sys
+
+## Description
+
+Upgrade the `libsqlite3-sys` dependency from `0.35.0` to `0.37.0`. The crate is used with `features = ["bundled"]` for static builds.
+
+## Version Notes
+
+- Current: `libsqlite3-sys 0.35.0` (pinned transitively by `matrix-sdk 0.16.0` → `matrix-sdk-sqlite` → `rusqlite 0.37.x`)
+- Target: `libsqlite3-sys 0.37.0`
+- Latest upstream rusqlite: `0.39.0`
+- **Blocker**: `matrix-sdk 0.16.0` pins `rusqlite 0.37.x` which pins `libsqlite3-sys 0.35.0`. A clean upgrade requires either waiting for matrix-sdk to bump their rusqlite dep, or upgrading matrix-sdk itself.
+- **Reverted 2026-03-17**: A previous coder vendored the entire rusqlite crate with a fake `0.37.99` version and patched its libsqlite3-sys dep. This was too hacky — reverted to clean `0.35.0`.
+
+## Acceptance Criteria
+
+- [ ] `libsqlite3-sys` is upgraded to `0.37.0` via a clean dependency path (no vendored forks)
+- [ ] `cargo build` succeeds
+- [ ] All tests pass
+- [ ] No `[patch.crates-io]` hacks or vendored crates

.story_kit/work/1_upcoming/282_story_matrix_bot_ambient_mode_toggle_via_chat_command.md

@@ -0,0 +1,23 @@
+---
+name: "Matrix bot ambient mode toggle via chat command"
+---
+
+# Story 282: Matrix bot ambient mode toggle via chat command
+
+## User Story
+
+As a user chatting with Timmy in a Matrix room, I want to toggle between "addressed mode" (bot only responds when mentioned by name) and "ambient mode" (bot responds to all messages) via a chat command, so that I don't have to @-mention the bot on every message when I'm the only one around.
+
+## Acceptance Criteria
+
+- [ ] Matrix bot defaults to addressed mode — only forwards messages containing the bot's name to Claude
+- [ ] Chat command "timmy ambient on" switches to ambient mode — bot forwards all room messages to Claude
+- [ ] Chat command "timmy ambient off" switches back to addressed mode
+- [ ] Mode persists until explicitly toggled (not across bot restarts)
+- [ ] Bot confirms the mode switch with a short response in chat
+- [ ] When other users join or are active, user can flip back to addressed mode to avoid noise
+- [ ] Ambient mode applies per-room (not globally across all rooms)
+
+## Out of Scope
+
+- TBD

.story_kit/work/1_upcoming/92_spike_stop_auto_committing_intermediate_pipeline_moves.md

@@ -1,55 +0,0 @@
----
-name: "Stop auto-committing intermediate pipeline moves"
----
-
-# Spike 92: Stop auto-committing intermediate pipeline moves
-
-## Goal
-
-Determine how to stop the filesystem watcher from auto-committing every pipeline stage move (upcoming -> current -> qa -> merge) while still committing at terminal states (creation in upcoming, acceptance in archived). This keeps git history clean while preserving cross-machine portability for completed work.
-
-## Context
-
-The watcher in `server/src/io/watcher.rs` currently auto-commits every file change in `.story_kit/work/`. A single story run generates 5+ commits just from pipeline moves:
-- `story-kit: create 42_story_foo`
-- `story-kit: start 42_story_foo`
-- `story-kit: queue 42_story_foo for QA`
-- `story-kit: queue 42_story_foo for merge`
-- `story-kit: accept 42_story_foo`
-
-Since story runs complete relatively quickly, the intermediate state (current/qa/merge) is transient and doesn't need to be committed. Only creation and archival are meaningful checkpoints.
-
-## Questions to Answer
-
-1. Can we filter `stage_metadata()` to only commit for `1_upcoming` and `5_archived` stages while still broadcasting `WatcherEvent`s for all stages (so the frontend stays in sync)?
-2. Should we keep `git add -A .story_kit/work/` for the committed stages, or narrow it to only the specific file?
-3. What happens if the server crashes mid-pipeline? Uncommitted moves are lost — is this acceptable given the story can just be re-run?
-4. Should intermediate moves be `.gitignore`d at the directory level, or is filtering in the watcher sufficient?
-5. Do any other parts of the system (agent worktree setup, merge_agent_work, sparse checkout) depend on intermediate pipeline files being committed to master?
-
-## Approach to Investigate
-
-### Option A: Filter in `flush_pending()`
-- In `flush_pending()`, still broadcast the `WatcherEvent` for all stages
-- Only call `git_add_work_and_commit()` for stages `1_upcoming` and `5_archived`
-- Simplest change — ~5 lines modified in `watcher.rs`
-
-### Option B: Two-tier watcher
-- Split into "commit-worthy" events (create, archive) and "notify-only" events (start, qa, merge)
-- Commit-worthy events go through git
-- Notify-only events just broadcast to WebSocket clients
-- More explicit but same end result as Option A
-
-### Option C: .gitignore intermediate directories
-- Add `2_current/`, `3_qa/`, `4_merge/` to `.gitignore`
-- Watcher still sees events (gitignore doesn't affect filesystem watching)
-- Git naturally ignores them
-- Risk: harder to debug, `git status` won't show pipeline state
-
-## Acceptance Criteria
-
-- [ ] Spike document updated with findings and recommendation
-- [ ] If Option A is viable: prototype the change and verify git log is clean during a full story run
-- [ ] Confirm frontend still receives real-time pipeline updates for all stages
-- [ ] Confirm no other system depends on intermediate pipeline commits being on master
-- [ ] Identify any edge cases (server crash, manual git operations, multi-machine sync)

.story_kit/work/5_done/245_bug_chat_history_persistence_lost_on_page_refresh_story_145_regression.md

@@ -1,36 +0,0 @@
----
-name: "Chat history persistence lost on page refresh (story 145 regression)"
----
-
-## Rejection Notes
-
-**2026-03-16:** Previous coder produced zero code changes — feature branch had no diff against master. The coder must actually use `git bisect` to find the breaking commit and produce a surgical fix. Do not submit with no code changes.
-
-# Bug 245: Chat history persistence lost on page refresh (story 145 regression)
-
-## Description
-
-Story 145 implemented localStorage persistence for chat history across page reloads. This is no longer working — refreshing the page loses all conversation context. This is a regression of the feature delivered in story 145.
-
-## How to Reproduce
-
-1. Open the web UI and have a conversation with the agent
-2. Refresh the page (F5 or Cmd+R)
-
-## Actual Result
-
-Chat history is gone after refresh — the UI shows a blank conversation.
-
-## Expected Result
-
-Chat history is restored from localStorage on page load, as implemented in story 145.
-
-## Acceptance Criteria
-
-- [ ] Chat messages survive a full page refresh
-- [ ] Chat messages are restored from localStorage on component mount
-- [ ] Behaviour matches the original acceptance criteria from story 145
-
-## Investigation Notes
-
-**Use `git bisect` to find the commit that broke this.** Story 145 delivered working localStorage persistence — something after that regressed it. Find the breaking commit, understand the root cause, and fix it there. Do NOT layer on a new implementation. Revert or surgically fix the regression.

.story_kit/work/5_done/266_story_matrix_bot_structured_conversation_history.md

@@ -0,0 +1,60 @@
+---
+name: "Matrix bot structured conversation history"
+agent: coder-opus
+---
+
+# Story 266: Matrix bot structured conversation history
+
+## User Story
+
+As a user chatting with the Matrix bot, I want it to remember and own its prior responses naturally, so that conversations feel like talking to one continuous entity rather than a new instance each message.
+
+## Acceptance Criteria
+
+- [ ] Conversation history is passed as structured API messages (user/assistant turns) rather than a flattened text prefix
+- [ ] Claude recognises its prior responses as its own, maintaining consistent personality across a conversation
+- [ ] Per-room history survives server restarts (persisted to disk or database)
+- [ ] Rolling window trimming still applies to keep context bounded
+- [ ] Multi-user rooms still attribute messages to the correct sender
+
+## Investigation Notes (2026-03-18)
+
+The current implementation attempts session resumption via `--resume <session_id>` but it's not working:
+
+### Code path: how session resumption is supposed to work
+
+1. `server/src/matrix/bot.rs:671-676` — `handle_message()` reads `conv.session_id` from the per-room `RoomConversation` to get the resume ID.
+2. `server/src/matrix/bot.rs:717` — passes `resume_session_id` to `provider.chat_stream()`.
+3. `server/src/llm/providers/claude_code.rs:57` — `chat_stream()` stores it as `resume_id`.
+4. `server/src/llm/providers/claude_code.rs:170-173` — if `resume_session_id` is `Some`, appends `--resume <id>` to the `claude -p` command.
+5. `server/src/llm/providers/claude_code.rs:348` — `process_json_event()` looks for `json["session_id"]` in each streamed NDJSON event and sends it via a oneshot channel (`sid_tx`).
+6. `server/src/llm/providers/claude_code.rs:122` — after the PTY exits, `sid_rx.await.ok()` captures the session ID (or `None` if never sent).
+7. `server/src/matrix/bot.rs:785-787` — stores `new_session_id` back into `conv.session_id` and persists via `save_history()`.
+
+### What's broken
+
+- **No session_id captured:** `.story_kit/matrix_history.json` contains conversation entries but no `session_id`. `RoomConversation.session_id` is always `None`.
+- **Root cause:** `claude -p --output-format stream-json` may not emit a `session_id` in its NDJSON events, or the parser at step 5 isn't matching the actual event shape. The oneshot channel never fires.
+- **Effect:** Every message spawns a fresh Claude Code process with no `--resume` flag. Each turn is a blank slate.
+- **History persistence works fine** — serialization round-trips correctly (test at `bot.rs:1335-1339`). The problem is purely that `--resume` is never invoked.
+
+### Debugging steps
+
+1. Run `claude -p "hello" --output-format stream-json --verbose 2>/dev/null` manually and inspect the NDJSON for a `session_id` field. Check what event type carries it and whether the key name matches what `process_json_event()` expects.
+2. If `session_id` is present but nested differently (e.g. inside an `event` wrapper), fix the JSON path at `claude_code.rs:348`.
+3. If `-p` mode doesn't emit `session_id` at all, consider an alternative: pass conversation history as a structured prompt prefix, or switch to the Claude API directly.
+
+### Previous attempt failed (2026-03-18)
+
+A sonnet coder attempted this story but did NOT fix the root cause. It rewrote the `chat_stream()` call in `bot.rs` to look identical to what was already there — it never investigated why `session_id` isn't being captured. The merge auto-resolver then jammed the duplicate call inside the `tokio::select!` permission loop, producing mismatched braces. The broken merge was reverted.
+
+**What the coder must actually do:**
+
+1. **Do NOT rewrite the `chat_stream()` call or the `tokio::select!` loop in `bot.rs`.** That code is correct and handles permission forwarding (story 275). Do not touch it.
+2. **The bug is in `claude_code.rs`, not `bot.rs`.** The `process_json_event()` function at line ~348 looks for `json["session_id"]` but it's likely never finding it. Start by running step 1 above to see what the actual NDJSON output looks like.
+3. **If `claude -p` doesn't emit `session_id` at all**, the `--resume` approach won't work. In that case, the fix is to pass conversation history as a prompt prefix (prepend prior turns to the user message) or use `--continue` instead of `--resume`, or call the Claude API directly instead of shelling out to the CLI.
+4. **Rebase onto current master before starting.** Master has changed significantly (spike 92, story 275 permission handling, gitignore changes).
+
+## Out of Scope
+
+- TBD

.story_kit/work/5_done/271_story_show_assigned_agent_in_expanded_work_item_view.md

@@ -0,0 +1,19 @@
+---
+name: "Show assigned agent in expanded work item view"
+---
+
+# Story 271: Show assigned agent in expanded work item view
+
+## User Story
+
+As a project owner viewing an expanded work item in the web UI, I want to see which agent (e.g. coder-opus) has been assigned via front matter, so that I know which coder is working on or will pick up the story.
+
+## Acceptance Criteria
+
+- [ ] Expanded work item view displays the agent front matter field if set
+- [ ] Shows the specific agent name (e.g. 'coder-opus') not just 'assigned'
+- [ ] If no agent is set in front matter, the field is omitted or shows unassigned
+
+## Out of Scope
+
+- TBD

.story_kit/work/5_done/273_story_matrix_bot_sends_typing_indicator_while_waiting_for_claude_response.md

@@ -0,0 +1,20 @@
+---
+name: "Matrix bot sends typing indicator while waiting for Claude response"
+---
+
+# Story 273: Matrix bot sends typing indicator while waiting for Claude response
+
+## User Story
+
+As a user chatting with the Matrix bot, I want to see a typing indicator in Element while the bot is processing my message, so that I know it received my request and is working on a response.
+
+## Acceptance Criteria
+
+- [ ] Bot sets m.typing on the room as soon as it starts the Claude API call
+- [ ] Typing indicator is cleared when the first response chunk is sent to the room
+- [ ] Typing indicator is cleared on error so it doesn't get stuck
+- [ ] No visible delay between sending a message and seeing the typing indicator
+
+## Out of Scope
+
+- TBD

.story_kit/work/5_done/274_story_mcp_pipeline_status_tool_with_agent_assignments.md

@@ -0,0 +1,20 @@
+---
+name: "MCP pipeline status tool with agent assignments"
+---
+
+# Story 274: MCP pipeline status tool with agent assignments
+
+## User Story
+
+As a user checking pipeline status, I want an MCP tool that returns a structured status report including which agent is assigned to each work item, so that I can quickly see what's active and spot stuck items.
+
+## Acceptance Criteria
+
+- [ ] New MCP tool (e.g. `get_pipeline_status`) returns all work items across all active pipeline stages (current, qa, merge, done) with their stage, name, and assigned agent
+- [ ] Upcoming backlog items are included with count or listing
+- [ ] Agent assignment info comes from story front matter (`agent` field) and/or the running agent list
+- [ ] Response is structured/deterministic (not free-form prose)
+
+## Out of Scope
+
+- TBD

.story_kit/work/5_done/277_story_matrix_bot_uses_its_configured_name_instead_of_claude.md

@@ -0,0 +1,19 @@
+---
+name: "Matrix bot uses its configured name instead of \"Claude\""
+---
+
+# Story 277: Matrix bot uses its configured name instead of "Claude"
+
+## User Story
+
+As a Matrix user, I want the bot to identify itself by its configured name (e.g., "Timmy") rather than "Claude", so that the bot feels like a distinct personality in the chat.
+
+## Acceptance Criteria
+
+- [ ] The Matrix bot refers to itself by its configured display name (e.g., 'Timmy') in conversations, not 'Claude'
+- [ ] The bot's self-referencing name is derived from configuration, not hardcoded
+- [ ] If no custom name is configured, the bot falls back to a sensible default
+
+## Out of Scope
+
+- TBD

.story_kit/work/5_done/278_story_auto_assign_agents_to_pipeline_items_on_server_startup.md

@@ -0,0 +1,17 @@
+---
+name: "Auto-assign agents to pipeline items on server startup"
+---
+
+# Story 278: Auto-assign agents to pipeline items on server startup
+
+## User Story
+
+As a ..., I want ..., so that ...
+
+## Acceptance Criteria
+
+- [ ] TODO
+
+## Out of Scope
+
+- TBD

.story_kit/work/5_done/279_story_auto_assign_should_respect_agent_stage_when_front_matter_specifies_agent.md

@@ -0,0 +1,20 @@
+---
+name: "Auto-assign should respect agent stage when front matter specifies agent"
+---
+
+# Story 279: Auto-assign should respect agent stage when front matter specifies agent
+
+## User Story
+
+As a project operator, I want auto-assign to respect the pipeline stage when a story's front matter specifies a preferred agent, so that a coder agent isn't assigned to do QA work just because the story originally requested that coder.
+
+## Acceptance Criteria
+
+- [ ] When a story in `3_qa/` has `agent: coder-opus` in front matter, auto-assign skips the preferred agent (stage mismatch) and assigns a free QA-stage agent instead
+- [ ] When a story in `2_current/` has `agent: coder-opus` in front matter, auto-assign still respects the preference (stage matches)
+- [ ] When the preferred agent's stage mismatches, auto-assign logs a message indicating the stage mismatch and fallback
+
+## Out of Scope
+
+- Changing the front matter `agent` field automatically when a story advances stages
+- Adding per-stage agent preferences to front matter

.story_kit/work/5_done/281_story_matrix_bot_announces_itself_when_it_comes_online.md

@@ -0,0 +1,20 @@
+---
+name: "Matrix bot announces itself when it comes online"
+---
+
+# Story 281: Matrix bot announces itself when it comes online
+
+## User Story
+
+As a user in the Matrix room, I want Timmy to post a message when he starts up, so that I know the bot is online and ready to accept commands.
+
+## Acceptance Criteria
+
+- [ ] Bot sends a brief greeting message to each configured room on startup (e.g. 'Timmy is online.')
+- [ ] Message uses the configured display_name, not a hardcoded name
+- [ ] Message is only sent once per startup, not on reconnects or sync resumptions
+- [ ] Bot does not announce if it was already running (e.g. after a brief network blip)
+
+## Out of Scope
+
+- TBD

.story_kit/work/5_done/92_spike_stop_auto_committing_intermediate_pipeline_moves.md

@@ -0,0 +1,119 @@
+---
+name: "Stop auto-committing intermediate pipeline moves"
+agent: "coder-opus"
+review_hold: true
+---
+
+# Spike 92: Stop auto-committing intermediate pipeline moves
+
+## Goal
+
+Determine how to stop the filesystem watcher from auto-committing every pipeline stage move (upcoming -> current -> qa -> merge -> done -> archive) while still committing at terminal states (creation in upcoming, acceptance in done and archived). This keeps git history clean while preserving cross-machine portability for completed work.
+
+## Context
+
+The watcher in `server/src/io/watcher.rs` currently auto-commits every file change in `.story_kit/work/`. A single story run generates 5+ commits just from pipeline moves:
+- `story-kit: create 42_story_foo`
+- `story-kit: start 42_story_foo`
+- `story-kit: queue 42_story_foo for QA`
+- `story-kit: queue 42_story_foo for merge`
+- `story-kit: accept 42_story_foo`
+
+Since story runs complete relatively quickly, the intermediate state (current/qa/merge) is transient and doesn't need to be committed. Only creation and archival are meaningful checkpoints.
+
+## Questions to Answer
+
+1. Can we filter `stage_metadata()` to only commit for `1_upcoming` and `6_archived` stages while still broadcasting `WatcherEvent`s for all stages (so the frontend stays in sync)?
+2. Should we keep `git add -A .story_kit/work/` for the committed stages, or narrow it to only the specific file?
+3. What happens if the server crashes mid-pipeline? Uncommitted moves are lost — is this acceptable given the story can just be re-run?
+4. Should intermediate moves be `.gitignore`d at the directory level, or is filtering in the watcher sufficient?
+5. Do any other parts of the system (agent worktree setup, merge_agent_work, sparse checkout) depend on intermediate pipeline files being committed to master?
+
+## Findings
+
+### Q1: Can we filter to only commit terminal stages?
+
+**Yes.** The fix is in `flush_pending()`, not `stage_metadata()`. We add a `should_commit_stage()` predicate that returns `true` only for `1_upcoming` and `6_archived`. The event broadcast path is decoupled from the commit path — `flush_pending()` always broadcasts a `WatcherEvent` regardless of whether it commits.
+
+Prototype implemented: added `COMMIT_WORTHY_STAGES` constant and `should_commit_stage()` function. The change is ~15 lines including the constant, predicate, and conditional in `flush_pending()`.
+
+### Q2: Keep `git add -A .story_kit/work/` or narrow to specific file?
+
+**Keep `git add -A .story_kit/work/`.** When committing a terminal stage (e.g. `6_archived`), the file has been moved from a previous stage (e.g. `5_done`). Using `-A` on the whole work directory captures both the addition in the new stage and the deletion from the old stage in a single commit. Narrowing to the specific file would miss the deletion side of the move.
+
+### Q3: Server crash mid-pipeline — acceptable?
+
+**Yes.** If the server crashes while a story is in `2_current`, `3_qa`, or `4_merge`, the file is lost from git but:
+- The story file still exists on the filesystem (it's just not committed)
+- The agent's work is in its own feature branch/worktree (independent of pipeline file state)
+- The story can be re-queued from `1_upcoming` which IS committed
+- Pipeline state is transient by nature — it reflects "what's happening right now", not permanent record
+
+### Q4: `.gitignore` vs watcher filtering?
+
+**Watcher filtering is sufficient.** `.gitignore` approach (Option C) has downsides:
+- `git status` won't show pipeline state, making debugging harder
+- If you ever need to commit an intermediate state (e.g. for a new feature), you'd have to fight `.gitignore`
+- Watcher filtering is explicit and easy to understand — a constant lists the commit-worthy stages
+- No risk of accidentally ignoring files that should be tracked
+
+### Q5: Dependencies on intermediate pipeline commits?
+
+**None found.** Thorough investigation confirmed:
+
+1. **`merge_agent_work`** (`agents/merge.rs`): Creates a temporary `merge-queue/` branch and worktree. Reads the feature branch, not pipeline files. After merge, calls `move_story_to_archived()` which is a filesystem operation.
+
+2. **Agent worktree setup** (`worktree.rs`): Creates worktrees from feature branches. Sparse checkout is a no-op (disabled). Does not read pipeline file state from git.
+
+3. **MCP tool handlers** (`agents/lifecycle.rs`): `move_story_to_current()`, `move_story_to_merge()`, `move_story_to_qa()`, `move_story_to_archived()` — all pure filesystem `fs::rename()` operations. None perform git commits.
+
+4. **Frontend** (`http/workflow.rs`): `load_pipeline_state()` reads directories from the filesystem directly via `fs::read_dir()`. Never calls git. WebSocket events keep the frontend in sync.
+
+5. **No git inspection commands** reference pipeline stage directories anywhere in the codebase.
+
+### Edge Cases
+
+- **Multi-machine sync:** Only `1_upcoming` and `6_archived` are committed. If you push/pull, you'll see story creation and archival but not intermediate pipeline state. This is correct — intermediate state is machine-local runtime state.
+- **Manual git operations:** `git status` will show uncommitted files in intermediate stages. This is actually helpful for debugging — you can see what's in the pipeline without grepping git log.
+- **Sweep (5_done → 6_archived):** The sweep moves files to `6_archived`, which triggers a watcher event that WILL commit (since `6_archived` is a terminal stage). This naturally captures the final state.
+
+## Approach to Investigate
+
+### Option A: Filter in `flush_pending()` ← **RECOMMENDED**
+- In `flush_pending()`, still broadcast the `WatcherEvent` for all stages
+- Only call `git_add_work_and_commit()` for stages `1_upcoming` and `6_archived`
+- Simplest change — ~15 lines modified in `watcher.rs`
+
+### Option B: Two-tier watcher
+- Split into "commit-worthy" events (create, archive) and "notify-only" events (start, qa, merge)
+- Commit-worthy events go through git
+- Notify-only events just broadcast to WebSocket clients
+- More explicit but same end result as Option A
+
+### Option C: .gitignore intermediate directories
+- Add `2_current/`, `3_qa/`, `4_merge/` to `.gitignore`
+- Watcher still sees events (gitignore doesn't affect filesystem watching)
+- Git naturally ignores them
+- Risk: harder to debug, `git status` won't show pipeline state
+
+## Recommendation
+
+**Option A is viable and implemented.** The prototype is in `server/src/io/watcher.rs`:
+- Added `COMMIT_WORTHY_STAGES` constant: `["1_upcoming", "6_archived"]`
+- Added `should_commit_stage()` predicate
+- Modified `flush_pending()` to conditionally commit based on stage, while always broadcasting events
+- All 872 tests pass, clippy clean
+
+A full story run will now produce only 2 pipeline commits instead of 5+:
+- `story-kit: create 42_story_foo` (creation in `1_upcoming`)
+- `story-kit: accept 42_story_foo` (archival in `6_archived`)
+
+The intermediate moves (`start`, `queue for QA`, `queue for merge`, `done`) are still broadcast to WebSocket clients for real-time frontend updates, but no longer clutter git history.
+
+## Acceptance Criteria
+
+- [x] Spike document updated with findings and recommendation
+- [x] If Option A is viable: prototype the change and verify git log is clean during a full story run
+- [x] Confirm frontend still receives real-time pipeline updates for all stages
+- [x] Confirm no other system depends on intermediate pipeline commits being on master
+- [x] Identify any edge cases (server crash, manual git operations, multi-machine sync)

.story_kit/work/6_archived/245_bug_chat_history_persistence_lost_on_page_refresh_story_145_regression.md

@@ -0,0 +1,68 @@
+---
+name: "Chat history persistence lost on page refresh (story 145 regression)"
+agent: coder-opus
+---
+
+## Rejection Notes
+
+**2026-03-16:** Previous coder produced zero code changes — feature branch had no diff against master. The coder must actually use `git bisect` to find the breaking commit and produce a surgical fix. Do not submit with no code changes.
+
+**2026-03-17:** Re-opened. Multiple fix attempts have failed. See investigation notes below for the actual root cause.
+
+# Bug 245: Chat history persistence lost on page refresh (story 145 regression)
+
+## Description
+
+Story 145 implemented localStorage persistence for chat history across page reloads. This is no longer working — refreshing the page loses all conversation context. This is a regression of the feature delivered in story 145.
+
+## How to Reproduce
+
+1. Open the web UI and have a conversation with the agent
+2. Refresh the page (F5 or Cmd+R)
+3. Send a new message
+4. The LLM has no knowledge of the prior conversation
+
+## Actual Result
+
+Chat history is gone after refresh — the UI shows a blank conversation. Even if messages appear in the UI (loaded from localStorage), the LLM does not receive them as context on the next exchange.
+
+## Expected Result
+
+Chat history is restored from localStorage on page load, as implemented in story 145. The LLM should receive the full conversation history when the user sends a new message after refresh.
+
+## Acceptance Criteria
+
+- [ ] Chat messages survive a full page refresh (visible in UI)
+- [ ] Chat messages are restored from localStorage on component mount
+- [ ] After refresh, the LLM receives full prior conversation history as context when the user sends the next message
+- [ ] Behaviour matches the original acceptance criteria from story 145
+
+## Investigation Notes (2026-03-17)
+
+### Root cause analysis
+
+The frontend correctly:
+1. Persists messages to localStorage in `useChatHistory.ts` (key: `storykit-chat-history:{projectPath}`)
+2. Loads them on mount
+3. Sends the FULL history array to the backend via `wsRef.current?.sendChat(newHistory, config)` in `Chat.tsx` line ~558
+
+The backend bug is in `server/src/llm/chat.rs`:
+- The `chat()` function receives the full `messages: Vec<Message>` from the client
+- Line ~283: `let mut current_history = messages.clone()` — correctly clones full history
+- Lines ~299-318: Adds 2 system prompts at position 0 and 1
+- Lines ~323-404: Main LLM loop generates new assistant/tool messages
+- **Line ~407: `ChatResult { messages: new_messages }` — BUG: returns ONLY the newly generated turn, not the full `current_history`**
+
+During streaming, the `on_update()` callbacks DO send `current_history[2..]` (full history minus system prompts), which is correct. But there may be a reconciliation issue on the frontend where the final state doesn't include the full history.
+
+### Key files
+- `frontend/src/hooks/useChatHistory.ts` — localStorage persistence
+- `frontend/src/components/Chat.tsx` — sends full history, handles `onUpdate` callbacks
+- `frontend/src/api/client.ts` — WebSocket client
+- `server/src/http/ws.rs` — WebSocket handler, passes messages to chat()
+- `server/src/llm/chat.rs` — **THE BUG** at line ~407, ChatResult returns only new_messages
+
+### What NOT to do
+- Do NOT layer on a new localStorage implementation. The localStorage code works fine.
+- Do NOT add server-side persistence. The "dumb pipe" architecture is correct.
+- The fix should be surgical — ensure the full conversation history round-trips correctly through the backend.

.story_kit/work/6_archived/256_story_bot_must_verify_other_users_cross_signing_identity_before_checking_device_verification.md

@@ -1,5 +1,6 @@
 ---
 name: "Bot must verify other users' cross-signing identity before checking device verification"
+agent: mergemaster
 ---
 
 # Story 256: Bot must verify other users' cross-signing identity before checking device verification
@@ -18,3 +19,16 @@ As a Matrix user messaging the bot, I want the bot to correctly recognize my cro
 ## Out of Scope
 
 - TBD
+
+## Test Results
+
+<!-- story-kit-test-results: {"unit":[{"name":"sender_with_cross_signing_identity_is_accepted","status":"pass","details":"Verifies get_user_identity Some(_) → accepted"},{"name":"sender_without_cross_signing_identity_is_rejected","status":"pass","details":"Verifies get_user_identity None → rejected"}],"integration":[]} -->
+
+### Unit Tests (2 passed, 0 failed)
+
+- ✅ sender_with_cross_signing_identity_is_accepted — Verifies get_user_identity Some(_) → accepted
+- ✅ sender_without_cross_signing_identity_is_rejected — Verifies get_user_identity None → rejected
+
+### Integration Tests (0 passed, 0 failed)
+
+*No integration tests recorded.*

.story_kit/work/6_archived/258_bug_auto_assign_not_called_after_merge_failure.md

@@ -0,0 +1,26 @@
+---
+name: "Auto-assign not called after merge failure"
+---
+
+# Bug 258: Auto-assign not called after merge failure
+
+## Description
+
+When the background merge pipeline fails (e.g. quality gate timeout), `auto_assign_available_work` is never called. The story stays in `4_merge/` with no agent assigned, requiring manual intervention.
+
+### Root cause
+
+In `pool.rs`, `start_merge_agent_work` spawns a tokio task that calls `run_merge_pipeline`. On failure, the task updates the job status to `Failed` but does NOT call `auto_assign_available_work`. The only call to `auto_assign` in the merge pipeline is inside `run_merge_pipeline` on the success path (line ~1251).
+
+The `spawn_pipeline_advance` completion handler does call `auto_assign` after the mergemaster agent exits, but only on the success path (post-merge tests pass → move to done → auto_assign). On failure, it returns early without triggering auto-assign.
+
+There is no periodic sweep — auto-assign is purely reactive (watcher events, agent completions, startup).
+
+### Impact
+
+After a merge failure, the story is permanently stuck in `4_merge/` with no agent. The only way to unstick it is to restart the server or manually trigger a watcher event.
+
+## Acceptance Criteria
+
+- [ ] After a merge pipeline failure, `auto_assign_available_work` is called so the mergemaster can retry
+- [ ] Stories in `4_merge/` do not get permanently stuck after transient merge failures

.story_kit/work/6_archived/259_story_move_story_kit_ignores_into_story_kit_gitignore.md

@@ -0,0 +1,20 @@
+---
+name: "Move story-kit ignores into .story_kit/.gitignore"
+---
+
+# Story 259: Move story-kit ignores into .story_kit/.gitignore
+
+## User Story
+
+As a developer using story-kit, I want story-kit-specific gitignore patterns to live inside .story_kit/.gitignore, so that the host project's root .gitignore stays clean and story-kit concerns are self-contained.
+
+## Acceptance Criteria
+
+- [ ] A .gitignore file exists at .story_kit/.gitignore containing all story-kit-specific ignore patterns
+- [ ] The root .gitignore no longer contains story-kit-specific ignore patterns
+- [ ] The deterministic project scaffold process creates .story_kit/.gitignore when initialising a new project
+- [ ] Existing repos continue to work correctly after the change (no previously-ignored files become tracked)
+
+## Out of Scope
+
+- TBD

.story_kit/work/6_archived/261_story_bot_notifications_when_stories_move_between_stages.md

@@ -0,0 +1,19 @@
+---
+name: "Bot notifications when stories move between stages"
+agent: coder-opus
+---
+
+# Story 261: Bot notifications when stories move between stages
+
+## User Story
+
+As a user, I want to receive bot notifications in the channel whenever a story moves between pipeline stages, so that I can track progress without manually checking status.
+
+## Acceptance Criteria
+
+- [ ] Bot sends a notification to the channel each time a story transitions between stages (e.g. upcoming → current, current → QA, QA → merge, merge → done)
+- [ ] Notification includes the story number, name, and the stage transition (from → to)
+
+## Out of Scope
+
+- TBD

.story_kit/work/6_archived/262_story_bot_error_notifications_for_story_failures.md

@@ -0,0 +1,24 @@
+---
+name: "Bot error notifications for story failures (with shared messaging)"
+---
+
+# Story 262: Bot error notifications for story failures
+
+## User Story
+
+As a user, I want to receive bot notifications with an error icon in the channel whenever a story errors out (e.g. merge failure), so that I'm immediately aware of problems.
+
+## Design Constraint
+
+Story 261 adds stage-transition notifications using the same Matrix messaging path. Extract a shared utility/module for sending Matrix messages so that both error notifications (this story) and stage-transition notifications (261) use the same code path. Do not duplicate Matrix message-sending logic.
+
+## Acceptance Criteria
+
+- [ ] Bot sends an error notification to the channel when a story encounters a failure (e.g. merge failure)
+- [ ] Notification includes an error icon to distinguish it from normal stage-transition notifications
+- [ ] Notification includes the story number, name, and a description of the error
+- [ ] Matrix message-sending logic is in a shared module usable by both error and stage-transition notifications
+
+## Out of Scope
+
+- Stage-transition notifications (covered by story 261)

.story_kit/work/6_archived/263_story_matrix_bot_self_signs_device_keys_at_startup_for_verified_encryption.md

@@ -0,0 +1,21 @@
+---
+name: "Matrix bot self-signs device keys at startup for verified encryption"
+agent: mergemaster
+---
+
+# Story 263: Matrix bot self-signs device keys at startup for verified encryption
+
+## User Story
+
+As a Matrix room participant, I want the bot's messages to not show "encrypted by a device not verified by its owner" warnings, so that I have confidence the bot's encryption is fully verified.
+
+## Acceptance Criteria
+
+- [ ] At startup the bot checks whether its own device keys have been self-signed (cross-signed by its own user identity)
+- [ ] If the device keys are not self-signed, the bot signs them automatically
+- [ ] After signing, the bot uploads the new signatures to the homeserver
+- [ ] After a clean start (fresh matrix_store / device_id) the bot's messages no longer show the 'encrypted by a device not verified by its owner' warning
+
+## Out of Scope
+
+- TBD

.story_kit/work/6_archived/264_bug_claude_code_session_id_not_persisted_across_browser_refresh.md

@@ -0,0 +1,43 @@
+---
+name: "Claude Code session ID not persisted across browser refresh"
+---
+
+# Bug 264: Claude Code session ID not persisted across browser refresh
+
+## Description
+
+The Claude Code provider uses a session_id to resume conversations via `--resume <id>`. This session_id is stored in React state (`claudeSessionId`) but is NOT persisted to localStorage. After a browser refresh, the session_id is lost (`null`), so Claude Code cannot resume the prior session.
+
+A fallback exists (`build_claude_code_context_prompt` in `server/src/llm/chat.rs:188`) that injects prior messages as flattened text inside a `<conversation_history>` block, but this loses structure (tool calls, tool results, reasoning) and Claude Code treats it as informational text rather than actual conversation turns. In practice, the LLM does not retain meaningful context after refresh.
+
+This is the root cause behind bug 245 (chat history persistence regression). The localStorage message persistence from story 145 works correctly for the UI, but the LLM context is not properly restored because the session cannot be resumed.
+
+Key files:
+- `frontend/src/components/Chat.tsx:174` — `claudeSessionId` is ephemeral React state
+- `frontend/src/components/Chat.tsx:553` — session_id only sent when non-null
+- `server/src/llm/chat.rs:278` — backend branches on session_id presence
+- `server/src/llm/providers/claude_code.rs:44` — `--resume` flag passed to Claude CLI
+
+## How to Reproduce
+
+1. Open the Story Kit web UI and select claude-code-pty as the model
+2. Have a multi-turn conversation with the agent
+3. Refresh the browser (F5 or Cmd+R)
+4. Send a new message referencing the prior conversation
+5. The LLM has no knowledge of the prior conversation
+
+## Actual Result
+
+After refresh, claudeSessionId is null. Claude Code spawns a fresh session without --resume. The fallback text injection is too lossy to provide meaningful context. The LLM behaves as if the conversation never happened.
+
+## Expected Result
+
+After refresh, the Claude Code session is resumed via --resume, giving the LLM full context of the prior conversation including tool calls, reasoning, and all turns.
+
+## Acceptance Criteria
+
+- [ ] claudeSessionId is persisted to localStorage (scoped by project path) and restored on component mount
+- [ ] After browser refresh, the next chat message includes session_id in the ProviderConfig
+- [ ] Claude Code receives --resume with the persisted session_id after refresh
+- [ ] Clearing the session (clear button) also clears the persisted session_id
+- [ ] After server restart with session files intact on disk, conversation resumes correctly

.story_kit/work/6_archived/265_story_spikes_skip_merge_and_stop_for_human_review.md

@@ -0,0 +1,33 @@
+---
+name: "Spikes skip merge and stop for human review"
+agent: coder-opus
+---
+
+# Story 265: Spikes skip merge and stop for human review
+
+## User Story
+
+As a user, I want spike work items to stop after QA instead of auto-advancing to the merge stage, so that I can review the spike's findings and prototype code in the worktree before deciding what to do with them.
+
+## Context
+
+Spikes are investigative — their value is the findings and any prototype code, not a merge to master. The user needs to:
+- Read the spike document with findings
+- Review prototype code in the worktree
+- Optionally build and run the prototype to validate the approach
+- Then manually decide: archive the spike and create follow-up stories, or reject and re-investigate
+
+Currently all work items follow the same pipeline: coder → QA → merge → done. Spikes should diverge after QA and wait for human review instead of auto-advancing to merge.
+
+## Acceptance Criteria
+
+- [ ] Items with `_spike_` in the filename skip the merge stage after QA passes
+- [ ] After QA, spike items remain accessible for human review (worktree preserved, not cleaned up)
+- [ ] Spikes do not auto-advance to `4_merge/` — they stay in `3_qa/` or move to a review-hold state
+- [ ] The human can manually archive the spike when done reviewing
+- [ ] Non-spike items (stories, bugs, refactors) continue through the full pipeline as before
+
+## Out of Scope
+
+- New UI for spike review (manual file inspection is fine)
+- Changes to the spike creation flow

.story_kit/work/6_archived/267_story_mcp_update_story_tool_should_support_front_matter_fields.md

@@ -0,0 +1,19 @@
+---
+name: "MCP update_story tool should support front matter fields"
+---
+
+# Story 267: MCP update_story tool should support front matter fields
+
+## User Story
+
+As an operator using the MCP tools, I want update_story to accept optional front matter fields (like agent, manual_qa, etc.) so that I can update story metadata without editing files by hand.
+
+## Acceptance Criteria
+
+- [ ] update_story MCP tool accepts optional agent parameter to set/change the agent front matter field
+- [ ] update_story MCP tool accepts optional arbitrary front matter key-value pairs
+- [ ] Front matter updates are auto-committed via the filesystem watcher like other story mutations
+
+## Out of Scope
+
+- TBD

.story_kit/work/6_archived/268_refactor_upgrade_tokio_tungstenite_to_0_29_0.md

@@ -0,0 +1,23 @@
+---
+name: "Upgrade tokio-tungstenite to 0.29.0"
+---
+
+# Refactor 268: Upgrade tokio-tungstenite to 0.29.0
+
+## Current State
+
+- TBD
+
+## Desired State
+
+Upgrade tokio-tungstenite from 0.28.0 to 0.29.0 in workspace Cargo.toml and fix any breaking API changes.
+
+## Acceptance Criteria
+
+- [ ] tokio-tungstenite = "0.29.0" in workspace Cargo.toml
+- [ ] All code compiles without errors
+- [ ] All tests pass
+
+## Out of Scope
+
+- TBD

.story_kit/work/6_archived/269_story_file_references_in_web_ui_chat_input.md

@@ -0,0 +1,22 @@
+---
+name: "@ file references in web UI chat input"
+---
+
+# Story 269: @ file references in web UI chat input
+
+## User Story
+
+As a user chatting in the web UI, I want to type @ to get an autocomplete overlay listing project files, so that I can reference specific files in my messages the same way Zed and Claude Code do.
+
+## Acceptance Criteria
+
+- [ ] Typing @ in the chat input triggers a file picker overlay
+- [ ] Overlay searches project files with fuzzy matching as the user types after @
+- [ ] Selecting a file inserts a reference into the message (e.g. @path/to/file.rs)
+- [ ] The referenced file contents are included as context when the message is sent to the LLM
+- [ ] Overlay is dismissable with Escape
+- [ ] Multiple @ references can be used in a single message
+
+## Out of Scope
+
+- TBD

.story_kit/work/6_archived/270_bug_qa_test_server_overwrites_root_mcp_json_with_wrong_port.md

@@ -0,0 +1,31 @@
+---
+name: "QA test server overwrites root .mcp.json with wrong port"
+---
+
+# Bug 270: QA test server overwrites root .mcp.json with wrong port
+
+## Description
+
+When the QA agent starts a test server in a worktree (e.g. on port 3012), that server auto-detects the shared project root and calls open_project, which writes .mcp.json with the test server's port. This clobbers the root .mcp.json that should always point to the main server (port 3001).
+
+Root cause: open_project in server/src/io/fs.rs:527 unconditionally calls write_mcp_json(&p, port) with its own port. Because worktrees share .story_kit/ with the real project, the test server resolves to the real project root and overwrites the root .mcp.json instead of writing to its own worktree directory.
+
+Fix: Remove the write_mcp_json call from open_project entirely. Worktree .mcp.json files are already written correctly during worktree creation (worktree.rs:81,97), and the root .mcp.json is committed in git. open_project should not touch it.
+
+## How to Reproduce
+
+1. QA agent starts on a story\n2. QA agent starts a test server in the worktree on a non-default port (e.g. 3012)\n3. Test server auto-opens the project root\n4. Root .mcp.json is overwritten with test port
+
+## Actual Result
+
+Root .mcp.json contains the QA test server's port (e.g. 3012) instead of the main server's port (3001). Interactive Claude sessions lose MCP connectivity.
+
+## Expected Result
+
+Root .mcp.json always points to the primary server's port. Test servers started by QA agents should not overwrite it.
+
+## Acceptance Criteria
+
+- [ ] QA test servers do not overwrite root .mcp.json
+- [ ] Root .mcp.json always reflects the primary server's port
+- [ ] Worktree .mcp.json files are only written during worktree creation

.story_kit/work/6_archived/272_story_clear_merge_error_front_matter_when_story_leaves_merge_stage.md

@@ -0,0 +1,19 @@
+---
+name: "Clear merge error front matter when story leaves merge stage"
+---
+
+# Story 272: Clear merge error front matter when story leaves merge stage
+
+## User Story
+
+As an operator, I want merge error front matter to be automatically removed when a story is moved out of the merge stage via MCP, so that stale error metadata doesn't persist when the story is retried.
+
+## Acceptance Criteria
+
+- [ ] When a story with merge_error front matter is moved out of 4_merge via MCP, the merge_error field is automatically stripped
+- [ ] Works for all destinations: back to 2_current, back to 1_upcoming, or forward to 5_done
+- [ ] Stories without merge_error front matter are unaffected
+
+## Out of Scope
+
+- TBD

.story_kit/work/6_archived/275_story_matrix_bot_surfaces_claude_code_permission_prompts_to_chat.md

@@ -0,0 +1,22 @@
+---
+name: "Matrix bot surfaces Claude Code permission prompts to chat"
+agent: coder-opus
+---
+
+# Story 275: Matrix bot surfaces Claude Code permission prompts to chat
+
+## User Story
+
+As a user chatting with the Matrix bot, I want to see permission prompts from Claude Code in the chat and be able to approve or deny them, so that headless Claude Code sessions don't silently hang when they need authorization to proceed.
+
+## Acceptance Criteria
+
+- [ ] When Claude Code hits a permission prompt during a bot-initiated session, the bot sends the prompt text to the Matrix room as a message
+- [ ] The user can approve or deny the permission by replying in chat (e.g. yes/no or a reaction)
+- [ ] The bot relays the user decision back to the Claude Code subprocess so execution continues
+- [ ] If the user does not respond within a configurable timeout, the permission is denied (fail-closed)
+- [ ] The bot does not hang or timeout silently when a permission prompt is pending - the user always sees what is happening
+
+## Out of Scope
+
+- TBD

.story_kit/work/6_archived/276_story_detect_and_log_when_root_mcp_json_port_is_modified.md

@@ -0,0 +1,17 @@
+---
+name: "Detect and log when root .mcp.json port is modified"
+---
+
+# Story 276: Detect and log when root .mcp.json port is modified
+
+## User Story
+
+As a ..., I want ..., so that ...
+
+## Acceptance Criteria
+
+- [ ] TODO
+
+## Out of Scope
+
+- TBD

Cargo.lock

@@ -3997,7 +3997,7 @@ checksum = "6ce2be8dc25455e1f91df71bfa12ad37d7af1092ae736f3a6cd0e37bc7810596"
 
 [[package]]
 name = "story-kit"
-version = "0.1.0"
+version = "0.3.0"
 dependencies = [
  "async-stream",
  "async-trait",
@@ -4025,7 +4025,7 @@ dependencies = [
  "strip-ansi-escapes",
  "tempfile",
  "tokio",
- "tokio-tungstenite 0.28.0",
+ "tokio-tungstenite 0.29.0",
  "toml 1.0.6+spec-1.1.0",
  "uuid",
  "wait-timeout",
@@ -4333,14 +4333,14 @@ dependencies = [
 
 [[package]]
 name = "tokio-tungstenite"
-version = "0.28.0"
+version = "0.29.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "d25a406cddcc431a75d3d9afc6a7c0f7428d4891dd973e4d54c56b46127bf857"
+checksum = "8f72a05e828585856dacd553fba484c242c46e391fb0e58917c942ee9202915c"
 dependencies = [
  "futures-util",
  "log",
  "tokio",
- "tungstenite 0.28.0",
+ "tungstenite 0.29.0",
 ]
 
 [[package]]
@@ -4562,9 +4562,9 @@ dependencies = [
 
 [[package]]
 name = "tungstenite"
-version = "0.28.0"
+version = "0.29.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "8628dcc84e5a09eb3d8423d6cb682965dea9133204e8fb3efee74c2a0c259442"
+checksum = "6c01152af293afb9c7c2a57e4b559c5620b421f6d133261c60dd2d0cdb38e6b8"
 dependencies = [
  "bytes 1.11.1",
  "data-encoding",
@@ -4574,7 +4574,6 @@ dependencies = [
  "rand 0.9.2",
  "sha1",
  "thiserror 2.0.18",
- "utf-8",
 ]
 
 [[package]]

Cargo.toml

@@ -26,7 +26,7 @@ tempfile = "3"
 tokio = { version = "1", features = ["rt-multi-thread", "macros", "sync"] }
 toml = "1.0.6"
 uuid = { version = "1.22.0", features = ["v4", "serde"] }
-tokio-tungstenite = "0.28.0"
+tokio-tungstenite = "0.29.0"
 walkdir = "2.5.0"
 filetime = "0.2"
 matrix-sdk = { version = "0.16.0", default-features = false, features = [

frontend/src/api/client.ts

@@ -115,6 +115,7 @@ export interface WorkItemContent {
 	content: string;
 	stage: string;
 	name: string | null;
+	agent: string | null;
 }
 
 export interface TestCaseResult {
@@ -277,6 +278,9 @@ export const api = {
 	getHomeDirectory(baseUrl?: string) {
 		return requestJson<string>("/io/fs/home", {}, baseUrl);
 	},
+	listProjectFiles(baseUrl?: string) {
+		return requestJson<string[]>("/io/fs/files", {}, baseUrl);
+	},
 	searchFiles(query: string, baseUrl?: string) {
 		return requestJson<SearchResult[]>(
 			"/fs/search",

frontend/src/components/Chat.test.tsx

@@ -26,6 +26,8 @@ type WsHandlers = {
 	) => void;
 };
 let capturedWsHandlers: WsHandlers | null = null;
+// Captures the last sendChat call's arguments for assertion.
+let lastSendChatArgs: { messages: Message[]; config: unknown } | null = null;
 
 vi.mock("../api/client", () => {
 	const api = {
@@ -36,13 +38,17 @@ vi.mock("../api/client", () => {
 		setModelPreference: vi.fn(),
 		cancelChat: vi.fn(),
 		setAnthropicApiKey: vi.fn(),
+		readFile: vi.fn(),
+		listProjectFiles: vi.fn(),
 	};
 	class ChatWebSocket {
 		connect(handlers: WsHandlers) {
 			capturedWsHandlers = handlers;
 		}
 		close() {}
-		sendChat() {}
+		sendChat(messages: Message[], config: unknown) {
+			lastSendChatArgs = { messages, config };
+		}
 		cancel() {}
 	}
 	return { api, ChatWebSocket };
@@ -56,6 +62,8 @@ const mockedApi = {
 	setModelPreference: vi.mocked(api.setModelPreference),
 	cancelChat: vi.mocked(api.cancelChat),
 	setAnthropicApiKey: vi.mocked(api.setAnthropicApiKey),
+	readFile: vi.mocked(api.readFile),
+	listProjectFiles: vi.mocked(api.listProjectFiles),
 };
 
 function setupMocks() {
@@ -64,6 +72,8 @@ function setupMocks() {
 	mockedApi.getAnthropicModels.mockResolvedValue([]);
 	mockedApi.getModelPreference.mockResolvedValue(null);
 	mockedApi.setModelPreference.mockResolvedValue(true);
+	mockedApi.readFile.mockResolvedValue("");
+	mockedApi.listProjectFiles.mockResolvedValue([]);
 	mockedApi.cancelChat.mockResolvedValue(true);
 	mockedApi.setAnthropicApiKey.mockResolvedValue(true);
 }
@@ -580,6 +590,63 @@ describe("Chat localStorage persistence (Story 145)", () => {
 		expect(storedAfterRemount).toEqual(history);
 	});
 
+	it("Bug 245: after refresh, sendChat includes full prior history", async () => {
+		// Step 1: Render, populate messages via onUpdate, then unmount (simulate refresh)
+		const { unmount } = render(
+			<Chat projectPath={PROJECT_PATH} onCloseProject={vi.fn()} />,
+		);
+		await waitFor(() => expect(capturedWsHandlers).not.toBeNull());
+
+		const priorHistory: Message[] = [
+			{ role: "user", content: "What is Rust?" },
+			{ role: "assistant", content: "Rust is a systems programming language." },
+		];
+		act(() => {
+			capturedWsHandlers?.onUpdate(priorHistory);
+		});
+
+		// Verify localStorage has the prior history
+		const stored = JSON.parse(localStorage.getItem(STORAGE_KEY) ?? "[]");
+		expect(stored).toEqual(priorHistory);
+
+		unmount();
+
+		// Step 2: Remount (simulates page reload) — messages load from localStorage
+		capturedWsHandlers = null;
+		lastSendChatArgs = null;
+		render(<Chat projectPath={PROJECT_PATH} onCloseProject={vi.fn()} />);
+		await waitFor(() => expect(capturedWsHandlers).not.toBeNull());
+
+		// Verify prior messages are displayed
+		expect(await screen.findByText("What is Rust?")).toBeInTheDocument();
+
+		// Step 3: Send a new message — sendChat should include the full prior history
+		const input = screen.getByPlaceholderText("Send a message...");
+		await act(async () => {
+			fireEvent.change(input, { target: { value: "Tell me more" } });
+		});
+		await act(async () => {
+			fireEvent.keyDown(input, { key: "Enter", shiftKey: false });
+		});
+
+		// Verify sendChat was called with ALL prior messages + the new one
+		expect(lastSendChatArgs).not.toBeNull();
+		const args = lastSendChatArgs as unknown as { messages: Message[]; config: unknown };
+		expect(args.messages).toHaveLength(3);
+		expect(args.messages[0]).toEqual({
+			role: "user",
+			content: "What is Rust?",
+		});
+		expect(args.messages[1]).toEqual({
+			role: "assistant",
+			content: "Rust is a systems programming language.",
+		});
+		expect(args.messages[2]).toEqual({
+			role: "user",
+			content: "Tell me more",
+		});
+	});
+
 	it("AC5: uses project-scoped storage key", async () => {
 		const otherKey = "storykit-chat-history:/other/project";
 		localStorage.setItem(
@@ -1215,3 +1282,168 @@ describe("Remove bubble styling from streaming messages (Story 163)", () => {
 		expect(styleAttr).not.toContain("background: transparent");
 	});
 });
+
+describe("Bug 264: Claude Code session ID persisted across browser refresh", () => {
+	const PROJECT_PATH = "/tmp/project";
+	const SESSION_KEY = `storykit-claude-session-id:${PROJECT_PATH}`;
+	const STORAGE_KEY = `storykit-chat-history:${PROJECT_PATH}`;
+
+	beforeEach(() => {
+		capturedWsHandlers = null;
+		lastSendChatArgs = null;
+		localStorage.clear();
+		setupMocks();
+	});
+
+	afterEach(() => {
+		localStorage.clear();
+	});
+
+	it("AC1: session_id is persisted to localStorage when onSessionId fires", async () => {
+		render(<Chat projectPath={PROJECT_PATH} onCloseProject={vi.fn()} />);
+
+		await waitFor(() => expect(capturedWsHandlers).not.toBeNull());
+
+		act(() => {
+			capturedWsHandlers?.onSessionId("test-session-abc");
+		});
+
+		await waitFor(() => {
+			expect(localStorage.getItem(SESSION_KEY)).toBe("test-session-abc");
+		});
+	});
+
+	it("AC2: after remount, next sendChat includes session_id from localStorage", async () => {
+		// Step 1: Render, receive a session ID, then unmount (simulate refresh)
+		localStorage.setItem(SESSION_KEY, "persisted-session-xyz");
+		localStorage.setItem(
+			STORAGE_KEY,
+			JSON.stringify([
+				{ role: "user", content: "Prior message" },
+				{ role: "assistant", content: "Prior reply" },
+			]),
+		);
+
+		const { unmount } = render(
+			<Chat projectPath={PROJECT_PATH} onCloseProject={vi.fn()} />,
+		);
+		await waitFor(() => expect(capturedWsHandlers).not.toBeNull());
+		unmount();
+
+		// Step 2: Remount (simulates page reload)
+		capturedWsHandlers = null;
+		lastSendChatArgs = null;
+		render(<Chat projectPath={PROJECT_PATH} onCloseProject={vi.fn()} />);
+		await waitFor(() => expect(capturedWsHandlers).not.toBeNull());
+
+		// Prior messages should be visible
+		expect(await screen.findByText("Prior message")).toBeInTheDocument();
+
+		// Step 3: Send a new message — config should include session_id
+		const input = screen.getByPlaceholderText("Send a message...");
+		await act(async () => {
+			fireEvent.change(input, { target: { value: "Continue" } });
+		});
+		await act(async () => {
+			fireEvent.keyDown(input, { key: "Enter", shiftKey: false });
+		});
+
+		expect(lastSendChatArgs).not.toBeNull();
+		expect(
+			((lastSendChatArgs as unknown as { messages: Message[]; config: unknown })?.config as Record<string, unknown>).session_id,
+		).toBe("persisted-session-xyz");
+	});
+
+	it("AC3: clearing the session also clears the persisted session_id", async () => {
+		localStorage.setItem(SESSION_KEY, "session-to-clear");
+
+		const confirmSpy = vi.spyOn(window, "confirm").mockReturnValue(true);
+
+		render(<Chat projectPath={PROJECT_PATH} onCloseProject={vi.fn()} />);
+
+		await waitFor(() => expect(capturedWsHandlers).not.toBeNull());
+
+		const newSessionBtn = screen.getByText(/New Session/);
+		await act(async () => {
+			fireEvent.click(newSessionBtn);
+		});
+
+		expect(localStorage.getItem(SESSION_KEY)).toBeNull();
+
+		confirmSpy.mockRestore();
+	});
+
+	it("AC1: storage key is scoped to project path", async () => {
+		const otherPath = "/other/project";
+		const otherKey = `storykit-claude-session-id:${otherPath}`;
+		localStorage.setItem(otherKey, "other-session");
+
+		render(<Chat projectPath={PROJECT_PATH} onCloseProject={vi.fn()} />);
+		await waitFor(() => expect(capturedWsHandlers).not.toBeNull());
+
+		act(() => {
+			capturedWsHandlers?.onSessionId("my-session");
+		});
+
+		await waitFor(() => {
+			expect(localStorage.getItem(SESSION_KEY)).toBe("my-session");
+		});
+
+		// Other project's session should be untouched
+		expect(localStorage.getItem(otherKey)).toBe("other-session");
+	});
+});
+
+describe("File reference expansion (Story 269 AC4)", () => {
+	beforeEach(() => {
+		vi.clearAllMocks();
+		capturedWsHandlers = null;
+		lastSendChatArgs = null;
+		setupMocks();
+	});
+
+	it("includes file contents as context when message contains @file reference", async () => {
+		mockedApi.readFile.mockResolvedValue('fn main() { println!("hello"); }');
+
+		render(<Chat projectPath="/tmp/project" onCloseProject={vi.fn()} />);
+		await waitFor(() => expect(capturedWsHandlers).not.toBeNull());
+
+		const input = screen.getByPlaceholderText("Send a message...");
+		await act(async () => {
+			fireEvent.change(input, { target: { value: "explain @src/main.rs" } });
+		});
+		await act(async () => {
+			fireEvent.keyDown(input, { key: "Enter", shiftKey: false });
+		});
+
+		await waitFor(() => expect(lastSendChatArgs).not.toBeNull());
+		const sentMessages = (
+			lastSendChatArgs as NonNullable<typeof lastSendChatArgs>
+		).messages;
+		const userMsg = sentMessages[sentMessages.length - 1];
+		expect(userMsg.content).toContain("explain @src/main.rs");
+		expect(userMsg.content).toContain("[File: src/main.rs]");
+		expect(userMsg.content).toContain("fn main()");
+	});
+
+	it("sends message without modification when no @file references are present", async () => {
+		render(<Chat projectPath="/tmp/project" onCloseProject={vi.fn()} />);
+		await waitFor(() => expect(capturedWsHandlers).not.toBeNull());
+
+		const input = screen.getByPlaceholderText("Send a message...");
+		await act(async () => {
+			fireEvent.change(input, { target: { value: "hello world" } });
+		});
+		await act(async () => {
+			fireEvent.keyDown(input, { key: "Enter", shiftKey: false });
+		});
+
+		await waitFor(() => expect(lastSendChatArgs).not.toBeNull());
+		const sentMessages = (
+			lastSendChatArgs as NonNullable<typeof lastSendChatArgs>
+		).messages;
+		const userMsg = sentMessages[sentMessages.length - 1];
+		expect(userMsg.content).toBe("hello world");
+		expect(mockedApi.readFile).not.toHaveBeenCalled();
+	});
+});

frontend/src/components/Chat.tsx

@@ -171,7 +171,16 @@ export function Chat({ projectPath, onCloseProject }: ChatProps) {
 		merge: [],
 		done: [],
 	});
-	const [claudeSessionId, setClaudeSessionId] = useState<string | null>(null);
+	const [claudeSessionId, setClaudeSessionId] = useState<string | null>(() => {
+		try {
+			return (
+				localStorage.getItem(`storykit-claude-session-id:${projectPath}`) ??
+				null
+			);
+		} catch {
+			return null;
+		}
+	});
 	const [activityStatus, setActivityStatus] = useState<string | null>(null);
 	const [permissionQueue, setPermissionQueue] = useState<
 		{
@@ -247,6 +256,21 @@ export function Chat({ projectPath, onCloseProject }: ChatProps) {
 		};
 	}, [messages, streamingContent, model]);
 
+	useEffect(() => {
+		try {
+			if (claudeSessionId !== null) {
+				localStorage.setItem(
+					`storykit-claude-session-id:${projectPath}`,
+					claudeSessionId,
+				);
+			} else {
+				localStorage.removeItem(`storykit-claude-session-id:${projectPath}`);
+			}
+		} catch {
+			// Ignore — quota or security errors.
+		}
+	}, [claudeSessionId, projectPath]);
+
 	useEffect(() => {
 		api
 			.getOllamaModels()
@@ -530,7 +554,26 @@ export function Chat({ projectPath, onCloseProject }: ChatProps) {
 			}
 		}
 
-		const userMsg: Message = { role: "user", content: messageText };
+		// Expand @file references: append file contents as context
+		const fileRefs = [...messageText.matchAll(/(^|[\s\n])@([^\s@]+)/g)].map(
+			(m) => m[2],
+		);
+		let expandedText = messageText;
+		if (fileRefs.length > 0) {
+			const expansions = await Promise.allSettled(
+				fileRefs.map(async (ref) => {
+					const contents = await api.readFile(ref);
+					return { ref, contents };
+				}),
+			);
+			for (const result of expansions) {
+				if (result.status === "fulfilled") {
+					expandedText += `\n\n[File: ${result.value.ref}]\n\`\`\`\n${result.value.contents}\n\`\`\``;
+				}
+			}
+		}
+
+		const userMsg: Message = { role: "user", content: expandedText };
 		const newHistory = [...messages, userMsg];
 
 		setMessages(newHistory);
@@ -664,6 +707,11 @@ export function Chat({ projectPath, onCloseProject }: ChatProps) {
 			setLoading(false);
 			setActivityStatus(null);
 			setClaudeSessionId(null);
+			try {
+				localStorage.removeItem(`storykit-claude-session-id:${projectPath}`);
+			} catch {
+				// Ignore — quota or security errors.
+			}
 		}
 	};
 

frontend/src/components/ChatHeader.test.tsx

@@ -136,9 +136,9 @@ describe("ChatHeader", () => {
 		expect(screen.getByText("Built: 2026-01-01 00:00")).toBeInTheDocument();
 	});
 
-	it("displays StorkIt branding in the header", () => {
+	it("displays Story Kit branding in the header", () => {
 		render(<ChatHeader {...makeProps()} />);
-		expect(screen.getByText("StorkIt")).toBeInTheDocument();
+		expect(screen.getByText("Story Kit")).toBeInTheDocument();
 	});
 
 	it("labels the claude-pty optgroup as 'Claude Code'", () => {

frontend/src/components/ChatHeader.tsx

@@ -82,7 +82,7 @@ export function ChatHeader({
 						letterSpacing: "0.02em",
 					}}
 				>
-					StorkIt
+					Story Kit
 				</span>
 				<div
 					title={projectPath}

frontend/src/components/ChatInput.tsx

@@ -1,6 +1,7 @@
 import * as React from "react";
+import { api } from "../api/client";
 
-const { forwardRef, useEffect, useImperativeHandle, useRef, useState } = React;
+const { forwardRef, useCallback, useEffect, useImperativeHandle, useRef, useState } = React;
 
 export interface ChatInputHandle {
 	appendToInput(text: string): void;
@@ -14,6 +15,97 @@ interface ChatInputProps {
 	onRemoveQueuedMessage: (id: string) => void;
 }
 
+/** Fuzzy-match: returns true if all chars of `query` appear in order in `str`. */
+function fuzzyMatch(str: string, query: string): boolean {
+	if (!query) return true;
+	const lower = str.toLowerCase();
+	const q = query.toLowerCase();
+	let qi = 0;
+	for (let i = 0; i < lower.length && qi < q.length; i++) {
+		if (lower[i] === q[qi]) qi++;
+	}
+	return qi === q.length;
+}
+
+/** Score a fuzzy match: lower is better. Exact prefix match wins, then shorter paths. */
+function fuzzyScore(str: string, query: string): number {
+	const lower = str.toLowerCase();
+	const q = query.toLowerCase();
+	// Prefer matches where query appears as a contiguous substring
+	if (lower.includes(q)) return lower.indexOf(q);
+	return str.length;
+}
+
+interface FilePickerOverlayProps {
+	query: string;
+	files: string[];
+	selectedIndex: number;
+	onSelect: (file: string) => void;
+	onDismiss: () => void;
+	anchorRef: React.RefObject<HTMLTextAreaElement | null>;
+}
+
+function FilePickerOverlay({
+	query,
+	files,
+	selectedIndex,
+	onSelect,
+}: FilePickerOverlayProps) {
+	const filtered = files
+		.filter((f) => fuzzyMatch(f, query))
+		.sort((a, b) => fuzzyScore(a, query) - fuzzyScore(b, query))
+		.slice(0, 10);
+
+	if (filtered.length === 0) return null;
+
+	return (
+		<div
+			data-testid="file-picker-overlay"
+			style={{
+				position: "absolute",
+				bottom: "100%",
+				left: 0,
+				right: 0,
+				background: "#1e1e1e",
+				border: "1px solid #444",
+				borderRadius: "8px",
+				marginBottom: "6px",
+				overflow: "hidden",
+				zIndex: 100,
+				boxShadow: "0 4px 16px rgba(0,0,0,0.4)",
+				maxHeight: "240px",
+				overflowY: "auto",
+			}}
+		>
+			{filtered.map((file, idx) => (
+				<button
+					key={file}
+					type="button"
+					data-testid={`file-picker-item-${idx}`}
+					onClick={() => onSelect(file)}
+					style={{
+						display: "block",
+						width: "100%",
+						textAlign: "left",
+						padding: "8px 14px",
+						background: idx === selectedIndex ? "#2d4a6e" : "transparent",
+						border: "none",
+						color: idx === selectedIndex ? "#ececec" : "#aaa",
+						cursor: "pointer",
+						fontFamily: "monospace",
+						fontSize: "0.85rem",
+						whiteSpace: "nowrap",
+						overflow: "hidden",
+						textOverflow: "ellipsis",
+					}}
+				>
+					{file}
+				</button>
+			))}
+		</div>
+	);
+}
+
 export const ChatInput = forwardRef<ChatInputHandle, ChatInputProps>(
 	function ChatInput(
 		{ loading, queuedMessages, onSubmit, onCancel, onRemoveQueuedMessage },
@@ -22,6 +114,12 @@ export const ChatInput = forwardRef<ChatInputHandle, ChatInputProps>(
 		const [input, setInput] = useState("");
 		const inputRef = useRef<HTMLTextAreaElement>(null);
 
+		// File picker state
+		const [projectFiles, setProjectFiles] = useState<string[]>([]);
+		const [pickerQuery, setPickerQuery] = useState<string | null>(null);
+		const [pickerSelectedIndex, setPickerSelectedIndex] = useState(0);
+		const [pickerAtStart, setPickerAtStart] = useState(0);
+
 		useImperativeHandle(ref, () => ({
 			appendToInput(text: string) {
 				setInput((prev) => (prev ? `${prev}\n${text}` : text));
@@ -32,10 +130,104 @@ export const ChatInput = forwardRef<ChatInputHandle, ChatInputProps>(
 			inputRef.current?.focus();
 		}, []);
 
+		// Compute filtered files for current picker query
+		const filteredFiles = pickerQuery !== null
+			? projectFiles
+				.filter((f) => fuzzyMatch(f, pickerQuery))
+				.sort((a, b) => fuzzyScore(a, pickerQuery) - fuzzyScore(b, pickerQuery))
+				.slice(0, 10)
+			: [];
+
+		const dismissPicker = useCallback(() => {
+			setPickerQuery(null);
+			setPickerSelectedIndex(0);
+		}, []);
+
+		const selectFile = useCallback(
+			(file: string) => {
+				// Replace the @query portion with @file
+				const before = input.slice(0, pickerAtStart);
+				const cursorPos = inputRef.current?.selectionStart ?? input.length;
+				const after = input.slice(cursorPos);
+				setInput(`${before}@${file}${after}`);
+				dismissPicker();
+				// Restore focus after state update
+				setTimeout(() => inputRef.current?.focus(), 0);
+			},
+			[input, pickerAtStart, dismissPicker],
+		);
+
+		const handleInputChange = useCallback(
+			(e: React.ChangeEvent<HTMLTextAreaElement>) => {
+				const val = e.target.value;
+				setInput(val);
+
+				const cursor = e.target.selectionStart ?? val.length;
+				// Find the last @ before the cursor that starts a reference token
+				const textUpToCursor = val.slice(0, cursor);
+				// Match @ not preceded by non-whitespace (i.e. @ at start or after space/newline)
+				const atMatch = textUpToCursor.match(/(^|[\s\n])@([^\s@]*)$/);
+
+				if (atMatch) {
+					const query = atMatch[2];
+					const atPos = textUpToCursor.lastIndexOf("@");
+					setPickerAtStart(atPos);
+					setPickerQuery(query);
+					setPickerSelectedIndex(0);
+
+					// Lazily load files on first trigger
+					if (projectFiles.length === 0) {
+						api.listProjectFiles().then(setProjectFiles).catch(() => {});
+					}
+				} else {
+					if (pickerQuery !== null) dismissPicker();
+				}
+			},
+			[projectFiles.length, pickerQuery, dismissPicker],
+		);
+
+		const handleKeyDown = useCallback(
+			(e: React.KeyboardEvent<HTMLTextAreaElement>) => {
+				if (pickerQuery !== null && filteredFiles.length > 0) {
+					if (e.key === "ArrowDown") {
+						e.preventDefault();
+						setPickerSelectedIndex((i) => Math.min(i + 1, filteredFiles.length - 1));
+						return;
+					}
+					if (e.key === "ArrowUp") {
+						e.preventDefault();
+						setPickerSelectedIndex((i) => Math.max(i - 1, 0));
+						return;
+					}
+					if (e.key === "Enter" || e.key === "Tab") {
+						e.preventDefault();
+						selectFile(filteredFiles[pickerSelectedIndex] ?? filteredFiles[0]);
+						return;
+					}
+					if (e.key === "Escape") {
+						e.preventDefault();
+						dismissPicker();
+						return;
+					}
+				} else if (e.key === "Escape" && pickerQuery !== null) {
+					e.preventDefault();
+					dismissPicker();
+					return;
+				}
+
+				if (e.key === "Enter" && !e.shiftKey) {
+					e.preventDefault();
+					handleSubmit();
+				}
+			},
+			[pickerQuery, filteredFiles, pickerSelectedIndex, selectFile, dismissPicker],
+		);
+
 		const handleSubmit = () => {
 			if (!input.trim()) return;
 			onSubmit(input);
 			setInput("");
+			dismissPicker();
 		};
 
 		return (
@@ -135,24 +327,30 @@ export const ChatInput = forwardRef<ChatInputHandle, ChatInputProps>(
 							</button>
 						</div>
 					))}
-					{/* Input row */}
+					{/* Input row with file picker overlay */}
 					<div
 						style={{
 							display: "flex",
 							gap: "8px",
 							alignItems: "center",
+							position: "relative",
 						}}
 					>
+						{pickerQuery !== null && (
+							<FilePickerOverlay
+								query={pickerQuery}
+								files={projectFiles}
+								selectedIndex={pickerSelectedIndex}
+								onSelect={selectFile}
+								onDismiss={dismissPicker}
+								anchorRef={inputRef}
+							/>
+						)}
 						<textarea
 							ref={inputRef}
 							value={input}
-							onChange={(e) => setInput(e.target.value)}
+							onChange={handleInputChange}
-							onKeyDown={(e) => {
+							onKeyDown={handleKeyDown}
-								if (e.key === "Enter" && !e.shiftKey) {
-									e.preventDefault();
-									handleSubmit();
-								}
-							}}
 							placeholder="Send a message..."
 							rows={1}
 							style={{

frontend/src/components/ChatInputFilePicker.test.tsx

@@ -0,0 +1,194 @@
+import {
+	act,
+	fireEvent,
+	render,
+	screen,
+	waitFor,
+} from "@testing-library/react";
+import { beforeEach, describe, expect, it, vi } from "vitest";
+import { api } from "../api/client";
+import { ChatInput } from "./ChatInput";
+
+vi.mock("../api/client", () => ({
+	api: {
+		listProjectFiles: vi.fn(),
+	},
+}));
+
+const mockedListProjectFiles = vi.mocked(api.listProjectFiles);
+
+const defaultProps = {
+	loading: false,
+	queuedMessages: [],
+	onSubmit: vi.fn(),
+	onCancel: vi.fn(),
+	onRemoveQueuedMessage: vi.fn(),
+};
+
+beforeEach(() => {
+	vi.clearAllMocks();
+	mockedListProjectFiles.mockResolvedValue([
+		"src/main.rs",
+		"src/lib.rs",
+		"frontend/index.html",
+		"README.md",
+	]);
+});
+
+describe("File picker overlay (Story 269 AC1)", () => {
+	it("shows file picker overlay when @ is typed", async () => {
+		render(<ChatInput {...defaultProps} />);
+		const textarea = screen.getByPlaceholderText("Send a message...");
+
+		await act(async () => {
+			fireEvent.change(textarea, { target: { value: "@" } });
+		});
+
+		await waitFor(() => {
+			expect(screen.getByTestId("file-picker-overlay")).toBeInTheDocument();
+		});
+	});
+
+	it("does not show file picker overlay for text without @", async () => {
+		render(<ChatInput {...defaultProps} />);
+		const textarea = screen.getByPlaceholderText("Send a message...");
+
+		await act(async () => {
+			fireEvent.change(textarea, { target: { value: "hello world" } });
+		});
+
+		expect(screen.queryByTestId("file-picker-overlay")).not.toBeInTheDocument();
+	});
+});
+
+describe("File picker fuzzy matching (Story 269 AC2)", () => {
+	it("filters files by query typed after @", async () => {
+		render(<ChatInput {...defaultProps} />);
+		const textarea = screen.getByPlaceholderText("Send a message...");
+
+		await act(async () => {
+			fireEvent.change(textarea, { target: { value: "@main" } });
+		});
+
+		await waitFor(() => {
+			expect(screen.getByTestId("file-picker-overlay")).toBeInTheDocument();
+		});
+
+		// main.rs should be visible, README.md should not
+		expect(screen.getByText("src/main.rs")).toBeInTheDocument();
+		expect(screen.queryByText("README.md")).not.toBeInTheDocument();
+	});
+
+	it("shows all files when @ is typed with no query", async () => {
+		render(<ChatInput {...defaultProps} />);
+		const textarea = screen.getByPlaceholderText("Send a message...");
+
+		await act(async () => {
+			fireEvent.change(textarea, { target: { value: "@" } });
+		});
+
+		await waitFor(() => {
+			expect(screen.getByTestId("file-picker-overlay")).toBeInTheDocument();
+		});
+
+		// All 4 files should be visible
+		expect(screen.getByText("src/main.rs")).toBeInTheDocument();
+		expect(screen.getByText("src/lib.rs")).toBeInTheDocument();
+		expect(screen.getByText("README.md")).toBeInTheDocument();
+	});
+});
+
+describe("File picker selection (Story 269 AC3)", () => {
+	it("clicking a file inserts @path into the message", async () => {
+		render(<ChatInput {...defaultProps} />);
+		const textarea = screen.getByPlaceholderText("Send a message...");
+
+		await act(async () => {
+			fireEvent.change(textarea, { target: { value: "@" } });
+		});
+
+		await waitFor(() => {
+			expect(screen.getByTestId("file-picker-item-0")).toBeInTheDocument();
+		});
+
+		await act(async () => {
+			fireEvent.click(screen.getByTestId("file-picker-item-0"));
+		});
+
+		// Picker should be dismissed and the file reference inserted
+		expect(screen.queryByTestId("file-picker-overlay")).not.toBeInTheDocument();
+		expect((textarea as HTMLTextAreaElement).value).toMatch(/^@\S+/);
+	});
+
+	it("Enter key selects highlighted file and inserts it into message", async () => {
+		render(<ChatInput {...defaultProps} />);
+		const textarea = screen.getByPlaceholderText("Send a message...");
+
+		await act(async () => {
+			fireEvent.change(textarea, { target: { value: "@main" } });
+		});
+
+		await waitFor(() => {
+			expect(screen.getByTestId("file-picker-overlay")).toBeInTheDocument();
+		});
+
+		await act(async () => {
+			fireEvent.keyDown(textarea, { key: "Enter" });
+		});
+
+		expect(screen.queryByTestId("file-picker-overlay")).not.toBeInTheDocument();
+		expect((textarea as HTMLTextAreaElement).value).toContain("@src/main.rs");
+	});
+});
+
+describe("File picker dismiss (Story 269 AC5)", () => {
+	it("Escape key dismisses the file picker", async () => {
+		render(<ChatInput {...defaultProps} />);
+		const textarea = screen.getByPlaceholderText("Send a message...");
+
+		await act(async () => {
+			fireEvent.change(textarea, { target: { value: "@" } });
+		});
+
+		await waitFor(() => {
+			expect(screen.getByTestId("file-picker-overlay")).toBeInTheDocument();
+		});
+
+		await act(async () => {
+			fireEvent.keyDown(textarea, { key: "Escape" });
+		});
+
+		expect(screen.queryByTestId("file-picker-overlay")).not.toBeInTheDocument();
+	});
+});
+
+describe("Multiple @ references (Story 269 AC6)", () => {
+	it("typing @ after a completed reference triggers picker again", async () => {
+		render(<ChatInput {...defaultProps} />);
+		const textarea = screen.getByPlaceholderText("Send a message...");
+
+		// First reference
+		await act(async () => {
+			fireEvent.change(textarea, { target: { value: "@main" } });
+		});
+
+		await waitFor(() => {
+			expect(screen.getByTestId("file-picker-overlay")).toBeInTheDocument();
+		});
+
+		// Select file
+		await act(async () => {
+			fireEvent.keyDown(textarea, { key: "Enter" });
+		});
+
+		// Type a second @
+		await act(async () => {
+			const current = (textarea as HTMLTextAreaElement).value;
+			fireEvent.change(textarea, { target: { value: `${current} @` } });
+		});
+
+		await waitFor(() => {
+			expect(screen.getByTestId("file-picker-overlay")).toBeInTheDocument();
+		});
+	});
+});

frontend/src/components/WorkItemDetailPanel.test.tsx

@@ -37,6 +37,7 @@ const DEFAULT_CONTENT = {
 	content: "# Big Title\n\nSome content here.",
 	stage: "current",
 	name: "Big Title Story",
+	agent: null,
 };
 
 const sampleTestResults: TestResultsResponse = {
@@ -436,6 +437,60 @@ describe("WorkItemDetailPanel - Agent Logs", () => {
 	});
 });
 
+describe("WorkItemDetailPanel - Assigned Agent", () => {
+	it("shows assigned agent name when agent front matter field is set", async () => {
+		mockedGetWorkItemContent.mockResolvedValue({
+			...DEFAULT_CONTENT,
+			agent: "coder-opus",
+		});
+
+		render(
+			<WorkItemDetailPanel
+				storyId="271_story_test"
+				pipelineVersion={0}
+				onClose={() => {}}
+			/>,
+		);
+
+		const agentEl = await screen.findByTestId("detail-panel-assigned-agent");
+		expect(agentEl).toHaveTextContent("coder-opus");
+	});
+
+	it("omits assigned agent field when no agent is set in front matter", async () => {
+		render(
+			<WorkItemDetailPanel
+				storyId="271_story_test"
+				pipelineVersion={0}
+				onClose={() => {}}
+			/>,
+		);
+
+		await screen.findByTestId("detail-panel-content");
+		expect(
+			screen.queryByTestId("detail-panel-assigned-agent"),
+		).not.toBeInTheDocument();
+	});
+
+	it("shows the specific agent name not just 'assigned'", async () => {
+		mockedGetWorkItemContent.mockResolvedValue({
+			...DEFAULT_CONTENT,
+			agent: "coder-haiku",
+		});
+
+		render(
+			<WorkItemDetailPanel
+				storyId="271_story_test"
+				pipelineVersion={0}
+				onClose={() => {}}
+			/>,
+		);
+
+		const agentEl = await screen.findByTestId("detail-panel-assigned-agent");
+		expect(agentEl).toHaveTextContent("coder-haiku");
+		expect(agentEl).not.toHaveTextContent("assigned");
+	});
+});
+
 describe("WorkItemDetailPanel - Test Results", () => {
 	it("shows empty test results message when no results exist", async () => {
 		mockedGetTestResults.mockResolvedValue(null);

frontend/src/components/WorkItemDetailPanel.tsx

@@ -113,6 +113,7 @@ export function WorkItemDetailPanel({
 	const [content, setContent] = useState<string | null>(null);
 	const [stage, setStage] = useState<string>("");
 	const [name, setName] = useState<string | null>(null);
+	const [assignedAgent, setAssignedAgent] = useState<string | null>(null);
 	const [loading, setLoading] = useState(true);
 	const [error, setError] = useState<string | null>(null);
 	const [agentInfo, setAgentInfo] = useState<AgentInfo | null>(null);
@@ -133,6 +134,7 @@ export function WorkItemDetailPanel({
 				setContent(data.content);
 				setStage(data.stage);
 				setName(data.name);
+				setAssignedAgent(data.agent);
 			})
 			.catch((err: unknown) => {
 				setError(err instanceof Error ? err.message : "Failed to load content");
@@ -278,6 +280,14 @@ export function WorkItemDetailPanel({
 							{stageLabel}
 						</div>
 					)}
+					{assignedAgent ? (
+						<div
+							data-testid="detail-panel-assigned-agent"
+							style={{ fontSize: "0.75em", color: "#888" }}
+						>
+							Agent: {assignedAgent}
+						</div>
+					) : null}
 				</div>
 				<button
 					type="button"

frontend/vite.config.ts

@@ -16,8 +16,25 @@ export default defineConfig(() => {
         "/api": {
           target: `http://127.0.0.1:${String(backendPort)}`,
           timeout: 120000,
+          configure: (proxy) => {
+            proxy.on("error", (_err) => {
+              // Swallow proxy errors (e.g. ECONNREFUSED during backend restart)
+              // so the vite dev server doesn't crash.
+            });
+          },
         },
       },
+      watch: {
+        ignored: [
+          "**/.story_kit/**",
+          "**/target/**",
+          "**/.git/**",
+          "**/server/**",
+          "**/Cargo.*",
+          "**/vendor/**",
+          "**/node_modules/**",
+        ],
+      },
     },
     build: {
       outDir: "dist",

script/release

@@ -71,20 +71,93 @@ ls -lh "${DIST}"/
 echo "==> Generating changelog..."
 PREV_TAG=$(git describe --tags --abbrev=0 2>/dev/null || echo "")
 if [ -n "$PREV_TAG" ]; then
-  CHANGELOG=$(git log "${PREV_TAG}..HEAD" --pretty=format:"- %s" --no-merges)
+  LOG_RANGE="${PREV_TAG}..HEAD"
   RANGE="${PREV_TAG}...${TAG}"
 else
-  CHANGELOG=$(git log --pretty=format:"- %s" --no-merges)
+  LOG_RANGE=""
   RANGE="initial...${TAG}"
 fi
 
-if [ -z "$CHANGELOG" ]; then
+# Extract completed stories/bugs/refactors from "story-kit: merge <id>" commits.
-  CHANGELOG="- No changes since last release"
+# Deduplicate (a story may have been merged more than once after reverts).
+if [ -n "$LOG_RANGE" ]; then
+  MERGED_RAW=$(git log "$LOG_RANGE" --pretty=format:"%s" --no-merges \
+    | grep "^story-kit: merge " | sed 's/^story-kit: merge //' | sort -u)
+else
+  MERGED_RAW=$(git log --pretty=format:"%s" --no-merges \
+    | grep "^story-kit: merge " | sed 's/^story-kit: merge //' | sort -u)
 fi
 
-RELEASE_BODY="## What's Changed
+# Categorise merged work items and format names.
+FEATURES=""
+FIXES=""
+REFACTORS=""
+while IFS= read -r item; do
+  [ -z "$item" ] && continue
+  # Strip the numeric prefix and type to get the human name.
+  name=$(echo "$item" | sed -E 's/^[0-9]+_(story|bug|refactor|spike)_//' | tr '_' ' ')
+  # Capitalise first letter.
+  name="$(echo "${name:0:1}" | tr '[:lower:]' '[:upper:]')${name:1}"
+  case "$item" in
+    *_bug_*)     FIXES="${FIXES}- ${name}\n" ;;
+    *_refactor_*) REFACTORS="${REFACTORS}- ${name}\n" ;;
+    *)           FEATURES="${FEATURES}- ${name}\n" ;;
+  esac
+done <<< "$MERGED_RAW"
 
-${CHANGELOG}
+# Collect non-automation manual commits (direct fixes, version bumps, etc).
+if [ -n "$LOG_RANGE" ]; then
+  MANUAL=$(git log "$LOG_RANGE" --pretty=format:"%s" --no-merges \
+    | grep -v "^story-kit: " \
+    | grep -v "^Revert \"story-kit: " \
+    | grep -v "^Bump version" \
+    | sed 's/^/- /')
+else
+  MANUAL=$(git log --pretty=format:"%s" --no-merges \
+    | grep -v "^story-kit: " \
+    | grep -v "^Revert \"story-kit: " \
+    | grep -v "^Bump version" \
+    | sed 's/^/- /')
+fi
+
+# Assemble the release body.
+RELEASE_BODY="## What's Changed"
+
+if [ -n "$FEATURES" ]; then
+  RELEASE_BODY="${RELEASE_BODY}
+
+### Features
+$(echo -e "$FEATURES")"
+fi
+
+if [ -n "$FIXES" ]; then
+  RELEASE_BODY="${RELEASE_BODY}
+
+### Bug Fixes
+$(echo -e "$FIXES")"
+fi
+
+if [ -n "$REFACTORS" ]; then
+  RELEASE_BODY="${RELEASE_BODY}
+
+### Refactors
+$(echo -e "$REFACTORS")"
+fi
+
+if [ -n "$MANUAL" ]; then
+  RELEASE_BODY="${RELEASE_BODY}
+
+### Other Changes
+${MANUAL}"
+fi
+
+if [ -z "$FEATURES" ] && [ -z "$FIXES" ] && [ -z "$REFACTORS" ] && [ -z "$MANUAL" ]; then
+  RELEASE_BODY="${RELEASE_BODY}
+
+- No changes since last release"
+fi
+
+RELEASE_BODY="${RELEASE_BODY}
 
 **Full diff:** ${GITEA_URL}/${REPO}/compare/${RANGE}"
 

script/test

@@ -8,10 +8,16 @@ echo "=== Running Rust tests ==="
 cargo test --manifest-path "$PROJECT_ROOT/Cargo.toml"
 
 echo "=== Running frontend unit tests ==="
-cd "$PROJECT_ROOT/frontend"
+if [ -d "$PROJECT_ROOT/frontend" ]; then
-npm test
+  cd "$PROJECT_ROOT/frontend"
+  npm test
+else
+  echo "Skipping frontend tests (no frontend directory)"
+fi
 
 # Disabled: e2e tests may be causing merge pipeline hangs (no running server
 # in merge workspace → Playwright blocks indefinitely). Re-enable once confirmed.
+# Disabled: e2e tests cause merge pipeline hangs (no running server
+# in merge workspace → Playwright blocks indefinitely).
 # echo "=== Running e2e tests ==="
 # npm run test:e2e

server/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "story-kit"
-version = "0.1.0"
+version = "0.3.1"
 edition = "2024"
 build = "build.rs"
 

server/src/agents/gates.rs

@@ -93,6 +93,10 @@ pub(crate) fn run_project_tests(path: &Path) -> Result<(bool, String), String> {
 
 /// Run a command with a timeout. Returns `(success, combined_output)`.
 /// Kills the child process if it exceeds `TEST_TIMEOUT`.
+///
+/// Stdout and stderr are drained in background threads to avoid a pipe-buffer
+/// deadlock: if the child fills the 64 KB OS pipe buffer while the parent
+/// blocks on `waitpid`, neither side can make progress.
 fn run_command_with_timeout(
     program: impl AsRef<std::ffi::OsStr>,
     args: &[&str],
@@ -106,19 +110,32 @@ fn run_command_with_timeout(
         .spawn()
         .map_err(|e| format!("Failed to spawn command: {e}"))?;
 
+    // Drain stdout/stderr in background threads so the pipe buffers never fill.
+    let stdout_handle = child.stdout.take().map(|r| {
+        std::thread::spawn(move || {
+            let mut s = String::new();
+            let mut r = r;
+            std::io::Read::read_to_string(&mut r, &mut s).ok();
+            s
+        })
+    });
+    let stderr_handle = child.stderr.take().map(|r| {
+        std::thread::spawn(move || {
+            let mut s = String::new();
+            let mut r = r;
+            std::io::Read::read_to_string(&mut r, &mut s).ok();
+            s
+        })
+    });
+
     match child.wait_timeout(TEST_TIMEOUT) {
         Ok(Some(status)) => {
-            // Process exited within the timeout — collect output.
+            let stdout = stdout_handle
-            let stdout = child.stdout.take().map(|mut r| {
+                .and_then(|h| h.join().ok())
-                let mut s = String::new();
+                .unwrap_or_default();
-                std::io::Read::read_to_string(&mut r, &mut s).ok();
+            let stderr = stderr_handle
-                s
+                .and_then(|h| h.join().ok())
-            }).unwrap_or_default();
+                .unwrap_or_default();
-            let stderr = child.stderr.take().map(|mut r| {
-                let mut s = String::new();
-                std::io::Read::read_to_string(&mut r, &mut s).ok();
-                s
-            }).unwrap_or_default();
             Ok((status.success(), format!("{stdout}{stderr}")))
         }
         Ok(None) => {

server/src/agents/lifecycle.rs

@@ -4,8 +4,7 @@ use std::process::Command;
 use crate::io::story_metadata::clear_front_matter_field;
 use crate::slog;
 
-#[allow(dead_code)]
+pub(super) fn item_type_from_id(item_id: &str) -> &'static str {
-fn item_type_from_id(item_id: &str) -> &'static str {
     // New format: {digits}_{type}_{slug}
     let after_num = item_id.trim_start_matches(|c: char| c.is_ascii_digit());
     if after_num.starts_with("_bug_") {

server/src/agents/merge.rs

@@ -1,5 +1,6 @@
 use std::path::Path;
 use std::process::Command;
+use std::sync::Mutex;
 
 use serde::Serialize;
 
@@ -7,6 +8,29 @@ use crate::config::ProjectConfig;
 
 use super::gates::run_project_tests;
 
+/// Global lock ensuring only one squash-merge runs at a time.
+///
+/// The merge pipeline uses a shared `.story_kit/merge_workspace` directory and
+/// temporary `merge-queue/{story_id}` branches.  If two merges run concurrently,
+/// the second call's initial cleanup destroys the first call's branch mid-flight,
+/// causing `git cherry-pick merge-queue/…` to fail with "bad revision".
+static MERGE_LOCK: Mutex<()> = Mutex::new(());
+
+/// Status of an async merge job.
+#[derive(Debug, Clone, Serialize)]
+pub enum MergeJobStatus {
+    Running,
+    Completed(MergeReport),
+    Failed(String),
+}
+
+/// Tracks a background merge job started by `merge_agent_work`.
+#[derive(Debug, Clone, Serialize)]
+pub struct MergeJob {
+    pub story_id: String,
+    pub status: MergeJobStatus,
+}
+
 /// Result of a mergemaster merge operation.
 #[derive(Debug, Serialize, Clone)]
 pub struct MergeReport {
@@ -57,6 +81,11 @@ pub(crate) fn run_squash_merge(
     branch: &str,
     story_id: &str,
 ) -> Result<SquashMergeResult, String> {
+    // Acquire the merge lock so concurrent calls don't clobber each other.
+    let _lock = MERGE_LOCK
+        .lock()
+        .map_err(|e| format!("Merge lock poisoned: {e}"))?;
+
     let mut all_output = String::new();
     let merge_branch = format!("merge-queue/{story_id}");
     let merge_wt_path = project_root

server/src/agents/pool.rs

@@ -124,6 +124,10 @@ pub struct AgentPool {
     /// an `AgentStateChanged` event is emitted so the frontend can refresh the
     /// pipeline board without waiting for a filesystem event.
     watcher_tx: broadcast::Sender<WatcherEvent>,
+    /// Tracks background merge jobs started by `merge_agent_work`, keyed by story_id.
+    /// The MCP tool returns immediately and the mergemaster agent polls
+    /// `get_merge_status` until the job reaches a terminal state.
+    merge_jobs: Arc<Mutex<HashMap<String, super::merge::MergeJob>>>,
 }
 
 impl AgentPool {
@@ -133,6 +137,7 @@ impl AgentPool {
             port,
             child_killers: Arc::new(Mutex::new(HashMap::new())),
             watcher_tx,
+            merge_jobs: Arc::new(Mutex::new(HashMap::new())),
         }
     }
 
@@ -884,21 +889,39 @@ impl AgentPool {
                     };
 
                     if coverage_passed {
-                        slog!(
+                        // Spikes skip merge — they stay in 3_qa/ for human review.
-                            "[pipeline] QA passed gates and coverage for '{story_id}'. Moving to merge."
+                        if super::lifecycle::item_type_from_id(story_id) == "spike" {
-                        );
+                            // Mark the spike as held for review so auto-assign won't
-                        if let Err(e) = super::lifecycle::move_story_to_merge(&project_root, story_id) {
+                            // restart QA on it.
-                            slog_error!("[pipeline] Failed to move '{story_id}' to 4_merge/: {e}");
+                            let qa_dir = project_root.join(".story_kit/work/3_qa");
-                            return;
+                            let spike_path = qa_dir.join(format!("{story_id}.md"));
+                            if let Err(e) = crate::io::story_metadata::write_review_hold(&spike_path) {
+                                slog_error!("[pipeline] Failed to set review_hold on '{story_id}': {e}");
+                            }
+                            slog!(
+                                "[pipeline] QA passed for spike '{story_id}'. \
+                                 Stopping for human review (skipping merge). \
+                                 Worktree preserved at: {worktree_path:?}"
+                            );
+                            // Free up the QA slot without advancing the spike.
+                            self.auto_assign_available_work(&project_root).await;
+                        } else {
+                            slog!(
+                                "[pipeline] QA passed gates and coverage for '{story_id}'. Moving to merge."
+                            );
+                            if let Err(e) = super::lifecycle::move_story_to_merge(&project_root, story_id) {
+                                slog_error!("[pipeline] Failed to move '{story_id}' to 4_merge/: {e}");
+                                return;
+                            }
+                            if let Err(e) = self
+                                .start_agent(&project_root, story_id, Some("mergemaster"), None)
+                                .await
+                            {
+                                slog_error!("[pipeline] Failed to start mergemaster for '{story_id}': {e}");
+                            }
+                            // QA slot is now free — pick up any other unassigned work in 3_qa/.
+                            self.auto_assign_available_work(&project_root).await;
                         }
-                        if let Err(e) = self
-                            .start_agent(&project_root, story_id, Some("mergemaster"), None)
-                            .await
-                        {
-                            slog_error!("[pipeline] Failed to start mergemaster for '{story_id}': {e}");
-                        }
-                        // QA slot is now free — pick up any other unassigned work in 3_qa/.
-                        self.auto_assign_available_work(&project_root).await;
                     } else {
                         slog!(
                             "[pipeline] QA coverage gate failed for '{story_id}'. Restarting QA."
@@ -1110,6 +1133,7 @@ impl AgentPool {
             port: self.port,
             child_killers: Arc::clone(&self.child_killers),
             watcher_tx: self.watcher_tx.clone(),
+            merge_jobs: Arc::clone(&self.merge_jobs),
         };
         let sid = story_id.to_string();
         let aname = agent_name.to_string();
@@ -1138,8 +1162,71 @@ impl AgentPool {
     /// 4. If gates pass: cherry-pick the squash commit onto master and archive the story.
     ///
     /// Returns a `MergeReport` with full details of what happened.
-    pub async fn merge_agent_work(
+    /// Start the merge pipeline as a background task.
-        &self,
+    ///
+    /// Returns immediately so the MCP tool call doesn't time out (the full
+    /// pipeline — squash merge + quality gates — takes well over 60 seconds,
+    /// exceeding Claude Code's MCP tool-call timeout).
+    ///
+    /// The mergemaster agent should poll [`get_merge_status`](Self::get_merge_status)
+    /// until the job reaches a terminal state.
+    pub fn start_merge_agent_work(
+        self: &Arc<Self>,
+        project_root: &Path,
+        story_id: &str,
+    ) -> Result<(), String> {
+        // Guard against double-starts.
+        {
+            let jobs = self.merge_jobs.lock().map_err(|e| e.to_string())?;
+            if let Some(job) = jobs.get(story_id)
+                && matches!(job.status, super::merge::MergeJobStatus::Running)
+            {
+                return Err(format!(
+                    "Merge already in progress for '{story_id}'. \
+                     Use get_merge_status to poll for completion."
+                ));
+            }
+        }
+
+        // Insert Running job.
+        {
+            let mut jobs = self.merge_jobs.lock().map_err(|e| e.to_string())?;
+            jobs.insert(
+                story_id.to_string(),
+                super::merge::MergeJob {
+                    story_id: story_id.to_string(),
+                    status: super::merge::MergeJobStatus::Running,
+                },
+            );
+        }
+
+        let pool = Arc::clone(self);
+        let root = project_root.to_path_buf();
+        let sid = story_id.to_string();
+
+        tokio::spawn(async move {
+            let report = pool.run_merge_pipeline(&root, &sid).await;
+            let failed = report.is_err();
+            let status = match report {
+                Ok(r) => super::merge::MergeJobStatus::Completed(r),
+                Err(e) => super::merge::MergeJobStatus::Failed(e),
+            };
+            if let Ok(mut jobs) = pool.merge_jobs.lock()
+                && let Some(job) = jobs.get_mut(&sid)
+            {
+                job.status = status;
+            }
+            if failed {
+                pool.auto_assign_available_work(&root).await;
+            }
+        });
+
+        Ok(())
+    }
+
+    /// The actual merge pipeline, run inside a background task.
+    async fn run_merge_pipeline(
+        self: &Arc<Self>,
         project_root: &Path,
         story_id: &str,
     ) -> Result<super::merge::MergeReport, String> {
@@ -1149,8 +1236,6 @@ impl AgentPool {
         let sid = story_id.to_string();
         let br = branch.clone();
 
-        // Run blocking operations (git + cargo + quality gates) off the async runtime.
-        // Quality gates now run inside run_squash_merge before the fast-forward.
         let merge_result =
             tokio::task::spawn_blocking(move || super::merge::run_squash_merge(&root, &br, &sid))
                 .await
@@ -1170,13 +1255,11 @@ impl AgentPool {
             });
         }
 
-        // Merge + gates both passed — archive the story and clean up agent entries.
         let story_archived = super::lifecycle::move_story_to_archived(project_root, story_id).is_ok();
         if story_archived {
             self.remove_agents_for_story(story_id);
         }
 
-        // Clean up the worktree if it exists.
         let worktree_cleaned_up = if wt_path.exists() {
             let config = crate::config::ProjectConfig::load(project_root)
                 .unwrap_or_default();
@@ -1187,10 +1270,6 @@ impl AgentPool {
             false
         };
 
-        // Mergemaster slot is now free — trigger auto-assign so remaining
-        // items in 4_merge/ (or other stages) get picked up.  The normal
-        // server-owned completion handler won't run because we already
-        // removed the agent entry above.
         self.auto_assign_available_work(project_root).await;
 
         Ok(super::merge::MergeReport {
@@ -1206,9 +1285,12 @@ impl AgentPool {
         })
     }
 
-    /// Return the port this server is running on.
+    /// Check the status of a background merge job.
-    pub fn port(&self) -> u16 {
+    pub fn get_merge_status(&self, story_id: &str) -> Option<super::merge::MergeJob> {
-        self.port
+        self.merge_jobs
+            .lock()
+            .ok()
+            .and_then(|jobs| jobs.get(story_id).cloned())
     }
 
     /// Get project root helper.
@@ -1375,15 +1457,23 @@ impl AgentPool {
             }
 
             for story_id in &items {
+                // Items marked with review_hold (e.g. spikes after QA passes) stay
+                // in their current stage for human review — don't auto-assign agents.
+                if has_review_hold(project_root, stage_dir, story_id) {
+                    continue;
+                }
+
                 // Re-acquire the lock on each iteration to see state changes
                 // from previous start_agent calls in the same pass.
                 let preferred_agent =
                     read_story_front_matter_agent(project_root, stage_dir, story_id);
 
-                // Outcome: (already_assigned, chosen_agent, preferred_busy)
+                // Outcome: (already_assigned, chosen_agent, preferred_busy, stage_mismatch)
                 // preferred_busy=true means the story has a specific agent requested but it is
                 // currently occupied — the story should wait rather than fall back.
-                let (already_assigned, free_agent, preferred_busy) = {
+                // stage_mismatch=true means the preferred agent's stage doesn't match the
+                // pipeline stage, so we fell back to a generic stage agent.
+                let (already_assigned, free_agent, preferred_busy, stage_mismatch) = {
                     let agents = match self.agents.lock() {
                         Ok(a) => a,
                         Err(e) => {
@@ -1393,18 +1483,29 @@ impl AgentPool {
                     };
                     let assigned = is_story_assigned_for_stage(&config, &agents, story_id, stage);
                     if assigned {
-                        (true, None, false)
+                        (true, None, false, false)
                     } else if let Some(ref pref) = preferred_agent {
                         // Story has a front-matter agent preference.
-                        if is_agent_free(&agents, pref) {
+                        // Verify the preferred agent's stage matches the current
-                            (false, Some(pref.clone()), false)
+                        // pipeline stage — a coder shouldn't be assigned to QA.
+                        let pref_stage_matches = config
+                            .find_agent(pref)
+                            .map(|cfg| agent_config_stage(cfg) == *stage)
+                            .unwrap_or(false);
+                        if !pref_stage_matches {
+                            // Stage mismatch — fall back to any free agent for this stage.
+                            let free = find_free_agent_for_stage(&config, &agents, stage)
+                                .map(|s| s.to_string());
+                            (false, free, false, true)
+                        } else if is_agent_free(&agents, pref) {
+                            (false, Some(pref.clone()), false, false)
                         } else {
-                            (false, None, true)
+                            (false, None, true, false)
                         }
                     } else {
                         let free = find_free_agent_for_stage(&config, &agents, stage)
                             .map(|s| s.to_string());
-                        (false, free, false)
+                        (false, free, false, false)
                     }
                 };
 
@@ -1423,6 +1524,13 @@ impl AgentPool {
                     continue;
                 }
 
+                if stage_mismatch {
+                    slog!(
+                        "[auto-assign] Preferred agent '{}' stage mismatch for '{story_id}' in {stage_dir}/; falling back to stage-appropriate agent.",
+                        preferred_agent.as_deref().unwrap_or("?")
+                    );
+                }
+
                 match free_agent {
                     Some(agent_name) => {
                         slog!(
@@ -1638,7 +1746,25 @@ impl AgentPool {
                 };
 
                 if coverage_passed {
-                    if let Err(e) = super::lifecycle::move_story_to_merge(project_root, story_id) {
+                    // Spikes skip the merge stage — stay in 3_qa/ for human review.
+                    if super::lifecycle::item_type_from_id(story_id) == "spike" {
+                        let spike_path = project_root
+                            .join(".story_kit/work/3_qa")
+                            .join(format!("{story_id}.md"));
+                        if let Err(e) = crate::io::story_metadata::write_review_hold(&spike_path) {
+                            eprintln!(
+                                "[startup:reconcile] Failed to set review_hold on spike '{story_id}': {e}"
+                            );
+                        }
+                        eprintln!(
+                            "[startup:reconcile] Spike '{story_id}' passed QA — holding for human review."
+                        );
+                        let _ = progress_tx.send(ReconciliationEvent {
+                            story_id: story_id.clone(),
+                            status: "review_hold".to_string(),
+                            message: "Spike passed QA — waiting for human review.".to_string(),
+                        });
+                    } else if let Err(e) = super::lifecycle::move_story_to_merge(project_root, story_id) {
                         eprintln!(
                             "[startup:reconcile] Failed to move '{story_id}' to 4_merge/: {e}"
                         );
@@ -1853,6 +1979,24 @@ fn read_story_front_matter_agent(project_root: &Path, stage_dir: &str, story_id:
     parse_front_matter(&contents).ok()?.agent
 }
 
+/// Return `true` if the story file in the given stage has `review_hold: true` in its front matter.
+fn has_review_hold(project_root: &Path, stage_dir: &str, story_id: &str) -> bool {
+    use crate::io::story_metadata::parse_front_matter;
+    let path = project_root
+        .join(".story_kit")
+        .join("work")
+        .join(stage_dir)
+        .join(format!("{story_id}.md"));
+    let contents = match std::fs::read_to_string(path) {
+        Ok(c) => c,
+        Err(_) => return false,
+    };
+    parse_front_matter(&contents)
+        .ok()
+        .and_then(|m| m.review_hold)
+        .unwrap_or(false)
+}
+
 /// Return `true` if `agent_name` has no active (pending/running) entry in the pool.
 fn is_agent_free(agents: &HashMap<String, StoryAgent>, agent_name: &str) -> bool {
     !agents.values().any(|a| {
@@ -2128,6 +2272,7 @@ fn spawn_pipeline_advance(
             port,
             child_killers: Arc::new(Mutex::new(HashMap::new())),
             watcher_tx,
+            merge_jobs: Arc::new(Mutex::new(HashMap::new())),
         };
         pool.run_pipeline_advance(
             &sid,
@@ -2144,6 +2289,7 @@ fn spawn_pipeline_advance(
 #[cfg(test)]
 mod tests {
     use super::*;
+    use crate::agents::merge::{MergeJob, MergeJobStatus};
     use crate::agents::{
         AgentEvent, AgentStatus, CompletionReport, PipelineStage, ReconciliationEvent,
         lifecycle::move_story_to_archived,
@@ -4087,6 +4233,23 @@ stage = "coder"
 
     // ── merge_agent_work tests ────────────────────────────────────────────────
 
+    /// Helper: start a merge and poll until terminal state.
+    async fn run_merge_to_completion(
+        pool: &Arc<AgentPool>,
+        repo: &std::path::Path,
+        story_id: &str,
+    ) -> MergeJob {
+        pool.start_merge_agent_work(repo, story_id).unwrap();
+        loop {
+            tokio::time::sleep(std::time::Duration::from_millis(50)).await;
+            if let Some(job) = pool.get_merge_status(story_id)
+                && !matches!(job.status, MergeJobStatus::Running)
+            {
+                return job;
+            }
+        }
+    }
+
     #[tokio::test]
     async fn merge_agent_work_returns_error_when_branch_not_found() {
         use tempfile::tempdir;
@@ -4095,14 +4258,19 @@ stage = "coder"
         let repo = tmp.path();
         init_git_repo(repo);
 
-        let pool = AgentPool::new_test(3001);
+        let pool = Arc::new(AgentPool::new_test(3001));
-        // branch feature/story-99_nonexistent does not exist
+        let job = run_merge_to_completion(&pool, repo, "99_nonexistent").await;
-        let result = pool
+        match &job.status {
-            .merge_agent_work(repo, "99_nonexistent")
+            MergeJobStatus::Completed(report) => {
-            .await
+                assert!(!report.success, "should fail when branch missing");
-            .unwrap();
+            }
-        // Should fail (no branch) — not panic
+            MergeJobStatus::Failed(_) => {
-        assert!(!result.success, "should fail when branch missing");
+                // Also acceptable — the pipeline errored out
+            }
+            MergeJobStatus::Running => {
+                panic!("should not still be running");
+            }
+        }
     }
 
     #[tokio::test]
@@ -4155,22 +4323,29 @@ stage = "coder"
             .output()
             .unwrap();
 
-        let pool = AgentPool::new_test(3001);
+        let pool = Arc::new(AgentPool::new_test(3001));
-        let report = pool.merge_agent_work(repo, "23_test").await.unwrap();
+        let job = run_merge_to_completion(&pool, repo, "23_test").await;
 
-        // Merge should succeed (gates will run but cargo/pnpm results will depend on env)
+        match &job.status {
-        // At minimum the merge itself should succeed
+            MergeJobStatus::Completed(report) => {
-        assert!(!report.had_conflicts, "should have no conflicts");
+                assert!(!report.had_conflicts, "should have no conflicts");
-        // Note: gates_passed may be false in test env without Rust project, that's OK
+                assert!(
-        // The important thing is the merge itself ran
+                    report.success || report.gate_output.contains("Failed to run") || !report.gates_passed,
-        assert!(
+                    "report should be coherent: {report:?}"
-            report.success || report.gate_output.contains("Failed to run") || !report.gates_passed,
+                );
-            "report should be coherent: {report:?}"
+                if report.story_archived {
-        );
+                    let done = repo.join(".story_kit/work/5_done/23_test.md");
-        // Story should be in done if gates passed
+                    assert!(done.exists(), "done file should exist");
-        if report.story_archived {
+                }
-            let done = repo.join(".story_kit/work/5_done/23_test.md");
+            }
-            assert!(done.exists(), "done file should exist");
+            MergeJobStatus::Failed(e) => {
+                // Gate failures are acceptable in test env
+                assert!(
+                    e.contains("Failed") || e.contains("failed"),
+                    "unexpected failure: {e}"
+                );
+            }
+            MergeJobStatus::Running => panic!("should not still be running"),
         }
     }
 
@@ -4348,8 +4523,8 @@ stage = "coder"
             .output()
             .unwrap();
 
-        let pool = AgentPool::new_test(3001);
+        let pool = Arc::new(AgentPool::new_test(3001));
-        let report = pool.merge_agent_work(repo, "42_story_foo").await.unwrap();
+        let job = run_merge_to_completion(&pool, repo, "42_story_foo").await;
 
         // Master should NEVER have conflict markers, regardless of merge outcome.
         let master_code = fs::read_to_string(repo.join("code.rs")).unwrap();
@@ -4363,7 +4538,15 @@ stage = "coder"
         );
 
         // The report should accurately reflect what happened.
-        assert!(report.had_conflicts, "should report conflicts");
+        match &job.status {
+            MergeJobStatus::Completed(report) => {
+                assert!(report.had_conflicts, "should report conflicts");
+            }
+            MergeJobStatus::Failed(_) => {
+                // Acceptable — merge aborted due to conflicts
+            }
+            MergeJobStatus::Running => panic!("should not still be running"),
+        }
     }
 
     // ── reconcile_on_startup tests ────────────────────────────────────────────
@@ -4513,4 +4696,202 @@ stage = "coder"
             "story should be in 2_current/ or 3_qa/ after reconciliation"
         );
     }
+
+    #[test]
+    fn has_review_hold_returns_true_when_set() {
+        let tmp = tempfile::tempdir().unwrap();
+        let qa_dir = tmp.path().join(".story_kit/work/3_qa");
+        std::fs::create_dir_all(&qa_dir).unwrap();
+        let spike_path = qa_dir.join("10_spike_research.md");
+        std::fs::write(
+            &spike_path,
+            "---\nname: Research spike\nreview_hold: true\n---\n# Spike\n",
+        )
+        .unwrap();
+        assert!(has_review_hold(tmp.path(), "3_qa", "10_spike_research"));
+    }
+
+    #[test]
+    fn has_review_hold_returns_false_when_not_set() {
+        let tmp = tempfile::tempdir().unwrap();
+        let qa_dir = tmp.path().join(".story_kit/work/3_qa");
+        std::fs::create_dir_all(&qa_dir).unwrap();
+        let spike_path = qa_dir.join("10_spike_research.md");
+        std::fs::write(
+            &spike_path,
+            "---\nname: Research spike\n---\n# Spike\n",
+        )
+        .unwrap();
+        assert!(!has_review_hold(tmp.path(), "3_qa", "10_spike_research"));
+    }
+
+    #[test]
+    fn has_review_hold_returns_false_when_file_missing() {
+        let tmp = tempfile::tempdir().unwrap();
+        assert!(!has_review_hold(tmp.path(), "3_qa", "99_spike_missing"));
+    }
+
+    /// Story 265: auto_assign_available_work must skip spikes in 3_qa/ that
+    /// have review_hold: true set in their front matter.
+    #[tokio::test]
+    async fn auto_assign_skips_spikes_with_review_hold() {
+        let tmp = tempfile::tempdir().unwrap();
+        let root = tmp.path();
+
+        // Create project.toml with a QA agent.
+        let sk = root.join(".story_kit");
+        std::fs::create_dir_all(&sk).unwrap();
+        std::fs::write(
+            sk.join("project.toml"),
+            "[[agents]]\nname = \"qa\"\nrole = \"qa\"\nmodel = \"test\"\nprompt = \"test\"\n",
+        )
+        .unwrap();
+
+        // Put a spike in 3_qa/ with review_hold: true.
+        let qa_dir = root.join(".story_kit/work/3_qa");
+        std::fs::create_dir_all(&qa_dir).unwrap();
+        std::fs::write(
+            qa_dir.join("20_spike_test.md"),
+            "---\nname: Test Spike\nreview_hold: true\n---\n# Spike\n",
+        )
+        .unwrap();
+
+        let (watcher_tx, _) = broadcast::channel::<WatcherEvent>(4);
+        let pool = AgentPool::new(3001, watcher_tx);
+
+        pool.auto_assign_available_work(root).await;
+
+        // No agent should have been started for the spike.
+        let agents = pool.agents.lock().unwrap();
+        assert!(
+            agents.is_empty(),
+            "No agents should be assigned to a spike with review_hold"
+        );
+    }
+
+    // ── Story 279: auto-assign respects agent stage from front matter ──────────
+
+    /// When a story in 3_qa/ has `agent: coder-1` in its front matter but
+    /// coder-1 is a coder-stage agent, auto-assign must NOT assign coder-1.
+    /// Instead it should fall back to a free QA-stage agent.
+    #[tokio::test]
+    async fn auto_assign_ignores_coder_preference_when_story_is_in_qa_stage() {
+        let tmp = tempfile::tempdir().unwrap();
+        let sk = tmp.path().join(".story_kit");
+        let qa_dir = sk.join("work/3_qa");
+        std::fs::create_dir_all(&qa_dir).unwrap();
+        std::fs::write(
+            sk.join("project.toml"),
+            "[[agent]]\nname = \"coder-1\"\nstage = \"coder\"\n\n\
+             [[agent]]\nname = \"qa-1\"\nstage = \"qa\"\n",
+        )
+        .unwrap();
+        // Story in 3_qa/ with a preferred coder-stage agent.
+        std::fs::write(
+            qa_dir.join("story-qa1.md"),
+            "---\nname: QA Story\nagent: coder-1\n---\n",
+        )
+        .unwrap();
+
+        let pool = AgentPool::new_test(3001);
+
+        pool.auto_assign_available_work(tmp.path()).await;
+
+        let agents = pool.agents.lock().unwrap();
+        // coder-1 must NOT have been assigned (wrong stage for 3_qa/).
+        let coder_assigned = agents
+            .values()
+            .any(|a| a.agent_name == "coder-1" && matches!(a.status, AgentStatus::Pending | AgentStatus::Running));
+        assert!(
+            !coder_assigned,
+            "coder-1 should not be assigned to a QA-stage story"
+        );
+        // qa-1 should have been assigned instead.
+        let qa_assigned = agents
+            .values()
+            .any(|a| a.agent_name == "qa-1" && matches!(a.status, AgentStatus::Pending | AgentStatus::Running));
+        assert!(
+            qa_assigned,
+            "qa-1 should be assigned as fallback for the QA-stage story"
+        );
+    }
+
+    /// When a story in 2_current/ has `agent: coder-1` in its front matter and
+    /// coder-1 is a coder-stage agent, auto-assign must respect the preference
+    /// and assign coder-1 (not fall back to some other coder).
+    #[tokio::test]
+    async fn auto_assign_respects_coder_preference_when_story_is_in_current_stage() {
+        let tmp = tempfile::tempdir().unwrap();
+        let sk = tmp.path().join(".story_kit");
+        let current_dir = sk.join("work/2_current");
+        std::fs::create_dir_all(&current_dir).unwrap();
+        std::fs::write(
+            sk.join("project.toml"),
+            "[[agent]]\nname = \"coder-1\"\nstage = \"coder\"\n\n\
+             [[agent]]\nname = \"coder-2\"\nstage = \"coder\"\n",
+        )
+        .unwrap();
+        // Story in 2_current/ with a preferred coder-1 agent.
+        std::fs::write(
+            current_dir.join("story-pref.md"),
+            "---\nname: Coder Story\nagent: coder-1\n---\n",
+        )
+        .unwrap();
+
+        let pool = AgentPool::new_test(3001);
+
+        pool.auto_assign_available_work(tmp.path()).await;
+
+        let agents = pool.agents.lock().unwrap();
+        // coder-1 should have been picked (it matches the stage and is preferred).
+        let coder1_assigned = agents
+            .values()
+            .any(|a| a.agent_name == "coder-1" && matches!(a.status, AgentStatus::Pending | AgentStatus::Running));
+        assert!(
+            coder1_assigned,
+            "coder-1 should be assigned when it matches the stage and is preferred"
+        );
+        // coder-2 must NOT be assigned (not preferred).
+        let coder2_assigned = agents
+            .values()
+            .any(|a| a.agent_name == "coder-2" && matches!(a.status, AgentStatus::Pending | AgentStatus::Running));
+        assert!(
+            !coder2_assigned,
+            "coder-2 should not be assigned when coder-1 is explicitly preferred"
+        );
+    }
+
+    /// When the preferred agent's stage mismatches and no other agent of the
+    /// correct stage is available, auto-assign must not start any agent for that
+    /// story (no panic, no error).
+    #[tokio::test]
+    async fn auto_assign_stage_mismatch_with_no_fallback_starts_no_agent() {
+        let tmp = tempfile::tempdir().unwrap();
+        let sk = tmp.path().join(".story_kit");
+        let qa_dir = sk.join("work/3_qa");
+        std::fs::create_dir_all(&qa_dir).unwrap();
+        // Only a coder agent is configured — no QA agent exists.
+        std::fs::write(
+            sk.join("project.toml"),
+            "[[agent]]\nname = \"coder-1\"\nstage = \"coder\"\n",
+        )
+        .unwrap();
+        // Story in 3_qa/ requests coder-1 (wrong stage) and no QA agent exists.
+        std::fs::write(
+            qa_dir.join("story-noqa.md"),
+            "---\nname: QA Story No Agent\nagent: coder-1\n---\n",
+        )
+        .unwrap();
+
+        let pool = AgentPool::new_test(3001);
+
+        // Must not panic.
+        pool.auto_assign_available_work(tmp.path()).await;
+
+        let agents = pool.agents.lock().unwrap();
+        assert!(
+            agents.is_empty(),
+            "No agent should be started when no stage-appropriate agent is available"
+        );
+    }
 }

server/src/http/agents.rs

@@ -68,6 +68,7 @@ struct WorkItemContentResponse {
     content: String,
     stage: String,
     name: Option<String>,
+    agent: Option<String>,
 }
 
 /// A single test case result for the OpenAPI response.
@@ -354,13 +355,14 @@ impl AgentsApi {
             if file_path.exists() {
                 let content = std::fs::read_to_string(&file_path)
                     .map_err(|e| bad_request(format!("Failed to read work item: {e}")))?;
-                let name = crate::io::story_metadata::parse_front_matter(&content)
+                let metadata = crate::io::story_metadata::parse_front_matter(&content).ok();
-                    .ok()
+                let name = metadata.as_ref().and_then(|m| m.name.clone());
-                    .and_then(|m| m.name);
+                let agent = metadata.and_then(|m| m.agent);
                 return Ok(Json(WorkItemContentResponse {
                     content,
                     stage: stage_name.to_string(),
                     name,
+                    agent,
                 }));
             }
         }

server/src/http/io.rs

@@ -103,6 +103,15 @@ impl IoApi {
         Ok(Json(home))
     }
 
+    /// List all files in the project recursively, respecting .gitignore.
+    #[oai(path = "/io/fs/files", method = "get")]
+    async fn list_project_files(&self) -> OpenApiResult<Json<Vec<String>>> {
+        let files = io_fs::list_project_files(&self.ctx.state)
+            .await
+            .map_err(bad_request)?;
+        Ok(Json(files))
+    }
+
     /// Search the currently open project for files containing the provided query string.
     #[oai(path = "/io/search", method = "post")]
     async fn search_files(
@@ -316,6 +325,53 @@ mod tests {
         );
     }
 
+    // --- list_project_files ---
+
+    #[tokio::test]
+    async fn list_project_files_returns_file_paths() {
+        let dir = TempDir::new().unwrap();
+        std::fs::create_dir(dir.path().join("src")).unwrap();
+        std::fs::write(dir.path().join("src/main.rs"), "fn main() {}").unwrap();
+        std::fs::write(dir.path().join("README.md"), "# readme").unwrap();
+
+        let api = make_api(&dir);
+        let result = api.list_project_files().await.unwrap();
+        let files = &result.0;
+
+        assert!(files.contains(&"README.md".to_string()));
+        assert!(files.contains(&"src/main.rs".to_string()));
+    }
+
+    #[tokio::test]
+    async fn list_project_files_excludes_directories() {
+        let dir = TempDir::new().unwrap();
+        std::fs::create_dir(dir.path().join("subdir")).unwrap();
+        std::fs::write(dir.path().join("file.txt"), "").unwrap();
+
+        let api = make_api(&dir);
+        let result = api.list_project_files().await.unwrap();
+        let files = &result.0;
+
+        assert!(files.contains(&"file.txt".to_string()));
+        // Directories should not appear
+        assert!(!files.iter().any(|f| f == "subdir"));
+    }
+
+    #[tokio::test]
+    async fn list_project_files_returns_sorted_paths() {
+        let dir = TempDir::new().unwrap();
+        std::fs::write(dir.path().join("z_last.txt"), "").unwrap();
+        std::fs::write(dir.path().join("a_first.txt"), "").unwrap();
+
+        let api = make_api(&dir);
+        let result = api.list_project_files().await.unwrap();
+        let files = &result.0;
+
+        let a_idx = files.iter().position(|f| f == "a_first.txt").unwrap();
+        let z_idx = files.iter().position(|f| f == "z_last.txt").unwrap();
+        assert!(a_idx < z_idx);
+    }
+
     // --- list_directory (project-scoped) ---
 
     #[tokio::test]
@@ -345,4 +401,5 @@ mod tests {
         let result = api.list_directory(payload).await;
         assert!(result.is_err());
     }
+
 }

server/src/http/mcp.rs

@@ -8,7 +8,7 @@ use crate::http::settings::get_editor_command_from_store;
 use crate::http::workflow::{
     add_criterion_to_file, check_criterion_in_file, create_bug_file, create_refactor_file,
     create_spike_file, create_story_file, list_bug_files, list_refactor_files,
-    load_upcoming_stories, update_story_in_file, validate_story_dirs,
+    load_pipeline_state, load_upcoming_stories, update_story_in_file, validate_story_dirs,
 };
 use crate::worktree;
 use crate::io::story_metadata::{parse_front_matter, parse_unchecked_todos, write_merge_failure};
@@ -19,6 +19,7 @@ use poem::web::Data;
 use poem::{Body, Request, Response};
 use serde::{Deserialize, Serialize};
 use serde_json::{json, Value};
+use std::collections::HashMap;
 use std::fs;
 use std::sync::Arc;
 
@@ -638,7 +639,7 @@ fn handle_tools_list(id: Option<Value>) -> JsonRpcResponse {
                 },
                 {
                     "name": "update_story",
-                    "description": "Update the user story text and/or description of an existing story file. Replaces the content of the '## User Story' and/or '## Description' section in place. Auto-commits via the filesystem watcher.",
+                    "description": "Update an existing story file. Can replace the '## User Story' and/or '## Description' section content, and/or set YAML front matter fields (e.g. agent, manual_qa). Auto-commits via the filesystem watcher.",
                     "inputSchema": {
                         "type": "object",
                         "properties": {
@@ -653,6 +654,17 @@ fn handle_tools_list(id: Option<Value>) -> JsonRpcResponse {
                             "description": {
                                 "type": "string",
                                 "description": "New description text to replace the '## Description' section content"
+                            },
+                            "agent": {
+                                "type": "string",
+                                "description": "Set or change the 'agent' YAML front matter field"
+                            },
+                            "front_matter": {
+                                "type": "object",
+                                "description": "Arbitrary YAML front matter key-value pairs to set or update",
+                                "additionalProperties": {
+                                    "type": "string"
+                                }
                             }
                         },
                         "required": ["story_id"]
@@ -766,7 +778,7 @@ fn handle_tools_list(id: Option<Value>) -> JsonRpcResponse {
                 },
                 {
                     "name": "merge_agent_work",
-                    "description": "Trigger the mergemaster pipeline for a completed story: squash-merge the feature branch into master, run quality gates (cargo clippy, cargo test, pnpm build, pnpm test), move the story from work/4_merge/ or work/2_current/ to work/5_done/, and clean up the worktree and branch. Reports success/failure with details including any conflicts found and gate output.",
+                    "description": "Start the mergemaster pipeline for a completed story as a background job. Returns immediately — poll get_merge_status(story_id) until the merge completes or fails. The pipeline squash-merges the feature branch into master, runs quality gates, moves the story to done, and cleans up.",
                     "inputSchema": {
                         "type": "object",
                         "properties": {
@@ -782,6 +794,20 @@ fn handle_tools_list(id: Option<Value>) -> JsonRpcResponse {
                         "required": ["story_id"]
                     }
                 },
+                {
+                    "name": "get_merge_status",
+                    "description": "Check the status of a merge_agent_work background job. Returns running/completed/failed. When completed, includes the full merge report with conflict details, gate output, and whether the story was archived.",
+                    "inputSchema": {
+                        "type": "object",
+                        "properties": {
+                            "story_id": {
+                                "type": "string",
+                                "description": "Story identifier (same as passed to merge_agent_work)"
+                            }
+                        },
+                        "required": ["story_id"]
+                    }
+                },
                 {
                     "name": "move_story_to_merge",
                     "description": "Move a story or bug from work/2_current/ to work/4_merge/ to queue it for the mergemaster pipeline and automatically spawn the mergemaster agent to squash-merge, run quality gates, and archive.",
@@ -836,6 +862,14 @@ fn handle_tools_list(id: Option<Value>) -> JsonRpcResponse {
                         "required": ["story_id"]
                     }
                 },
+                {
+                    "name": "get_pipeline_status",
+                    "description": "Return a structured snapshot of the full work item pipeline. Includes all active stages (current, qa, merge, done) with each item's stage, name, and assigned agent. Also includes upcoming backlog items.",
+                    "inputSchema": {
+                        "type": "object",
+                        "properties": {}
+                    }
+                },
                 {
                     "name": "get_server_logs",
                     "description": "Return recent server log lines captured in the in-process ring buffer. Useful for diagnosing runtime behaviour such as WebSocket events, MCP call flow, and filesystem watcher activity.",
@@ -931,11 +965,14 @@ async fn handle_tools_call(
         "create_refactor" => tool_create_refactor(&args, ctx),
         "list_refactors" => tool_list_refactors(ctx),
         // Mergemaster tools
-        "merge_agent_work" => tool_merge_agent_work(&args, ctx).await,
+        "merge_agent_work" => tool_merge_agent_work(&args, ctx),
+        "get_merge_status" => tool_get_merge_status(&args, ctx),
         "move_story_to_merge" => tool_move_story_to_merge(&args, ctx).await,
         "report_merge_failure" => tool_report_merge_failure(&args, ctx),
         // QA tools
         "request_qa" => tool_request_qa(&args, ctx).await,
+        // Pipeline status
+        "get_pipeline_status" => tool_get_pipeline_status(ctx),
         // Diagnostics
         "get_server_logs" => tool_get_server_logs(&args),
         // Permission bridge (Claude Code → frontend dialog)
@@ -1017,6 +1054,47 @@ fn tool_list_upcoming(ctx: &AppContext) -> Result<String, String> {
     .map_err(|e| format!("Serialization error: {e}"))
 }
 
+fn tool_get_pipeline_status(ctx: &AppContext) -> Result<String, String> {
+    let state = load_pipeline_state(ctx)?;
+
+    fn map_items(items: &[crate::http::workflow::UpcomingStory], stage: &str) -> Vec<Value> {
+        items
+            .iter()
+            .map(|s| {
+                json!({
+                    "story_id": s.story_id,
+                    "name": s.name,
+                    "stage": stage,
+                    "agent": s.agent.as_ref().map(|a| json!({
+                        "agent_name": a.agent_name,
+                        "model": a.model,
+                        "status": a.status,
+                    })),
+                })
+            })
+            .collect()
+    }
+
+    let mut active: Vec<Value> = Vec::new();
+    active.extend(map_items(&state.current, "current"));
+    active.extend(map_items(&state.qa, "qa"));
+    active.extend(map_items(&state.merge, "merge"));
+    active.extend(map_items(&state.done, "done"));
+
+    let upcoming: Vec<Value> = state
+        .upcoming
+        .iter()
+        .map(|s| json!({ "story_id": s.story_id, "name": s.name }))
+        .collect();
+
+    serde_json::to_string_pretty(&json!({
+        "active": active,
+        "upcoming": upcoming,
+        "upcoming_count": upcoming.len(),
+    }))
+    .map_err(|e| format!("Serialization error: {e}"))
+}
+
 fn tool_get_story_todos(args: &Value, ctx: &AppContext) -> Result<String, String> {
     let story_id = args
         .get("story_id")
@@ -1529,8 +1607,24 @@ fn tool_update_story(args: &Value, ctx: &AppContext) -> Result<String, String> {
     let user_story = args.get("user_story").and_then(|v| v.as_str());
     let description = args.get("description").and_then(|v| v.as_str());
 
+    // Collect front matter fields: explicit `agent` param + arbitrary `front_matter` object.
+    let mut front_matter: HashMap<String, String> = HashMap::new();
+    if let Some(agent) = args.get("agent").and_then(|v| v.as_str()) {
+        front_matter.insert("agent".to_string(), agent.to_string());
+    }
+    if let Some(obj) = args.get("front_matter").and_then(|v| v.as_object()) {
+        for (k, v) in obj {
+            let val = match v {
+                Value::String(s) => s.clone(),
+                other => other.to_string(),
+            };
+            front_matter.insert(k.clone(), val);
+        }
+    }
+    let front_matter_opt = if front_matter.is_empty() { None } else { Some(&front_matter) };
+
     let root = ctx.state.get_project_root()?;
-    update_story_in_file(&root, story_id, user_story, description)?;
+    update_story_in_file(&root, story_id, user_story, description, front_matter_opt)?;
 
     Ok(format!("Updated story '{story_id}'."))
 }
@@ -1651,54 +1745,81 @@ fn tool_list_refactors(ctx: &AppContext) -> Result<String, String> {
 
 // ── Mergemaster tool implementations ─────────────────────────────
 
-async fn tool_merge_agent_work(args: &Value, ctx: &AppContext) -> Result<String, String> {
+fn tool_merge_agent_work(args: &Value, ctx: &AppContext) -> Result<String, String> {
     let story_id = args
         .get("story_id")
         .and_then(|v| v.as_str())
         .ok_or("Missing required argument: story_id")?;
-    let agent_name = args.get("agent_name").and_then(|v| v.as_str());
 
-    // TRACE:MERGE-DEBUG — remove once root cause is found
-    crate::slog!(
-        "[MERGE-DEBUG] tool_merge_agent_work called for story_id={:?}, agent_name={:?}",
-        story_id,
-        agent_name
-    );
     let project_root = ctx.agents.get_project_root(&ctx.state)?;
-    crate::slog!(
+    ctx.agents.start_merge_agent_work(&project_root, story_id)?;
-        "[MERGE-DEBUG] tool_merge_agent_work: project_root resolved to {:?}",
-        project_root
-    );
-    let report = ctx.agents.merge_agent_work(&project_root, story_id).await?;
-
-    let status_msg = if report.success && report.gates_passed && report.conflicts_resolved {
-        "Merge complete: conflicts were auto-resolved and all quality gates passed. Story moved to done and worktree cleaned up."
-    } else if report.success && report.gates_passed {
-        "Merge complete: all quality gates passed. Story moved to done and worktree cleaned up."
-    } else if report.had_conflicts && !report.conflicts_resolved {
-        "Merge failed: conflicts detected that could not be auto-resolved. Merge was aborted — master is untouched. Call report_merge_failure with the conflict details so the human can resolve them. Do NOT manually move the story file or call accept_story."
-    } else if report.success && !report.gates_passed {
-        "Merge committed but quality gates failed. Review gate_output and fix issues before re-running."
-    } else {
-        "Merge failed. Review gate_output for details. Call report_merge_failure to record the failure. Do NOT manually move the story file or call accept_story."
-    };
 
     serde_json::to_string_pretty(&json!({
         "story_id": story_id,
-        "agent_name": agent_name,
+        "status": "started",
-        "success": report.success,
+        "message": "Merge pipeline started. Poll get_merge_status(story_id) every 10-15 seconds until status is 'completed' or 'failed'."
-        "had_conflicts": report.had_conflicts,
-        "conflicts_resolved": report.conflicts_resolved,
-        "conflict_details": report.conflict_details,
-        "gates_passed": report.gates_passed,
-        "gate_output": report.gate_output,
-        "worktree_cleaned_up": report.worktree_cleaned_up,
-        "story_archived": report.story_archived,
-        "message": status_msg,
     }))
     .map_err(|e| format!("Serialization error: {e}"))
 }
 
+fn tool_get_merge_status(args: &Value, ctx: &AppContext) -> Result<String, String> {
+    let story_id = args
+        .get("story_id")
+        .and_then(|v| v.as_str())
+        .ok_or("Missing required argument: story_id")?;
+
+    let job = ctx.agents.get_merge_status(story_id)
+        .ok_or_else(|| format!("No merge job found for story '{story_id}'. Call merge_agent_work first."))?;
+
+    match &job.status {
+        crate::agents::merge::MergeJobStatus::Running => {
+            serde_json::to_string_pretty(&json!({
+                "story_id": story_id,
+                "status": "running",
+                "message": "Merge pipeline is still running. Poll again in 10-15 seconds."
+            }))
+            .map_err(|e| format!("Serialization error: {e}"))
+        }
+        crate::agents::merge::MergeJobStatus::Completed(report) => {
+            let status_msg = if report.success && report.gates_passed && report.conflicts_resolved {
+                "Merge complete: conflicts were auto-resolved and all quality gates passed. Story moved to done and worktree cleaned up."
+            } else if report.success && report.gates_passed {
+                "Merge complete: all quality gates passed. Story moved to done and worktree cleaned up."
+            } else if report.had_conflicts && !report.conflicts_resolved {
+                "Merge failed: conflicts detected that could not be auto-resolved. Merge was aborted — master is untouched. Call report_merge_failure with the conflict details so the human can resolve them. Do NOT manually move the story file or call accept_story."
+            } else if report.success && !report.gates_passed {
+                "Merge committed but quality gates failed. Review gate_output and fix issues before re-running."
+            } else {
+                "Merge failed. Review gate_output for details. Call report_merge_failure to record the failure. Do NOT manually move the story file or call accept_story."
+            };
+
+            serde_json::to_string_pretty(&json!({
+                "story_id": story_id,
+                "status": "completed",
+                "success": report.success,
+                "had_conflicts": report.had_conflicts,
+                "conflicts_resolved": report.conflicts_resolved,
+                "conflict_details": report.conflict_details,
+                "gates_passed": report.gates_passed,
+                "gate_output": report.gate_output,
+                "worktree_cleaned_up": report.worktree_cleaned_up,
+                "story_archived": report.story_archived,
+                "message": status_msg,
+            }))
+            .map_err(|e| format!("Serialization error: {e}"))
+        }
+        crate::agents::merge::MergeJobStatus::Failed(err) => {
+            serde_json::to_string_pretty(&json!({
+                "story_id": story_id,
+                "status": "failed",
+                "error": err,
+                "message": format!("Merge pipeline failed: {err}. Call report_merge_failure to record the failure.")
+            }))
+            .map_err(|e| format!("Serialization error: {e}"))
+        }
+    }
+}
+
 async fn tool_move_story_to_merge(args: &Value, ctx: &AppContext) -> Result<String, String> {
     let story_id = args
         .get("story_id")
@@ -1746,6 +1867,13 @@ fn tool_report_merge_failure(args: &Value, ctx: &AppContext) -> Result<String, S
     slog!("[mergemaster] Merge failure reported for '{story_id}': {reason}");
     ctx.agents.set_merge_failure_reported(story_id);
 
+    // Broadcast the failure so the Matrix notification listener can post an
+    // error message to configured rooms without coupling this tool to the bot.
+    let _ = ctx.watcher_tx.send(crate::io::watcher::WatcherEvent::MergeFailure {
+        story_id: story_id.to_string(),
+        reason: reason.to_string(),
+    });
+
     // Persist the failure reason to the story file's front matter so it
     // survives server restarts and is visible in the web UI.
     if let Ok(project_root) = ctx.state.get_project_root() {
@@ -2147,12 +2275,14 @@ mod tests {
         assert!(names.contains(&"create_refactor"));
         assert!(names.contains(&"list_refactors"));
         assert!(names.contains(&"merge_agent_work"));
+        assert!(names.contains(&"get_merge_status"));
         assert!(names.contains(&"move_story_to_merge"));
         assert!(names.contains(&"report_merge_failure"));
         assert!(names.contains(&"request_qa"));
         assert!(names.contains(&"get_server_logs"));
         assert!(names.contains(&"prompt_permission"));
-        assert_eq!(tools.len(), 33);
+        assert!(names.contains(&"get_pipeline_status"));
+        assert_eq!(tools.len(), 35);
     }
 
     #[test]
@@ -2219,6 +2349,81 @@ mod tests {
         assert!(result.unwrap_err().contains("Missing required argument"));
     }
 
+    #[test]
+    fn tool_get_pipeline_status_returns_structured_response() {
+        let tmp = tempfile::tempdir().unwrap();
+        let root = tmp.path();
+
+        for (stage, id, name) in &[
+            ("1_upcoming", "10_story_upcoming", "Upcoming Story"),
+            ("2_current", "20_story_current", "Current Story"),
+            ("3_qa", "30_story_qa", "QA Story"),
+            ("4_merge", "40_story_merge", "Merge Story"),
+            ("5_done", "50_story_done", "Done Story"),
+        ] {
+            let dir = root.join(".story_kit/work").join(stage);
+            std::fs::create_dir_all(&dir).unwrap();
+            std::fs::write(
+                dir.join(format!("{id}.md")),
+                format!("---\nname: \"{name}\"\n---\n"),
+            )
+            .unwrap();
+        }
+
+        let ctx = test_ctx(root);
+        let result = tool_get_pipeline_status(&ctx).unwrap();
+        let parsed: Value = serde_json::from_str(&result).unwrap();
+
+        // Active stages include current, qa, merge, done
+        let active = parsed["active"].as_array().unwrap();
+        assert_eq!(active.len(), 4);
+
+        let stages: Vec<&str> = active.iter().map(|i| i["stage"].as_str().unwrap()).collect();
+        assert!(stages.contains(&"current"));
+        assert!(stages.contains(&"qa"));
+        assert!(stages.contains(&"merge"));
+        assert!(stages.contains(&"done"));
+
+        // Upcoming backlog
+        let upcoming = parsed["upcoming"].as_array().unwrap();
+        assert_eq!(upcoming.len(), 1);
+        assert_eq!(upcoming[0]["story_id"], "10_story_upcoming");
+        assert_eq!(parsed["upcoming_count"], 1);
+    }
+
+    #[test]
+    fn tool_get_pipeline_status_includes_agent_assignment() {
+        let tmp = tempfile::tempdir().unwrap();
+        let root = tmp.path();
+
+        let current = root.join(".story_kit/work/2_current");
+        std::fs::create_dir_all(&current).unwrap();
+        std::fs::write(
+            current.join("20_story_active.md"),
+            "---\nname: \"Active Story\"\n---\n",
+        )
+        .unwrap();
+
+        let ctx = test_ctx(root);
+        ctx.agents.inject_test_agent(
+            "20_story_active",
+            "coder-1",
+            crate::agents::AgentStatus::Running,
+        );
+
+        let result = tool_get_pipeline_status(&ctx).unwrap();
+        let parsed: Value = serde_json::from_str(&result).unwrap();
+
+        let active = parsed["active"].as_array().unwrap();
+        assert_eq!(active.len(), 1);
+        let item = &active[0];
+        assert_eq!(item["story_id"], "20_story_active");
+        assert_eq!(item["stage"], "current");
+        assert!(!item["agent"].is_null(), "agent should be present");
+        assert_eq!(item["agent"]["agent_name"], "coder-1");
+        assert_eq!(item["agent"]["status"], "running");
+    }
+
     #[test]
     fn tool_get_story_todos_missing_file() {
         let tmp = tempfile::tempdir().unwrap();
@@ -2787,11 +2992,11 @@ mod tests {
         assert!(!req_names.contains(&"agent_name"));
     }
 
-    #[tokio::test]
+    #[test]
-    async fn tool_merge_agent_work_missing_story_id() {
+    fn tool_merge_agent_work_missing_story_id() {
         let tmp = tempfile::tempdir().unwrap();
         let ctx = test_ctx(tmp.path());
-        let result = tool_merge_agent_work(&json!({}), &ctx).await;
+        let result = tool_merge_agent_work(&json!({}), &ctx);
         assert!(result.is_err());
         assert!(result.unwrap_err().contains("story_id"));
     }
@@ -2838,28 +3043,54 @@ mod tests {
     }
 
     #[tokio::test]
-    async fn tool_merge_agent_work_returns_coherent_report() {
+    async fn tool_merge_agent_work_returns_started() {
         let tmp = tempfile::tempdir().unwrap();
         setup_git_repo_in(tmp.path());
         let ctx = test_ctx(tmp.path());
 
-        // Try to merge a non-existent branch — should return a report (not panic)
         let result = tool_merge_agent_work(
             &json!({"story_id": "99_nonexistent", "agent_name": "coder-1"}),
             &ctx,
         )
-        .await
         .unwrap();
         let parsed: Value = serde_json::from_str(&result).unwrap();
         assert_eq!(parsed["story_id"], "99_nonexistent");
-        assert_eq!(parsed["agent_name"], "coder-1");
+        assert_eq!(parsed["status"], "started");
-        assert!(parsed.get("success").is_some());
-        assert!(parsed.get("had_conflicts").is_some());
-        assert!(parsed.get("gates_passed").is_some());
-        assert!(parsed.get("gate_output").is_some());
         assert!(parsed.get("message").is_some());
     }
 
+    #[test]
+    fn tool_get_merge_status_no_job() {
+        let tmp = tempfile::tempdir().unwrap();
+        let ctx = test_ctx(tmp.path());
+        let result = tool_get_merge_status(&json!({"story_id": "99_nonexistent"}), &ctx);
+        assert!(result.is_err());
+        assert!(result.unwrap_err().contains("No merge job"));
+    }
+
+    #[tokio::test]
+    async fn tool_get_merge_status_returns_running() {
+        let tmp = tempfile::tempdir().unwrap();
+        setup_git_repo_in(tmp.path());
+        let ctx = test_ctx(tmp.path());
+
+        // Start a merge (it will run in background)
+        tool_merge_agent_work(
+            &json!({"story_id": "99_nonexistent"}),
+            &ctx,
+        )
+        .unwrap();
+
+        // Immediately check — should be running (or already finished if very fast)
+        let result = tool_get_merge_status(&json!({"story_id": "99_nonexistent"}), &ctx).unwrap();
+        let parsed: Value = serde_json::from_str(&result).unwrap();
+        let status = parsed["status"].as_str().unwrap();
+        assert!(
+            status == "running" || status == "completed" || status == "failed",
+            "unexpected status: {status}"
+        );
+    }
+
     // ── report_merge_failure tool tests ─────────────────────────────
 
     #[test]

server/src/http/project.rs

@@ -39,7 +39,6 @@ impl ProjectApi {
             payload.0.path,
             &self.ctx.state,
             self.ctx.store.as_ref(),
-            self.ctx.agents.port(),
         )
         .await
         .map_err(bad_request)?;

server/src/http/workflow.rs

@@ -1,6 +1,6 @@
 use crate::agents::AgentStatus;
 use crate::http::context::AppContext;
-use crate::io::story_metadata::{parse_front_matter, write_coverage_baseline};
+use crate::io::story_metadata::{parse_front_matter, set_front_matter_field, write_coverage_baseline};
 use crate::workflow::{StoryTestResults, TestCaseResult, TestStatus};
 use serde::Serialize;
 use std::collections::HashMap;
@@ -706,10 +706,13 @@ pub fn update_story_in_file(
     story_id: &str,
     user_story: Option<&str>,
     description: Option<&str>,
+    front_matter: Option<&HashMap<String, String>>,
 ) -> Result<(), String> {
-    if user_story.is_none() && description.is_none() {
+    let has_front_matter_updates = front_matter.map(|m| !m.is_empty()).unwrap_or(false);
+    if user_story.is_none() && description.is_none() && !has_front_matter_updates {
         return Err(
-            "At least one of 'user_story' or 'description' must be provided.".to_string(),
+            "At least one of 'user_story', 'description', or 'front_matter' must be provided."
+                .to_string(),
         );
     }
 
@@ -717,6 +720,13 @@ pub fn update_story_in_file(
     let mut contents = fs::read_to_string(&filepath)
         .map_err(|e| format!("Failed to read story file: {e}"))?;
 
+    if let Some(fields) = front_matter {
+        for (key, value) in fields {
+            let yaml_value = format!("\"{}\"", value.replace('"', "\\\"").replace('\n', " ").replace('\r', ""));
+            contents = set_front_matter_field(&contents, key, &yaml_value);
+        }
+    }
+
     if let Some(us) = user_story {
         contents = replace_section_content(&contents, "User Story", us)?;
     }
@@ -1597,7 +1607,7 @@ mod tests {
         let content = "---\nname: T\n---\n\n## User Story\n\nOld text\n\n## Acceptance Criteria\n\n- [ ] AC\n";
         fs::write(&filepath, content).unwrap();
 
-        update_story_in_file(tmp.path(), "20_test", Some("New user story text"), None).unwrap();
+        update_story_in_file(tmp.path(), "20_test", Some("New user story text"), None, None).unwrap();
 
         let result = fs::read_to_string(&filepath).unwrap();
         assert!(result.contains("New user story text"), "new text should be present");
@@ -1614,7 +1624,7 @@ mod tests {
         let content = "---\nname: T\n---\n\n## Description\n\nOld description\n\n## Acceptance Criteria\n\n- [ ] AC\n";
         fs::write(&filepath, content).unwrap();
 
-        update_story_in_file(tmp.path(), "21_test", None, Some("New description")).unwrap();
+        update_story_in_file(tmp.path(), "21_test", None, Some("New description"), None).unwrap();
 
         let result = fs::read_to_string(&filepath).unwrap();
         assert!(result.contains("New description"), "new description present");
@@ -1628,7 +1638,7 @@ mod tests {
         fs::create_dir_all(&current).unwrap();
         fs::write(current.join("22_test.md"), "---\nname: T\n---\n").unwrap();
 
-        let result = update_story_in_file(tmp.path(), "22_test", None, None);
+        let result = update_story_in_file(tmp.path(), "22_test", None, None, None);
         assert!(result.is_err());
         assert!(result.unwrap_err().contains("At least one"));
     }
@@ -1644,11 +1654,65 @@ mod tests {
         )
         .unwrap();
 
-        let result = update_story_in_file(tmp.path(), "23_test", Some("new text"), None);
+        let result = update_story_in_file(tmp.path(), "23_test", Some("new text"), None, None);
         assert!(result.is_err());
         assert!(result.unwrap_err().contains("User Story"));
     }
 
+    #[test]
+    fn update_story_sets_agent_front_matter_field() {
+        let tmp = tempfile::tempdir().unwrap();
+        let current = tmp.path().join(".story_kit/work/2_current");
+        fs::create_dir_all(&current).unwrap();
+        let filepath = current.join("24_test.md");
+        fs::write(&filepath, "---\nname: T\n---\n\n## User Story\n\nSome story\n").unwrap();
+
+        let mut fields = HashMap::new();
+        fields.insert("agent".to_string(), "dev".to_string());
+        update_story_in_file(tmp.path(), "24_test", None, None, Some(&fields)).unwrap();
+
+        let result = fs::read_to_string(&filepath).unwrap();
+        assert!(result.contains("agent: \"dev\""), "agent field should be set");
+        assert!(result.contains("name: T"), "name field preserved");
+    }
+
+    #[test]
+    fn update_story_sets_arbitrary_front_matter_fields() {
+        let tmp = tempfile::tempdir().unwrap();
+        let current = tmp.path().join(".story_kit/work/2_current");
+        fs::create_dir_all(&current).unwrap();
+        let filepath = current.join("25_test.md");
+        fs::write(&filepath, "---\nname: T\n---\n\n## User Story\n\nSome story\n").unwrap();
+
+        let mut fields = HashMap::new();
+        fields.insert("manual_qa".to_string(), "true".to_string());
+        fields.insert("priority".to_string(), "high".to_string());
+        update_story_in_file(tmp.path(), "25_test", None, None, Some(&fields)).unwrap();
+
+        let result = fs::read_to_string(&filepath).unwrap();
+        assert!(result.contains("manual_qa: \"true\""), "manual_qa field should be set");
+        assert!(result.contains("priority: \"high\""), "priority field should be set");
+        assert!(result.contains("name: T"), "name field preserved");
+    }
+
+    #[test]
+    fn update_story_front_matter_only_no_section_required() {
+        let tmp = tempfile::tempdir().unwrap();
+        let current = tmp.path().join(".story_kit/work/2_current");
+        fs::create_dir_all(&current).unwrap();
+        // File without a User Story section — front matter update should succeed
+        let filepath = current.join("26_test.md");
+        fs::write(&filepath, "---\nname: T\n---\n\nNo sections here.\n").unwrap();
+
+        let mut fields = HashMap::new();
+        fields.insert("agent".to_string(), "dev".to_string());
+        let result = update_story_in_file(tmp.path(), "26_test", None, None, Some(&fields));
+        assert!(result.is_ok(), "front-matter-only update should not require body sections");
+
+        let contents = fs::read_to_string(&filepath).unwrap();
+        assert!(contents.contains("agent: \"dev\""));
+    }
+
     // ── Bug file helper tests ──────────────────────────────────────────────────
 
     #[test]

server/src/http/ws.rs

@@ -150,6 +150,9 @@ impl From<WatcherEvent> for Option<WsResponse> {
             }),
             WatcherEvent::ConfigChanged => Some(WsResponse::AgentConfigChanged),
             WatcherEvent::AgentStateChanged => Some(WsResponse::AgentStateChanged),
+            // MergeFailure is handled by the Matrix notification listener only;
+            // no WebSocket message is needed for the frontend.
+            WatcherEvent::MergeFailure { .. } => None,
         }
     }
 }

server/src/io/fs.rs

@@ -1,6 +1,5 @@
 use crate::state::SessionState;
 use crate::store::StoreOps;
-use crate::worktree::write_mcp_json as worktree_write_mcp_json;
 use serde::Serialize;
 use serde_json::json;
 use std::fs;
@@ -127,8 +126,8 @@ role = "Merges completed work into master, runs quality gates, and archives stor
 model = "sonnet"
 max_turns = 30
 max_budget_usd = 5.00
-prompt = "You are the mergemaster agent for story {{story_id}}. Call merge_agent_work(story_id='{{story_id}}') via the MCP tool to trigger the full merge pipeline. Report the result to the human. If the merge fails, call report_merge_failure."
+prompt = "You are the mergemaster agent for story {{story_id}}. Call merge_agent_work(story_id='{{story_id}}') to start the merge pipeline. Then poll get_merge_status(story_id='{{story_id}}') every 15 seconds until the status is 'completed' or 'failed'. Report the final result. If the merge fails, call report_merge_failure."
-system_prompt = "You are the mergemaster agent. Trigger merge_agent_work via MCP and report results. Never manually move story files. Call report_merge_failure when merges fail."
+system_prompt = "You are the mergemaster agent. Call merge_agent_work to start the merge, then poll get_merge_status every 15 seconds until done. Never manually move story files. Call report_merge_failure when merges fail."
 "#;
 
 /// Detect the tech stack from the project root and return TOML `[[component]]` entries.
@@ -313,17 +312,61 @@ fn write_script_if_missing(path: &Path, content: &str) -> Result<(), String> {
     Ok(())
 }
 
-/// Append Story Kit entries to `.gitignore` (or create one if missing).
+/// Write (or idempotently update) `.story_kit/.gitignore` with Story Kit–specific
-/// Does not duplicate entries already present.
+/// ignore patterns for files that live inside the `.story_kit/` directory.
-fn append_gitignore_entries(root: &Path) -> Result<(), String> {
+/// Patterns are relative to `.story_kit/` as git resolves `.gitignore` files
+/// relative to the directory that contains them.
+fn write_story_kit_gitignore(root: &Path) -> Result<(), String> {
+    // Entries that belong inside .story_kit/.gitignore (relative to .story_kit/).
     let entries = [
-        ".story_kit/worktrees/",
+        "bot.toml",
-        ".story_kit/merge_workspace/",
+        "matrix_store/",
-        ".story_kit/coverage/",
+        "matrix_device_id",
-        ".story_kit_port",
+        "worktrees/",
-        "store.json",
+        "merge_workspace/",
+        "coverage/",
     ];
 
+    let gitignore_path = root.join(".story_kit").join(".gitignore");
+    let existing = if gitignore_path.exists() {
+        fs::read_to_string(&gitignore_path)
+            .map_err(|e| format!("Failed to read .story_kit/.gitignore: {}", e))?
+    } else {
+        String::new()
+    };
+
+    let missing: Vec<&str> = entries
+        .iter()
+        .copied()
+        .filter(|e| !existing.lines().any(|l| l.trim() == *e))
+        .collect();
+
+    if missing.is_empty() {
+        return Ok(());
+    }
+
+    let mut new_content = existing;
+    if !new_content.is_empty() && !new_content.ends_with('\n') {
+        new_content.push('\n');
+    }
+    for entry in missing {
+        new_content.push_str(entry);
+        new_content.push('\n');
+    }
+
+    fs::write(&gitignore_path, new_content)
+        .map_err(|e| format!("Failed to write .story_kit/.gitignore: {}", e))?;
+
+    Ok(())
+}
+
+/// Append root-level Story Kit entries to the project `.gitignore`.
+/// Only `store.json` and `.story_kit_port` remain here because they live at
+/// the project root and git does not support `../` patterns in `.gitignore`
+/// files, so they cannot be expressed in `.story_kit/.gitignore`.
+fn append_root_gitignore_entries(root: &Path) -> Result<(), String> {
+    let entries = [".story_kit_port", "store.json"];
+
     let gitignore_path = root.join(".gitignore");
     let existing = if gitignore_path.exists() {
         fs::read_to_string(&gitignore_path)
@@ -402,7 +445,8 @@ fn scaffold_story_kit(root: &Path) -> Result<(), String> {
         .map_err(|e| format!("Failed to create .claude/ directory: {}", e))?;
     write_file_if_missing(&claude_dir.join("settings.json"), STORY_KIT_CLAUDE_SETTINGS)?;
 
-    append_gitignore_entries(root)?;
+    write_story_kit_gitignore(root)?;
+    append_root_gitignore_entries(root)?;
 
     // Run `git init` if the directory is not already a git repo, then make an initial commit
     if !root.join(".git").exists() {
@@ -470,17 +514,12 @@ pub async fn open_project(
     path: String,
     state: &SessionState,
     store: &dyn StoreOps,
-    port: u16,
 ) -> Result<String, String> {
     let p = PathBuf::from(&path);
 
     ensure_project_root_with_story_kit(p.clone()).await?;
     validate_project_path(p.clone()).await?;
 
-    // Write .mcp.json so that claude-code can connect to the MCP server.
-    // Best-effort: failure should not prevent the project from opening.
-    let _ = worktree_write_mcp_json(&p, port);
-
     {
         // TRACE:MERGE-DEBUG — remove once root cause is found
         crate::slog!("[MERGE-DEBUG] open_project: setting project_root to {:?}", p);
@@ -682,6 +721,42 @@ pub async fn create_directory_absolute(path: String) -> Result<bool, String> {
     .map_err(|e| format!("Task failed: {}", e))?
 }
 
+/// List all files in the project recursively, respecting .gitignore.
+/// Returns relative paths from the project root (files only, not directories).
+pub async fn list_project_files(state: &SessionState) -> Result<Vec<String>, String> {
+    let root = state.get_project_root()?;
+    list_project_files_impl(root).await
+}
+
+pub async fn list_project_files_impl(root: PathBuf) -> Result<Vec<String>, String> {
+    use ignore::WalkBuilder;
+
+    let root_clone = root.clone();
+    let files = tokio::task::spawn_blocking(move || {
+        let mut result = Vec::new();
+        let walker = WalkBuilder::new(&root_clone).git_ignore(true).build();
+
+        for entry in walker.flatten() {
+            if entry.file_type().map(|ft| ft.is_file()).unwrap_or(false) {
+                let relative = entry
+                    .path()
+                    .strip_prefix(&root_clone)
+                    .unwrap_or(entry.path())
+                    .to_string_lossy()
+                    .to_string();
+                result.push(relative);
+            }
+        }
+
+        result.sort();
+        result
+    })
+    .await
+    .map_err(|e| format!("Task failed: {e}"))?;
+
+    Ok(files)
+}
+
 #[cfg(test)]
 mod tests {
     use super::*;
@@ -732,7 +807,6 @@ mod tests {
             project_dir.to_string_lossy().to_string(),
             &state,
             &store,
-            3001,
         )
         .await;
 
@@ -742,7 +816,11 @@ mod tests {
     }
 
     #[tokio::test]
-    async fn open_project_writes_mcp_json_to_project_root() {
+    async fn open_project_does_not_write_mcp_json() {
+        // open_project must NOT overwrite .mcp.json — test servers started by QA
+        // agents share the real project root, so writing here would clobber the
+        // root .mcp.json with the wrong port.  .mcp.json is written once during
+        // worktree creation (worktree.rs) and should not be touched again.
         let dir = tempdir().unwrap();
         let project_dir = dir.path().join("myproject");
         fs::create_dir_all(&project_dir).unwrap();
@@ -753,17 +831,14 @@ mod tests {
             project_dir.to_string_lossy().to_string(),
             &state,
             &store,
-            4242,
         )
         .await
         .unwrap();
 
         let mcp_path = project_dir.join(".mcp.json");
-        assert!(mcp_path.exists(), ".mcp.json should be written to project root");
-        let content = fs::read_to_string(&mcp_path).unwrap();
         assert!(
-            content.contains("http://localhost:4242/mcp"),
+            !mcp_path.exists(),
-            ".mcp.json should contain the correct port"
+            "open_project must not write .mcp.json — that would overwrite the root with the wrong port"
         );
     }
 
@@ -823,7 +898,6 @@ mod tests {
             project_dir.to_string_lossy().to_string(),
             &state,
             &store,
-            3001,
         )
         .await
         .unwrap();
@@ -1122,12 +1196,17 @@ mod tests {
             toml_content
         );
 
-        let gitignore = fs::read_to_string(dir.path().join(".gitignore")).unwrap();
+        let story_kit_gitignore =
-        let count = gitignore
+            fs::read_to_string(dir.path().join(".story_kit/.gitignore")).unwrap();
+        let count = story_kit_gitignore
             .lines()
-            .filter(|l| l.trim() == ".story_kit/worktrees/")
+            .filter(|l| l.trim() == "worktrees/")
             .count();
-        assert_eq!(count, 1, ".gitignore should not have duplicate entries");
+        assert_eq!(
+            count,
+            1,
+            ".story_kit/.gitignore should not have duplicate entries"
+        );
     }
 
     #[test]
@@ -1173,53 +1252,56 @@ mod tests {
     }
 
     #[test]
-    fn scaffold_creates_gitignore_with_story_kit_entries() {
+    fn scaffold_creates_story_kit_gitignore_with_relative_entries() {
         let dir = tempdir().unwrap();
         scaffold_story_kit(dir.path()).unwrap();
 
-        let content = fs::read_to_string(dir.path().join(".gitignore")).unwrap();
+        // .story_kit/.gitignore must contain relative patterns for files under .story_kit/
-        assert!(content.contains(".story_kit/worktrees/"));
+        let sk_content =
-        assert!(content.contains(".story_kit/merge_workspace/"));
+            fs::read_to_string(dir.path().join(".story_kit/.gitignore")).unwrap();
-        assert!(content.contains(".story_kit/coverage/"));
+        assert!(sk_content.contains("worktrees/"));
-        assert!(content.contains(".story_kit_port"));
+        assert!(sk_content.contains("merge_workspace/"));
-        assert!(content.contains("store.json"));
+        assert!(sk_content.contains("coverage/"));
+        // Must NOT contain absolute .story_kit/ prefixed paths
+        assert!(!sk_content.contains(".story_kit/"));
+
+        // Root .gitignore must contain root-level story-kit entries
+        let root_content = fs::read_to_string(dir.path().join(".gitignore")).unwrap();
+        assert!(root_content.contains(".story_kit_port"));
+        assert!(root_content.contains("store.json"));
+        // Root .gitignore must NOT contain .story_kit/ sub-directory patterns
+        assert!(!root_content.contains(".story_kit/worktrees/"));
+        assert!(!root_content.contains(".story_kit/merge_workspace/"));
+        assert!(!root_content.contains(".story_kit/coverage/"));
     }
 
     #[test]
-    fn scaffold_gitignore_does_not_duplicate_existing_entries() {
+    fn scaffold_story_kit_gitignore_does_not_duplicate_existing_entries() {
         let dir = tempdir().unwrap();
-        // Pre-create .gitignore with some Story Kit entries already present
+        // Pre-create .story_kit dir and .gitignore with some entries already present
+        fs::create_dir_all(dir.path().join(".story_kit")).unwrap();
         fs::write(
-            dir.path().join(".gitignore"),
+            dir.path().join(".story_kit/.gitignore"),
-            ".story_kit/worktrees/\n.story_kit/coverage/\n",
+            "worktrees/\ncoverage/\n",
         )
         .unwrap();
 
         scaffold_story_kit(dir.path()).unwrap();
 
-        let content = fs::read_to_string(dir.path().join(".gitignore")).unwrap();
+        let content =
+            fs::read_to_string(dir.path().join(".story_kit/.gitignore")).unwrap();
         let worktrees_count = content
             .lines()
-            .filter(|l| l.trim() == ".story_kit/worktrees/")
+            .filter(|l| l.trim() == "worktrees/")
             .count();
-        assert_eq!(
+        assert_eq!(worktrees_count, 1, "worktrees/ should not be duplicated");
-            worktrees_count,
-            1,
-            ".story_kit/worktrees/ should not be duplicated"
-        );
         let coverage_count = content
             .lines()
-            .filter(|l| l.trim() == ".story_kit/coverage/")
+            .filter(|l| l.trim() == "coverage/")
             .count();
-        assert_eq!(
+        assert_eq!(coverage_count, 1, "coverage/ should not be duplicated");
-            coverage_count,
+        // The missing entry must have been added
-            1,
+        assert!(content.contains("merge_workspace/"));
-            ".story_kit/coverage/ should not be duplicated"
-        );
-        // The missing entries must have been added
-        assert!(content.contains(".story_kit/merge_workspace/"));
-        assert!(content.contains(".story_kit_port"));
-        assert!(content.contains("store.json"));
     }
 
     // --- CLAUDE.md scaffold ---
@@ -1276,7 +1358,6 @@ mod tests {
             project_dir.to_string_lossy().to_string(),
             &state,
             &store,
-            0,
         )
         .await
         .unwrap();
@@ -1300,7 +1381,6 @@ mod tests {
             project_dir.to_string_lossy().to_string(),
             &state,
             &store,
-            0,
         )
         .await
         .unwrap();
@@ -1535,4 +1615,68 @@ mod tests {
             "scaffold should not overwrite existing project.toml"
         );
     }
+
+    // --- list_project_files_impl ---
+
+    #[tokio::test]
+    async fn list_project_files_returns_all_files() {
+        let dir = tempdir().unwrap();
+        fs::create_dir(dir.path().join("src")).unwrap();
+        fs::write(dir.path().join("src/main.rs"), "fn main() {}").unwrap();
+        fs::write(dir.path().join("README.md"), "# readme").unwrap();
+
+        let files = list_project_files_impl(dir.path().to_path_buf())
+            .await
+            .unwrap();
+
+        assert!(files.contains(&"README.md".to_string()));
+        assert!(files.contains(&"src/main.rs".to_string()));
+    }
+
+    #[tokio::test]
+    async fn list_project_files_excludes_dirs_from_output() {
+        let dir = tempdir().unwrap();
+        fs::create_dir(dir.path().join("subdir")).unwrap();
+        fs::write(dir.path().join("file.txt"), "").unwrap();
+
+        let files = list_project_files_impl(dir.path().to_path_buf())
+            .await
+            .unwrap();
+
+        assert!(files.contains(&"file.txt".to_string()));
+        assert!(!files.iter().any(|f| f == "subdir"));
+    }
+
+    #[tokio::test]
+    async fn list_project_files_returns_sorted() {
+        let dir = tempdir().unwrap();
+        fs::write(dir.path().join("z.txt"), "").unwrap();
+        fs::write(dir.path().join("a.txt"), "").unwrap();
+
+        let files = list_project_files_impl(dir.path().to_path_buf())
+            .await
+            .unwrap();
+
+        let a_idx = files.iter().position(|f| f == "a.txt").unwrap();
+        let z_idx = files.iter().position(|f| f == "z.txt").unwrap();
+        assert!(a_idx < z_idx);
+    }
+
+    #[tokio::test]
+    async fn list_project_files_with_state() {
+        let dir = tempdir().unwrap();
+        fs::write(dir.path().join("hello.rs"), "").unwrap();
+        let state = make_state_with_root(dir.path().to_path_buf());
+
+        let files = list_project_files(&state).await.unwrap();
+
+        assert!(files.contains(&"hello.rs".to_string()));
+    }
+
+    #[tokio::test]
+    async fn list_project_files_errors_without_project() {
+        let state = SessionState::default();
+        let result = list_project_files(&state).await;
+        assert!(result.is_err());
+    }
 }

server/src/io/story_metadata.rs

@@ -8,6 +8,7 @@ pub struct StoryMetadata {
     pub coverage_baseline: Option<String>,
     pub merge_failure: Option<String>,
     pub agent: Option<String>,
+    pub review_hold: Option<bool>,
 }
 
 #[derive(Debug, Clone, PartialEq, Eq)]
@@ -31,6 +32,7 @@ struct FrontMatter {
     coverage_baseline: Option<String>,
     merge_failure: Option<String>,
     agent: Option<String>,
+    review_hold: Option<bool>,
 }
 
 pub fn parse_front_matter(contents: &str) -> Result<StoryMetadata, StoryMetaError> {
@@ -64,6 +66,7 @@ fn build_metadata(front: FrontMatter) -> StoryMetadata {
         coverage_baseline: front.coverage_baseline,
         merge_failure: front.merge_failure,
         agent: front.agent,
+        review_hold: front.review_hold,
     }
 }
 
@@ -98,6 +101,17 @@ pub fn write_merge_failure(path: &Path, reason: &str) -> Result<(), String> {
     Ok(())
 }
 
+/// Write `review_hold: true` to the YAML front matter of a story file.
+///
+/// Used to mark spikes that have passed QA and are waiting for human review.
+pub fn write_review_hold(path: &Path) -> Result<(), String> {
+    let contents =
+        fs::read_to_string(path).map_err(|e| format!("Failed to read story file: {e}"))?;
+    let updated = set_front_matter_field(&contents, "review_hold", "true");
+    fs::write(path, &updated).map_err(|e| format!("Failed to write story file: {e}"))?;
+    Ok(())
+}
+
 /// Remove a key from the YAML front matter of a story file on disk.
 ///
 /// If front matter is present and contains the key, the line is removed.
@@ -147,7 +161,7 @@ fn remove_front_matter_field(contents: &str, key: &str) -> String {
 /// Insert or update a key: value pair in the YAML front matter of a markdown string.
 ///
 /// If no front matter (opening `---`) is found, returns the content unchanged.
-fn set_front_matter_field(contents: &str, key: &str, value: &str) -> String {
+pub fn set_front_matter_field(contents: &str, key: &str, value: &str) -> String {
     let mut lines: Vec<String> = contents.lines().map(String::from).collect();
     if lines.is_empty() || lines[0].trim() != "---" {
         return contents.to_string();
@@ -328,4 +342,29 @@ workflow: tdd
         let input = "  - [ ] Indented item\n";
         assert_eq!(parse_unchecked_todos(input), vec!["Indented item"]);
     }
+
+    #[test]
+    fn parses_review_hold_from_front_matter() {
+        let input = "---\nname: Spike\nreview_hold: true\n---\n# Spike\n";
+        let meta = parse_front_matter(input).expect("front matter");
+        assert_eq!(meta.review_hold, Some(true));
+    }
+
+    #[test]
+    fn review_hold_defaults_to_none() {
+        let input = "---\nname: Story\n---\n# Story\n";
+        let meta = parse_front_matter(input).expect("front matter");
+        assert_eq!(meta.review_hold, None);
+    }
+
+    #[test]
+    fn write_review_hold_sets_field() {
+        let tmp = tempfile::tempdir().unwrap();
+        let path = tmp.path().join("spike.md");
+        std::fs::write(&path, "---\nname: My Spike\n---\n# Spike\n").unwrap();
+        write_review_hold(&path).unwrap();
+        let contents = std::fs::read_to_string(&path).unwrap();
+        assert!(contents.contains("review_hold: true"));
+        assert!(contents.contains("name: My Spike"));
+    }
 }

server/src/io/watcher.rs

@@ -20,6 +20,7 @@
 //! the event so connected clients stay in sync.
 
 use crate::config::{ProjectConfig, WatcherConfig};
+use crate::io::story_metadata::clear_front_matter_field;
 use crate::slog;
 use notify::{EventKind, RecommendedWatcher, RecursiveMode, Watcher, recommended_watcher};
 use serde::Serialize;
@@ -50,6 +51,14 @@ pub enum WatcherEvent {
     /// Triggers a pipeline state refresh so the frontend can update agent
     /// assignments without waiting for a filesystem event.
     AgentStateChanged,
+    /// A story encountered a failure (e.g. merge failure).
+    /// Triggers an error notification to configured Matrix rooms.
+    MergeFailure {
+        /// Work item ID (e.g. `"42_story_my_feature"`).
+        story_id: String,
+        /// Human-readable description of the failure.
+        reason: String,
+    },
 }
 
 /// Return `true` if `path` is the root-level `.story_kit/project.toml`, i.e.
@@ -146,11 +155,25 @@ fn git_add_work_and_commit(git_root: &Path, message: &str) -> Result<bool, Strin
     Err(format!("git commit failed: {stderr}"))
 }
 
+/// Stages that represent meaningful git checkpoints (creation and archival).
+/// Intermediate stages (current, qa, merge, done) are transient pipeline state
+/// that don't need to be committed — they're only relevant while the server is
+/// running and are broadcast to WebSocket clients for real-time UI updates.
+const COMMIT_WORTHY_STAGES: &[&str] = &["1_upcoming", "5_done", "6_archived"];
+
+/// Return `true` if changes in `stage` should be committed to git.
+fn should_commit_stage(stage: &str) -> bool {
+    COMMIT_WORTHY_STAGES.contains(&stage)
+}
+
 /// Process a batch of pending (path → stage) entries: commit and broadcast.
 ///
 /// Only files that still exist on disk are used to derive the commit message
 /// (they represent the destination of a move or a new file). Deletions are
 /// captured by `git add -A .story_kit/work/` automatically.
+///
+/// Only terminal stages (`1_upcoming` and `6_archived`) trigger git commits.
+/// All stages broadcast a [`WatcherEvent`] so the frontend stays in sync.
 fn flush_pending(
     pending: &HashMap<PathBuf, String>,
     git_root: &Path,
@@ -182,27 +205,46 @@ fn flush_pending(
         ("remove", item.to_string(), format!("story-kit: remove {item}"))
     };
 
-    slog!("[watcher] flush: {commit_msg}");
+    // Strip stale merge_failure front matter from any story that has left 4_merge/.
-    match git_add_work_and_commit(git_root, &commit_msg) {
+    for (path, stage) in &additions {
-        Ok(committed) => {
+        if *stage != "4_merge"
-            if committed {
+            && let Err(e) = clear_front_matter_field(path, "merge_failure")
-                slog!("[watcher] committed: {commit_msg}");
+        {
-            } else {
+            slog!("[watcher] Warning: could not clear merge_failure from {}: {e}", path.display());
-                slog!("[watcher] skipped (already committed): {commit_msg}");
-            }
-            let stage = additions.first().map_or("unknown", |(_, s)| s);
-            let evt = WatcherEvent::WorkItem {
-                stage: stage.to_string(),
-                item_id,
-                action: action.to_string(),
-                commit_msg,
-            };
-            let _ = event_tx.send(evt);
-        }
-        Err(e) => {
-            slog!("[watcher] git error: {e}");
         }
     }
+
+    // Only commit for terminal stages; intermediate moves are broadcast-only.
+    let dest_stage = additions.first().map_or("unknown", |(_, s)| *s);
+    let should_commit = should_commit_stage(dest_stage);
+
+    if should_commit {
+        slog!("[watcher] flush: {commit_msg}");
+        match git_add_work_and_commit(git_root, &commit_msg) {
+            Ok(committed) => {
+                if committed {
+                    slog!("[watcher] committed: {commit_msg}");
+                } else {
+                    slog!("[watcher] skipped (already committed): {commit_msg}");
+                }
+            }
+            Err(e) => {
+                slog!("[watcher] git error: {e}");
+                return;
+            }
+        }
+    } else {
+        slog!("[watcher] flush (broadcast-only): {commit_msg}");
+    }
+
+    // Always broadcast the event so connected WebSocket clients stay in sync.
+    let evt = WatcherEvent::WorkItem {
+        stage: dest_stage.to_string(),
+        item_id,
+        action: action.to_string(),
+        commit_msg,
+    };
+    let _ = event_tx.send(evt);
 }
 
 /// Scan `work/5_done/` and move any `.md` files whose mtime is older than
@@ -529,7 +571,50 @@ mod tests {
     // ── flush_pending ─────────────────────────────────────────────────────────
 
     #[test]
-    fn flush_pending_commits_and_broadcasts_work_item_for_addition() {
+    fn flush_pending_commits_and_broadcasts_for_terminal_stage() {
+        let tmp = TempDir::new().unwrap();
+        init_git_repo(tmp.path());
+        let stage_dir = make_stage_dir(tmp.path(), "1_upcoming");
+        let story_path = stage_dir.join("42_story_foo.md");
+        fs::write(&story_path, "---\nname: test\n---\n").unwrap();
+
+        let (tx, mut rx) = tokio::sync::broadcast::channel(16);
+        let mut pending = HashMap::new();
+        pending.insert(story_path, "1_upcoming".to_string());
+
+        flush_pending(&pending, tmp.path(), &tx);
+
+        let evt = rx.try_recv().expect("expected a broadcast event");
+        match evt {
+            WatcherEvent::WorkItem {
+                stage,
+                item_id,
+                action,
+                commit_msg,
+            } => {
+                assert_eq!(stage, "1_upcoming");
+                assert_eq!(item_id, "42_story_foo");
+                assert_eq!(action, "create");
+                assert_eq!(commit_msg, "story-kit: create 42_story_foo");
+            }
+            other => panic!("unexpected event: {other:?}"),
+        }
+
+        // Verify the file was actually committed.
+        let log = std::process::Command::new("git")
+            .args(["log", "--oneline", "-1"])
+            .current_dir(tmp.path())
+            .output()
+            .expect("git log");
+        let log_msg = String::from_utf8_lossy(&log.stdout);
+        assert!(
+            log_msg.contains("story-kit: create 42_story_foo"),
+            "terminal stage should produce a git commit"
+        );
+    }
+
+    #[test]
+    fn flush_pending_broadcasts_without_commit_for_intermediate_stage() {
         let tmp = TempDir::new().unwrap();
         init_git_repo(tmp.path());
         let stage_dir = make_stage_dir(tmp.path(), "2_current");
@@ -542,6 +627,7 @@ mod tests {
 
         flush_pending(&pending, tmp.path(), &tx);
 
+        // Event should still be broadcast for frontend sync.
         let evt = rx.try_recv().expect("expected a broadcast event");
         match evt {
             WatcherEvent::WorkItem {
@@ -557,6 +643,18 @@ mod tests {
             }
             other => panic!("unexpected event: {other:?}"),
         }
+
+        // Verify NO git commit was made (only the initial empty commit should exist).
+        let log = std::process::Command::new("git")
+            .args(["log", "--oneline"])
+            .current_dir(tmp.path())
+            .output()
+            .expect("git log");
+        let log_msg = String::from_utf8_lossy(&log.stdout);
+        assert!(
+            !log_msg.contains("story-kit:"),
+            "intermediate stage should NOT produce a git commit"
+        );
     }
 
     #[test]
@@ -582,6 +680,7 @@ mod tests {
 
             flush_pending(&pending, tmp.path(), &tx);
 
+            // All stages should broadcast events regardless of commit behavior.
             let evt = rx.try_recv().expect("expected broadcast for stage {stage}");
             match evt {
                 WatcherEvent::WorkItem {
@@ -664,6 +763,128 @@ mod tests {
         assert!(rx.try_recv().is_err(), "no event for empty pending map");
     }
 
+    // ── flush_pending clears merge_failure ─────────────────────────────────────
+
+    #[test]
+    fn flush_pending_clears_merge_failure_when_leaving_merge_stage() {
+        let tmp = TempDir::new().unwrap();
+        init_git_repo(tmp.path());
+        let stage_dir = make_stage_dir(tmp.path(), "2_current");
+        let story_path = stage_dir.join("50_story_retry.md");
+        fs::write(
+            &story_path,
+            "---\nname: Retry Story\nmerge_failure: \"conflicts detected\"\n---\n# Story\n",
+        )
+        .unwrap();
+
+        let (tx, _rx) = tokio::sync::broadcast::channel(16);
+        let mut pending = HashMap::new();
+        pending.insert(story_path.clone(), "2_current".to_string());
+
+        flush_pending(&pending, tmp.path(), &tx);
+
+        let contents = fs::read_to_string(&story_path).unwrap();
+        assert!(
+            !contents.contains("merge_failure"),
+            "merge_failure should be stripped when story lands in 2_current"
+        );
+        assert!(contents.contains("name: Retry Story"));
+    }
+
+    #[test]
+    fn flush_pending_clears_merge_failure_when_moving_to_upcoming() {
+        let tmp = TempDir::new().unwrap();
+        init_git_repo(tmp.path());
+        let stage_dir = make_stage_dir(tmp.path(), "1_upcoming");
+        let story_path = stage_dir.join("51_story_reset.md");
+        fs::write(
+            &story_path,
+            "---\nname: Reset Story\nmerge_failure: \"gate failed\"\n---\n# Story\n",
+        )
+        .unwrap();
+
+        let (tx, _rx) = tokio::sync::broadcast::channel(16);
+        let mut pending = HashMap::new();
+        pending.insert(story_path.clone(), "1_upcoming".to_string());
+
+        flush_pending(&pending, tmp.path(), &tx);
+
+        let contents = fs::read_to_string(&story_path).unwrap();
+        assert!(
+            !contents.contains("merge_failure"),
+            "merge_failure should be stripped when story lands in 1_upcoming"
+        );
+    }
+
+    #[test]
+    fn flush_pending_clears_merge_failure_when_moving_to_done() {
+        let tmp = TempDir::new().unwrap();
+        init_git_repo(tmp.path());
+        let stage_dir = make_stage_dir(tmp.path(), "5_done");
+        let story_path = stage_dir.join("52_story_done.md");
+        fs::write(
+            &story_path,
+            "---\nname: Done Story\nmerge_failure: \"stale error\"\n---\n# Story\n",
+        )
+        .unwrap();
+
+        let (tx, _rx) = tokio::sync::broadcast::channel(16);
+        let mut pending = HashMap::new();
+        pending.insert(story_path.clone(), "5_done".to_string());
+
+        flush_pending(&pending, tmp.path(), &tx);
+
+        let contents = fs::read_to_string(&story_path).unwrap();
+        assert!(
+            !contents.contains("merge_failure"),
+            "merge_failure should be stripped when story lands in 5_done"
+        );
+    }
+
+    #[test]
+    fn flush_pending_preserves_merge_failure_when_in_merge_stage() {
+        let tmp = TempDir::new().unwrap();
+        init_git_repo(tmp.path());
+        let stage_dir = make_stage_dir(tmp.path(), "4_merge");
+        let story_path = stage_dir.join("53_story_merging.md");
+        fs::write(
+            &story_path,
+            "---\nname: Merging Story\nmerge_failure: \"conflicts\"\n---\n# Story\n",
+        )
+        .unwrap();
+
+        let (tx, _rx) = tokio::sync::broadcast::channel(16);
+        let mut pending = HashMap::new();
+        pending.insert(story_path.clone(), "4_merge".to_string());
+
+        flush_pending(&pending, tmp.path(), &tx);
+
+        let contents = fs::read_to_string(&story_path).unwrap();
+        assert!(
+            contents.contains("merge_failure"),
+            "merge_failure should be preserved when story is in 4_merge"
+        );
+    }
+
+    #[test]
+    fn flush_pending_no_op_when_no_merge_failure() {
+        let tmp = TempDir::new().unwrap();
+        init_git_repo(tmp.path());
+        let stage_dir = make_stage_dir(tmp.path(), "2_current");
+        let story_path = stage_dir.join("54_story_clean.md");
+        let original = "---\nname: Clean Story\n---\n# Story\n";
+        fs::write(&story_path, original).unwrap();
+
+        let (tx, _rx) = tokio::sync::broadcast::channel(16);
+        let mut pending = HashMap::new();
+        pending.insert(story_path.clone(), "2_current".to_string());
+
+        flush_pending(&pending, tmp.path(), &tx);
+
+        let contents = fs::read_to_string(&story_path).unwrap();
+        assert_eq!(contents, original, "file without merge_failure should be unchanged");
+    }
+
     // ── stage_for_path (additional edge cases) ────────────────────────────────
 
     #[test]
@@ -713,6 +934,20 @@ mod tests {
         );
     }
 
+    #[test]
+    fn should_commit_stage_only_for_terminal_stages() {
+        // Terminal stages — should commit.
+        assert!(should_commit_stage("1_upcoming"));
+        assert!(should_commit_stage("5_done"));
+        assert!(should_commit_stage("6_archived"));
+        // Intermediate stages — broadcast-only, no commit.
+        assert!(!should_commit_stage("2_current"));
+        assert!(!should_commit_stage("3_qa"));
+        assert!(!should_commit_stage("4_merge"));
+        // Unknown — no commit.
+        assert!(!should_commit_stage("unknown"));
+    }
+
     #[test]
     fn stage_metadata_returns_correct_actions() {
         let (action, msg) = stage_metadata("2_current", "42_story_foo").unwrap();

server/src/llm/chat.rs

@@ -179,6 +179,44 @@ pub fn set_anthropic_api_key(store: &dyn StoreOps, api_key: String) -> Result<()
     set_anthropic_api_key_impl(store, &api_key)
 }
 
+/// Build a prompt for Claude Code that includes prior conversation history.
+///
+/// When a Claude Code session cannot be resumed (no session_id), we embed
+/// the prior messages as a structured preamble so the LLM retains context.
+/// If there is only one user message (the current one), the content is
+/// returned as-is with no preamble.
+fn build_claude_code_context_prompt(messages: &[Message], latest_user_content: &str) -> String {
+    // Collect prior messages (everything except the trailing user message).
+    let prior: Vec<&Message> = messages
+        .iter()
+        .rev()
+        .skip(1) // skip the latest user message
+        .collect::<Vec<_>>()
+        .into_iter()
+        .rev()
+        .collect();
+
+    if prior.is_empty() {
+        return latest_user_content.to_string();
+    }
+
+    let mut parts = Vec::new();
+    parts.push("<conversation_history>".to_string());
+    for msg in &prior {
+        let label = match msg.role {
+            Role::User => "User",
+            Role::Assistant => "Assistant",
+            Role::Tool => "Tool",
+            Role::System => continue,
+        };
+        parts.push(format!("[{}]: {}", label, msg.content));
+    }
+    parts.push("</conversation_history>".to_string());
+    parts.push(String::new());
+    parts.push(latest_user_content.to_string());
+    parts.join("\n")
+}
+
 #[allow(clippy::too_many_arguments)]
 pub async fn chat<F, U, T, A>(
     messages: Vec<Message>,
@@ -224,13 +262,25 @@ where
     if is_claude_code {
         use crate::llm::providers::claude_code::ClaudeCodeProvider;
 
-        let user_message = messages
+        let latest_user_content = messages
             .iter()
             .rev()
             .find(|m| m.role == Role::User)
             .map(|m| m.content.clone())
             .ok_or_else(|| "No user message found".to_string())?;
 
+        // When resuming with a session_id, Claude Code loads its own transcript
+        // from disk — the latest user message is sufficient.  Without a
+        // session_id (e.g. after a page refresh) the prior conversation context
+        // would be lost because Claude Code only receives a single prompt
+        // string.  In that case, prepend the conversation history so the LLM
+        // retains full context even though the session cannot be resumed.
+        let user_message = if config.session_id.is_some() {
+            latest_user_content
+        } else {
+            build_claude_code_context_prompt(&messages, &latest_user_content)
+        };
+
         let project_root = state
             .get_project_root()
             .unwrap_or_else(|_| std::path::PathBuf::from("."));
@@ -244,6 +294,7 @@ where
                 &user_message,
                 &project_root.to_string_lossy(),
                 config.session_id.as_deref(),
+                None,
                 &mut cancel_rx,
                 |token| on_token(token),
                 |thinking| on_thinking(thinking),
@@ -404,7 +455,7 @@ where
     }
 
     Ok(ChatResult {
-        messages: new_messages,
+        messages: current_history[2..].to_vec(),
         session_id: None,
     })
 }
@@ -1095,4 +1146,102 @@ mod tests {
         let result = execute_tool(&call, &state).await;
         assert!(result.starts_with("Error:"), "unexpected result: {result}");
     }
+
+    // ---------------------------------------------------------------------------
+    // build_claude_code_context_prompt (Bug 245)
+    // ---------------------------------------------------------------------------
+
+    #[test]
+    fn context_prompt_single_message_returns_content_as_is() {
+        let messages = vec![Message {
+            role: Role::User,
+            content: "hello".to_string(),
+            tool_calls: None,
+            tool_call_id: None,
+        }];
+        let result = build_claude_code_context_prompt(&messages, "hello");
+        assert_eq!(result, "hello");
+    }
+
+    #[test]
+    fn context_prompt_includes_prior_conversation() {
+        let messages = vec![
+            Message {
+                role: Role::User,
+                content: "What is Rust?".to_string(),
+                tool_calls: None,
+                tool_call_id: None,
+            },
+            Message {
+                role: Role::Assistant,
+                content: "Rust is a systems language.".to_string(),
+                tool_calls: None,
+                tool_call_id: None,
+            },
+            Message {
+                role: Role::User,
+                content: "Tell me more".to_string(),
+                tool_calls: None,
+                tool_call_id: None,
+            },
+        ];
+        let result = build_claude_code_context_prompt(&messages, "Tell me more");
+        assert!(
+            result.contains("<conversation_history>"),
+            "should have history preamble"
+        );
+        assert!(
+            result.contains("[User]: What is Rust?"),
+            "should include prior user message"
+        );
+        assert!(
+            result.contains("[Assistant]: Rust is a systems language."),
+            "should include prior assistant message"
+        );
+        assert!(
+            result.contains("</conversation_history>"),
+            "should close history block"
+        );
+        assert!(
+            result.ends_with("Tell me more"),
+            "should end with latest user message"
+        );
+    }
+
+    #[test]
+    fn context_prompt_skips_system_messages() {
+        let messages = vec![
+            Message {
+                role: Role::System,
+                content: "You are a helpful assistant.".to_string(),
+                tool_calls: None,
+                tool_call_id: None,
+            },
+            Message {
+                role: Role::User,
+                content: "hi".to_string(),
+                tool_calls: None,
+                tool_call_id: None,
+            },
+            Message {
+                role: Role::Assistant,
+                content: "hello".to_string(),
+                tool_calls: None,
+                tool_call_id: None,
+            },
+            Message {
+                role: Role::User,
+                content: "bye".to_string(),
+                tool_calls: None,
+                tool_call_id: None,
+            },
+        ];
+        let result = build_claude_code_context_prompt(&messages, "bye");
+        assert!(
+            !result.contains("helpful assistant"),
+            "should not include system messages"
+        );
+        assert!(result.contains("[User]: hi"));
+        assert!(result.contains("[Assistant]: hello"));
+    }
 }

server/src/llm/providers/claude_code.rs

@@ -42,6 +42,7 @@ impl ClaudeCodeProvider {
         user_message: &str,
         project_root: &str,
         session_id: Option<&str>,
+        system_prompt: Option<&str>,
         cancel_rx: &mut watch::Receiver<bool>,
         mut on_token: F,
         mut on_thinking: T,
@@ -55,6 +56,7 @@ impl ClaudeCodeProvider {
         let message = user_message.to_string();
         let cwd = project_root.to_string();
         let resume_id = session_id.map(|s| s.to_string());
+        let sys_prompt = system_prompt.map(|s| s.to_string());
         let cancelled = Arc::new(AtomicBool::new(false));
         let cancelled_clone = cancelled.clone();
 
@@ -79,6 +81,7 @@ impl ClaudeCodeProvider {
                 &message,
                 &cwd,
                 resume_id.as_deref(),
+                sys_prompt.as_deref(),
                 cancelled,
                 token_tx,
                 thinking_tx,
@@ -120,6 +123,7 @@ impl ClaudeCodeProvider {
             .map_err(|e| format!("PTY task panicked: {e}"))??;
 
         let captured_session_id = sid_rx.await.ok();
+        slog!("[pty-debug] RECEIVED session_id: {:?}", captured_session_id);
         let structured_messages: Vec<Message> = msg_rx.try_iter().collect();
 
         Ok(ClaudeCodeResult {
@@ -146,6 +150,7 @@ fn run_pty_session(
     user_message: &str,
     cwd: &str,
     resume_session_id: Option<&str>,
+    _system_prompt: Option<&str>,
     cancelled: Arc<AtomicBool>,
     token_tx: tokio::sync::mpsc::UnboundedSender<String>,
     thinking_tx: tokio::sync::mpsc::UnboundedSender<String>,
@@ -184,6 +189,8 @@ fn run_pty_session(
     // a tool requires user approval, instead of using PTY stdin/stdout.
     cmd.arg("--permission-prompt-tool");
     cmd.arg("mcp__story-kit__prompt_permission");
+    // Note: --system is not a valid Claude Code CLI flag. System-level
+    // instructions (like bot name) are prepended to the user prompt instead.
     cmd.cwd(cwd);
     // Keep TERM reasonable but disable color
     cmd.env("NO_COLOR", "1");
@@ -346,6 +353,7 @@ fn process_json_event(
     // Capture session_id from the first event that carries it
     if let Some(tx) = sid_tx.take() {
         if let Some(sid) = json.get("session_id").and_then(|s| s.as_str()) {
+            slog!("[pty-debug] CAPTURED session_id: {}", sid);
             let _ = tx.send(sid.to_string());
         } else {
             *sid_tx = Some(tx);

server/src/main.rs

@@ -58,7 +58,6 @@ async fn main() -> Result<(), std::io::Error> {
             explicit_root.to_string_lossy().to_string(),
             &app_state,
             store.as_ref(),
-            port,
         )
         .await
         {
@@ -81,7 +80,6 @@ async fn main() -> Result<(), std::io::Error> {
                 project_root.to_string_lossy().to_string(),
                 &app_state,
                 store.as_ref(),
-                port,
             )
             .await
             .unwrap_or_else(|e| {
@@ -167,6 +165,13 @@ async fn main() -> Result<(), std::io::Error> {
     // Permission channel: MCP prompt_permission → WebSocket handler.
     let (perm_tx, perm_rx) = tokio::sync::mpsc::unbounded_channel();
 
+    // Clone watcher_tx for the Matrix bot before it is moved into AppContext.
+    let watcher_tx_for_bot = watcher_tx.clone();
+    // Wrap perm_rx in Arc<Mutex> so it can be shared with both the WebSocket
+    // handler (via AppContext) and the Matrix bot.
+    let perm_rx = Arc::new(tokio::sync::Mutex::new(perm_rx));
+    let perm_rx_for_bot = Arc::clone(&perm_rx);
+
     // Capture project root, agents Arc, and reconciliation sender before ctx
     // is consumed by build_routes.
     let startup_root: Option<PathBuf> = app_state.project_root.lock().unwrap().clone();
@@ -182,7 +187,7 @@ async fn main() -> Result<(), std::io::Error> {
         watcher_tx,
         reconciliation_tx,
         perm_tx,
-        perm_rx: Arc::new(tokio::sync::Mutex::new(perm_rx)),
+        perm_rx,
     };
 
     let app = build_routes(ctx);
@@ -191,7 +196,7 @@ async fn main() -> Result<(), std::io::Error> {
     // Optional Matrix bot: connect to the homeserver and start listening for
     // messages if `.story_kit/bot.toml` is present and enabled.
     if let Some(ref root) = startup_root {
-        matrix::spawn_bot(root);
+        matrix::spawn_bot(root, watcher_tx_for_bot, perm_rx_for_bot);
     }
 
     // On startup:

server/src/matrix/config.rs

@@ -5,6 +5,10 @@ fn default_history_size() -> usize {
     20
 }
 
+fn default_permission_timeout_secs() -> u64 {
+    120
+}
+
 /// Configuration for the Matrix bot, read from `.story_kit/bot.toml`.
 #[derive(Deserialize, Clone, Debug)]
 pub struct BotConfig {
@@ -35,11 +39,20 @@ pub struct BotConfig {
     /// dropped. Defaults to 20.
     #[serde(default = "default_history_size")]
     pub history_size: usize,
+    /// Timeout in seconds for permission prompts surfaced to the Matrix room.
+    /// If the user does not respond within this window the permission is denied
+    /// (fail-closed). Defaults to 120 seconds.
+    #[serde(default = "default_permission_timeout_secs")]
+    pub permission_timeout_secs: u64,
     /// Previously used to select an Anthropic model. Now ignored — the bot
     /// uses Claude Code which manages its own model selection. Kept for
     /// backwards compatibility so existing bot.toml files still parse.
     #[allow(dead_code)]
     pub model: Option<String>,
+    /// Display name the bot uses to identify itself in conversations.
+    /// If unset, the bot falls back to "Assistant".
+    #[serde(default)]
+    pub display_name: Option<String>,
 }
 
 impl BotConfig {
@@ -256,6 +269,88 @@ history_size = 50
         assert_eq!(config.history_size, 50);
     }
 
+    #[test]
+    fn load_reads_display_name() {
+        let tmp = tempfile::tempdir().unwrap();
+        let sk = tmp.path().join(".story_kit");
+        fs::create_dir_all(&sk).unwrap();
+        fs::write(
+            sk.join("bot.toml"),
+            r#"
+homeserver = "https://matrix.example.com"
+username = "@bot:example.com"
+password = "secret"
+room_ids = ["!abc:example.com"]
+enabled = true
+display_name = "Timmy"
+"#,
+        )
+        .unwrap();
+        let config = BotConfig::load(tmp.path()).unwrap();
+        assert_eq!(config.display_name.as_deref(), Some("Timmy"));
+    }
+
+    #[test]
+    fn load_display_name_defaults_to_none_when_absent() {
+        let tmp = tempfile::tempdir().unwrap();
+        let sk = tmp.path().join(".story_kit");
+        fs::create_dir_all(&sk).unwrap();
+        fs::write(
+            sk.join("bot.toml"),
+            r#"
+homeserver = "https://matrix.example.com"
+username = "@bot:example.com"
+password = "secret"
+room_ids = ["!abc:example.com"]
+enabled = true
+"#,
+        )
+        .unwrap();
+        let config = BotConfig::load(tmp.path()).unwrap();
+        assert!(config.display_name.is_none());
+    }
+
+    #[test]
+    fn load_uses_default_permission_timeout() {
+        let tmp = tempfile::tempdir().unwrap();
+        let sk = tmp.path().join(".story_kit");
+        fs::create_dir_all(&sk).unwrap();
+        fs::write(
+            sk.join("bot.toml"),
+            r#"
+homeserver = "https://matrix.example.com"
+username = "@bot:example.com"
+password = "secret"
+room_ids = ["!abc:example.com"]
+enabled = true
+"#,
+        )
+        .unwrap();
+        let config = BotConfig::load(tmp.path()).unwrap();
+        assert_eq!(config.permission_timeout_secs, 120);
+    }
+
+    #[test]
+    fn load_respects_custom_permission_timeout() {
+        let tmp = tempfile::tempdir().unwrap();
+        let sk = tmp.path().join(".story_kit");
+        fs::create_dir_all(&sk).unwrap();
+        fs::write(
+            sk.join("bot.toml"),
+            r#"
+homeserver = "https://matrix.example.com"
+username = "@bot:example.com"
+password = "secret"
+room_ids = ["!abc:example.com"]
+enabled = true
+permission_timeout_secs = 60
+"#,
+        )
+        .unwrap();
+        let config = BotConfig::load(tmp.path()).unwrap();
+        assert_eq!(config.permission_timeout_secs, 60);
+    }
+
     #[test]
     fn load_ignores_legacy_require_verified_devices_key() {
         // Old bot.toml files that still have `require_verified_devices = true`

server/src/matrix/mod.rs

@@ -17,10 +17,15 @@
 
 mod bot;
 mod config;
+pub mod notifications;
 
 pub use config::BotConfig;
 
+use crate::http::context::PermissionForward;
+use crate::io::watcher::WatcherEvent;
 use std::path::Path;
+use std::sync::Arc;
+use tokio::sync::{Mutex as TokioMutex, broadcast, mpsc};
 
 /// Attempt to start the Matrix bot.
 ///
@@ -28,8 +33,20 @@ use std::path::Path;
 /// absent or `enabled = false`, this function returns immediately without
 /// spawning anything — the server continues normally.
 ///
+/// When the bot is enabled, a notification listener is also spawned that
+/// posts stage-transition messages to all configured rooms whenever a work
+/// item moves between pipeline stages.
+///
+/// `perm_rx` is the permission-request receiver shared with the MCP
+/// `prompt_permission` tool. The bot locks it during active chat sessions
+/// to surface permission prompts to the Matrix room and relay user decisions.
+///
 /// Must be called from within a Tokio runtime context (e.g., from `main`).
-pub fn spawn_bot(project_root: &Path) {
+pub fn spawn_bot(
+    project_root: &Path,
+    watcher_tx: broadcast::Sender<WatcherEvent>,
+    perm_rx: Arc<TokioMutex<mpsc::UnboundedReceiver<PermissionForward>>>,
+) {
     let config = match BotConfig::load(project_root) {
         Some(c) => c,
         None => {
@@ -45,8 +62,9 @@ pub fn spawn_bot(project_root: &Path) {
     );
 
     let root = project_root.to_path_buf();
+    let watcher_rx = watcher_tx.subscribe();
     tokio::spawn(async move {
-        if let Err(e) = bot::run_bot(config, root).await {
+        if let Err(e) = bot::run_bot(config, root, watcher_rx, perm_rx).await {
             crate::slog!("[matrix-bot] Fatal error: {e}");
         }
     });

server/src/matrix/notifications.rs

@@ -0,0 +1,376 @@
+//! Stage transition notifications for Matrix rooms.
+//!
+//! Subscribes to [`WatcherEvent`] broadcasts and posts a notification to all
+//! configured Matrix rooms whenever a work item moves between pipeline stages.
+
+use crate::io::story_metadata::parse_front_matter;
+use crate::io::watcher::WatcherEvent;
+use crate::slog;
+use matrix_sdk::ruma::events::room::message::RoomMessageEventContent;
+use matrix_sdk::ruma::OwnedRoomId;
+use matrix_sdk::Client;
+use std::path::{Path, PathBuf};
+use tokio::sync::broadcast;
+
+/// Human-readable display name for a pipeline stage directory.
+pub fn stage_display_name(stage: &str) -> &'static str {
+    match stage {
+        "1_upcoming" => "Upcoming",
+        "2_current" => "Current",
+        "3_qa" => "QA",
+        "4_merge" => "Merge",
+        "5_done" => "Done",
+        "6_archived" => "Archived",
+        _ => "Unknown",
+    }
+}
+
+/// Infer the previous pipeline stage for a given destination stage.
+///
+/// Returns `None` for `1_upcoming` since items are created there (not
+/// transitioned from another stage).
+pub fn inferred_from_stage(to_stage: &str) -> Option<&'static str> {
+    match to_stage {
+        "2_current" => Some("Upcoming"),
+        "3_qa" => Some("Current"),
+        "4_merge" => Some("QA"),
+        "5_done" => Some("Merge"),
+        "6_archived" => Some("Done"),
+        _ => None,
+    }
+}
+
+/// Extract the numeric story number from an item ID like `"261_story_slug"`.
+pub fn extract_story_number(item_id: &str) -> Option<&str> {
+    item_id
+        .split('_')
+        .next()
+        .filter(|s| !s.is_empty() && s.chars().all(|c| c.is_ascii_digit()))
+}
+
+/// Read the story name from the work item file's YAML front matter.
+///
+/// Returns `None` if the file doesn't exist or has no parseable name.
+pub fn read_story_name(project_root: &Path, stage: &str, item_id: &str) -> Option<String> {
+    let path = project_root
+        .join(".story_kit")
+        .join("work")
+        .join(stage)
+        .join(format!("{item_id}.md"));
+    let contents = std::fs::read_to_string(&path).ok()?;
+    let meta = parse_front_matter(&contents).ok()?;
+    meta.name
+}
+
+/// Format a stage transition notification message.
+///
+/// Returns `(plain_text, html)` suitable for `RoomMessageEventContent::text_html`.
+pub fn format_stage_notification(
+    item_id: &str,
+    story_name: Option<&str>,
+    from_stage: &str,
+    to_stage: &str,
+) -> (String, String) {
+    let number = extract_story_number(item_id).unwrap_or(item_id);
+    let name = story_name.unwrap_or(item_id);
+
+    let plain = format!("#{number} {name} \u{2014} {from_stage} \u{2192} {to_stage}");
+    let html = format!(
+        "<strong>#{number}</strong> <em>{name}</em> \u{2014} {from_stage} \u{2192} {to_stage}"
+    );
+    (plain, html)
+}
+
+/// Format an error notification message for a story failure.
+///
+/// Returns `(plain_text, html)` suitable for `RoomMessageEventContent::text_html`.
+pub fn format_error_notification(
+    item_id: &str,
+    story_name: Option<&str>,
+    reason: &str,
+) -> (String, String) {
+    let number = extract_story_number(item_id).unwrap_or(item_id);
+    let name = story_name.unwrap_or(item_id);
+
+    let plain = format!("\u{274c} #{number} {name} \u{2014} {reason}");
+    let html = format!(
+        "\u{274c} <strong>#{number}</strong> <em>{name}</em> \u{2014} {reason}"
+    );
+    (plain, html)
+}
+
+/// Spawn a background task that listens for watcher events and posts
+/// stage-transition notifications to all configured Matrix rooms.
+pub fn spawn_notification_listener(
+    client: Client,
+    room_ids: Vec<OwnedRoomId>,
+    watcher_rx: broadcast::Receiver<WatcherEvent>,
+    project_root: PathBuf,
+) {
+    tokio::spawn(async move {
+        let mut rx = watcher_rx;
+        loop {
+            match rx.recv().await {
+                Ok(WatcherEvent::WorkItem {
+                    ref stage,
+                    ref item_id,
+                    ..
+                }) => {
+                    // Only notify on stage transitions, not creations.
+                    let Some(from_display) = inferred_from_stage(stage) else {
+                        continue;
+                    };
+                    let to_display = stage_display_name(stage);
+
+                    let story_name = read_story_name(&project_root, stage, item_id);
+                    let (plain, html) = format_stage_notification(
+                        item_id,
+                        story_name.as_deref(),
+                        from_display,
+                        to_display,
+                    );
+
+                    slog!("[matrix-bot] Sending stage notification: {plain}");
+
+                    for room_id in &room_ids {
+                        if let Some(room) = client.get_room(room_id) {
+                            let content =
+                                RoomMessageEventContent::text_html(plain.clone(), html.clone());
+                            if let Err(e) = room.send(content).await {
+                                slog!(
+                                    "[matrix-bot] Failed to send notification to {room_id}: {e}"
+                                );
+                            }
+                        }
+                    }
+                }
+                Ok(WatcherEvent::MergeFailure {
+                    ref story_id,
+                    ref reason,
+                }) => {
+                    let story_name =
+                        read_story_name(&project_root, "4_merge", story_id);
+                    let (plain, html) = format_error_notification(
+                        story_id,
+                        story_name.as_deref(),
+                        reason,
+                    );
+
+                    slog!("[matrix-bot] Sending error notification: {plain}");
+
+                    for room_id in &room_ids {
+                        if let Some(room) = client.get_room(room_id) {
+                            let content =
+                                RoomMessageEventContent::text_html(plain.clone(), html.clone());
+                            if let Err(e) = room.send(content).await {
+                                slog!(
+                                    "[matrix-bot] Failed to send error notification to {room_id}: {e}"
+                                );
+                            }
+                        }
+                    }
+                }
+                Ok(_) => {} // Ignore non-work-item events
+                Err(broadcast::error::RecvError::Lagged(n)) => {
+                    slog!(
+                        "[matrix-bot] Notification listener lagged, skipped {n} events"
+                    );
+                }
+                Err(broadcast::error::RecvError::Closed) => {
+                    slog!(
+                        "[matrix-bot] Watcher channel closed, stopping notification listener"
+                    );
+                    break;
+                }
+            }
+        }
+    });
+}
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+
+    // ── stage_display_name ──────────────────────────────────────────────────
+
+    #[test]
+    fn stage_display_name_maps_all_known_stages() {
+        assert_eq!(stage_display_name("1_upcoming"), "Upcoming");
+        assert_eq!(stage_display_name("2_current"), "Current");
+        assert_eq!(stage_display_name("3_qa"), "QA");
+        assert_eq!(stage_display_name("4_merge"), "Merge");
+        assert_eq!(stage_display_name("5_done"), "Done");
+        assert_eq!(stage_display_name("6_archived"), "Archived");
+        assert_eq!(stage_display_name("unknown"), "Unknown");
+    }
+
+    // ── inferred_from_stage ─────────────────────────────────────────────────
+
+    #[test]
+    fn inferred_from_stage_returns_previous_stage() {
+        assert_eq!(inferred_from_stage("2_current"), Some("Upcoming"));
+        assert_eq!(inferred_from_stage("3_qa"), Some("Current"));
+        assert_eq!(inferred_from_stage("4_merge"), Some("QA"));
+        assert_eq!(inferred_from_stage("5_done"), Some("Merge"));
+        assert_eq!(inferred_from_stage("6_archived"), Some("Done"));
+    }
+
+    #[test]
+    fn inferred_from_stage_returns_none_for_upcoming() {
+        assert_eq!(inferred_from_stage("1_upcoming"), None);
+    }
+
+    #[test]
+    fn inferred_from_stage_returns_none_for_unknown() {
+        assert_eq!(inferred_from_stage("9_unknown"), None);
+    }
+
+    // ── extract_story_number ────────────────────────────────────────────────
+
+    #[test]
+    fn extract_story_number_parses_numeric_prefix() {
+        assert_eq!(
+            extract_story_number("261_story_bot_notifications"),
+            Some("261")
+        );
+        assert_eq!(extract_story_number("42_bug_fix_thing"), Some("42"));
+        assert_eq!(extract_story_number("1_spike_research"), Some("1"));
+    }
+
+    #[test]
+    fn extract_story_number_returns_none_for_non_numeric() {
+        assert_eq!(extract_story_number("abc_story_thing"), None);
+        assert_eq!(extract_story_number(""), None);
+    }
+
+    // ── read_story_name ─────────────────────────────────────────────────────
+
+    #[test]
+    fn read_story_name_reads_from_front_matter() {
+        let tmp = tempfile::tempdir().unwrap();
+        let stage_dir = tmp
+            .path()
+            .join(".story_kit")
+            .join("work")
+            .join("2_current");
+        std::fs::create_dir_all(&stage_dir).unwrap();
+        std::fs::write(
+            stage_dir.join("42_story_my_feature.md"),
+            "---\nname: My Cool Feature\n---\n# Story\n",
+        )
+        .unwrap();
+
+        let name = read_story_name(tmp.path(), "2_current", "42_story_my_feature");
+        assert_eq!(name.as_deref(), Some("My Cool Feature"));
+    }
+
+    #[test]
+    fn read_story_name_returns_none_for_missing_file() {
+        let tmp = tempfile::tempdir().unwrap();
+        let name = read_story_name(tmp.path(), "2_current", "99_story_missing");
+        assert_eq!(name, None);
+    }
+
+    #[test]
+    fn read_story_name_returns_none_for_missing_name_field() {
+        let tmp = tempfile::tempdir().unwrap();
+        let stage_dir = tmp
+            .path()
+            .join(".story_kit")
+            .join("work")
+            .join("2_current");
+        std::fs::create_dir_all(&stage_dir).unwrap();
+        std::fs::write(
+            stage_dir.join("42_story_no_name.md"),
+            "---\ncoverage_baseline: 50%\n---\n# Story\n",
+        )
+        .unwrap();
+
+        let name = read_story_name(tmp.path(), "2_current", "42_story_no_name");
+        assert_eq!(name, None);
+    }
+
+    // ── format_error_notification ────────────────────────────────────────────
+
+    #[test]
+    fn format_error_notification_with_story_name() {
+        let (plain, html) =
+            format_error_notification("262_story_bot_errors", Some("Bot error notifications"), "merge conflict in src/main.rs");
+        assert_eq!(
+            plain,
+            "\u{274c} #262 Bot error notifications \u{2014} merge conflict in src/main.rs"
+        );
+        assert_eq!(
+            html,
+            "\u{274c} <strong>#262</strong> <em>Bot error notifications</em> \u{2014} merge conflict in src/main.rs"
+        );
+    }
+
+    #[test]
+    fn format_error_notification_without_story_name_falls_back_to_item_id() {
+        let (plain, _html) =
+            format_error_notification("42_bug_fix_thing", None, "tests failed");
+        assert_eq!(
+            plain,
+            "\u{274c} #42 42_bug_fix_thing \u{2014} tests failed"
+        );
+    }
+
+    #[test]
+    fn format_error_notification_non_numeric_id_uses_full_id() {
+        let (plain, _html) =
+            format_error_notification("abc_story_thing", Some("Some Story"), "clippy errors");
+        assert_eq!(
+            plain,
+            "\u{274c} #abc_story_thing Some Story \u{2014} clippy errors"
+        );
+    }
+
+    // ── format_stage_notification ───────────────────────────────────────────
+
+    #[test]
+    fn format_notification_with_story_name() {
+        let (plain, html) = format_stage_notification(
+            "261_story_bot_notifications",
+            Some("Bot notifications"),
+            "Upcoming",
+            "Current",
+        );
+        assert_eq!(
+            plain,
+            "#261 Bot notifications \u{2014} Upcoming \u{2192} Current"
+        );
+        assert_eq!(
+            html,
+            "<strong>#261</strong> <em>Bot notifications</em> \u{2014} Upcoming \u{2192} Current"
+        );
+    }
+
+    #[test]
+    fn format_notification_without_story_name_falls_back_to_item_id() {
+        let (plain, _html) = format_stage_notification(
+            "42_bug_fix_thing",
+            None,
+            "Current",
+            "QA",
+        );
+        assert_eq!(
+            plain,
+            "#42 42_bug_fix_thing \u{2014} Current \u{2192} QA"
+        );
+    }
+
+    #[test]
+    fn format_notification_non_numeric_id_uses_full_id() {
+        let (plain, _html) = format_stage_notification(
+            "abc_story_thing",
+            Some("Some Story"),
+            "QA",
+            "Merge",
+        );
+        assert_eq!(
+            plain,
+            "#abc_story_thing Some Story \u{2014} QA \u{2192} Merge"
+        );
+    }
+}