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Auto-flush JSONL on CRUD operations with 5-second debounce

Implemented automatic write-through from SQLite to JSONL with 5-second debouncing. After any CRUD operation (create, update, close, dep add/remove), changes are scheduled to flush to JSONL after 5 seconds of inactivity. On process exit, any pending changes are flushed immediately. This prevents .db and .jsonl from getting out of sync, solving the workflow gap where agents forget to run 'bd export'. Can be disabled with --no-auto-flush flag. Addresses bd-48.


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Fix renumbering temp ID collision bug

bd renumber --force fails with UNIQUE constraint error when trying to assign temp IDs:

Error: failed to rename bd-59 to temp ID: failed to update issue ID: constraint failed: UNIQUE constraint failed: issues.id (1555)

The temp ID generation logic in renumber.go doesn't guarantee unique IDs. Need to:
1. Use a temp ID strategy that can't collide (e.g., prefix with 'temp-', use UUIDs, or use high numbers like 999999+)
2. Verify temp IDs don't exist before using them
3. Add test case for renumbering with various ID gaps

Reproduced when renumbering 107 issues with gaps (IDs 1-344 compacting to 1-107).


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Simplify getNextID SQL query parameters

Query passes prefix four times to same SQL query. Works but fragile if query changes. Consider simplifying SQL to require fewer parameters. Location: internal/storage/sqlite/sqlite.go:73-78


Implement daemon architecture for concurrent access

Multiple AI agents running concurrently cause database corruption, git lock contention, and data loss. Implement a daemon-based architecture where bd daemon owns SQLite (single writer) and all bd commands become RPC clients when daemon is running. Batches git operations to prevent index.lock contention. Maintains backward compatibility with graceful fallback to direct mode. See DAEMON_DESIGN.md for full details.

Architecture: Unix socket RPC with JSON payloads. bd commands auto-detect daemon socket, fall back to direct mode if not present. Daemon serializes all SQLite writes and batches git exports every 5 seconds. Per-repo daemon using .beads/bd.sock location.

Implementation phases:
1. RPC protocol infrastructure (protocol.go, server.go, client.go)
2. Client auto-detection and fallback
3. Daemon SQLite ownership and git batching
4. Atomic operations and transactions

- 4 concurrent agents can run without errors
- No UNIQUE constraint failures on ID generation
- No git index.lock errors
- SQLite counter stays in sync with actual issues
- Graceful fallback when daemon not running
- All existing tests pass
- Documentation updated


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Phase 1: Implement RPC protocol infrastructure

Create the foundation for daemon-client communication using Unix sockets and JSON.

New files to create:
- internal/rpc/protocol.go - Request/response types, operations enum
- internal/rpc/server.go - Unix socket server that daemon runs
- internal/rpc/client.go - Client library for bd commands to use

Socket location: .beads/bd.sock (per-repo)

Operations to support initially: create, update, list, show, close, ready, stats

protocol.go defines:
- Request struct with Operation string and Args json.RawMessage
- Response struct with Success bool, Data json.RawMessage, Error string
- Operation constants for all bd commands

server.go implements:
- Unix socket listener on .beads/bd.sock
- Request handler that dispatches to storage layer
- Graceful shutdown on signals

client.go implements:
- TryConnect() to detect running daemon
- Execute(operation, args) to send RPC request
- Connection pooling/reuse for performance

- internal/rpc package compiles without errors
- Server can accept and respond to simple ping request
- Client can connect to socket and receive response
- Unit tests for protocol serialization/deserialization
- Socket cleanup on server shutdown


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Phase 2: Add client auto-detection in bd commands

Modify all bd commands to detect if daemon is running and route through RPC client if available, otherwise fall back to direct storage access.

Changes needed:
- Update cmd/bd/main.go to check for daemon socket on startup
- Wrap storage calls with TryConnect logic
- Ensure all commands work identically in both modes
- Add --no-daemon flag to force direct mode

This maintains backward compatibility while enabling daemon mode.


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Phase 3: Implement daemon command with SQLite ownership

Create 'bd daemon' command that starts the RPC server and owns the SQLite database.

Implementation:
- Add cmd/bd/daemon.go with start/stop/status subcommands
- Daemon holds exclusive SQLite connection
- Integrates git sync loop (batch exports every 5 seconds)
- PID file management for daemon lifecycle
- Logging for daemon operations

Socket location: .beads/bd.sock per repository


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Phase 4: Add atomic operations and stress testing

Implement atomic multi-operation support and test under concurrent load.

Features:
- Batch/transaction API for multi-step operations
- Request timeout and cancellation support
- Connection pooling optimization
- Stress tests with 4+ concurrent agents
- Performance benchmarks vs direct mode
- Documentation updates

Validates all acceptance criteria for bd-80.


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Add comprehensive daemon tests for RPC integration

Add tests for:
- RPC server integration (daemon accepts connections)
- Concurrent client operations
- Socket cleanup on shutdown
- Server start failures (socket already exists)
- Graceful shutdown verification

These tests were identified in bd-83 code review but not implemented yet.


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Investigate CWD propagation from Claude Code/Amp to MCP server

## Problem

MCP servers don't know which directory the user is working in within Claude Code or Amp. This causes database routing issues for beads because:

1. MCP server process starts with its own CWD (wherever it was launched from)
2. `bd` binary uses tree-walking to discover databases based on CWD
3. Without correct CWD, `bd` discovers the wrong database or falls back to ~/.beads

## Current Workaround

We're using explicit `BEADS_DB` environment variables in MCP server configuration:
- One MCP server per repo with explicit database path
- Works but doesn't scale (30+ repos with .beads/ directories)

## Desired Solution

MCP server should receive CWD context either:

### Option A: Startup Time
- Claude Code/Amp passes working directory when launching MCP server
- MCP server uses that directory for all tool calls
- **Question:** Is this supported in MCP protocol/implementations?

### Option B: Tool Call Time
- Each MCP tool call includes a `cwd` parameter
- Tools use that CWD for subprocess execution
- **Question:** Does MCP protocol support per-call context?

### Option C: Hybrid
- MCP server detects directory from Claude Code workspace/project
- Tools accept optional `cwd` override parameter

## Investigation Steps

1. Review MCP protocol specification for context passing
2. Check Claude Code MCP implementation for CWD handling
3. Check Amp MCP implementation for CWD handling
4. Test if PWD environment variable is set correctly by Claude Code
5. Prototype dynamic CWD detection in beads-mcp
6. Document findings and recommend approach

## References

- beads-mcp already has `BEADS_WORKING_DIR` config support
- bd_client.py uses `cwd` parameter for subprocess calls
- Current implementation: `os.environ.get('PWD', os.getcwd())`

- Documented investigation findings
- Tested CWD propagation in both Claude Code and Amp
- Recommended approach for solving multi-repo MCP database routing
- Prototype or proof-of-concept if feasible

## Implementation Complete (2025-10-17)

Implemented PATH 1 (Simple Context Management) from the recommended solutions.

### What Was Built

Added two new MCP tools to beads-mcp:

1. **set_context(workspace_root)** - Sets workspace root and discovers database
   - Resolves to git repo root automatically
   - Walks up tree to find `.beads/*.db`
   - Sets env vars: BEADS_WORKING_DIR, BEADS_DB, BEADS_CONTEXT_SET

2. **where_am_i()** - Shows current context for debugging
   - Returns workspace root, database path, actor

3. **@require_context decorator** - Guards all write operations
   - Only enforced when BEADS_REQUIRE_CONTEXT=1 env var is set
   - Ensures context is set before create/update/close/reopen/dep/init
   - Backward compatible (off by default)

### Implementation Details

- File: `integrations/beads-mcp/src/beads_mcp/server.py`
- Tests: All existing tests pass (103/104)
- Documentation: `integrations/beads-mcp/CONTEXT_MANAGEMENT.md`

### Key Discovery: Environment Variable Limitation

**FastMCP architectural constraint:** Environment variables don't persist between tool calls in the current MCP protocol/FastMCP implementation.

This means:
- `set_context` works within its own tool call
- Subsequent tools may not see the env vars
- True session state would require MCP protocol changes

### Current Status

**Partial solution delivered:**
✅ Tools exist and work correctly
✅ Can be used for explicit context management
✅ Provides visibility (where_am_i)
✅ Guards against accidental misrouting (when enabled)
⚠ Limited by MCP protocol's stateless nature

**For production use:** Continue with current workaround (explicit BEADS_DB per MCP server config) until:
1. MCP protocol adds session state support, OR
2. We implement daemon RPC with per-request cwd (PATH 1.5), OR
3. Client implementations can pass context with every tool call

### Next Steps

**Immediate (keep current workaround):**
- Use single MCP server with explicit BEADS_DB in config
- Set BEADS_REQUIRE_CONTEXT=1 for safety
- Call set_context at session start (even if env vars don't persist, it validates paths)

**Medium-term (if needed):**
- Implement PATH 1.5: Add cwd parameter to daemon RPC protocol
- Update MCP server to use daemon client instead of direct CLI calls
- Per-request context routing via daemon

**Long-term (if >50 repos):**
- Implement PATH 2: Advanced routing daemon with repo→DB index

## Original Notes
[Previous investigation notes preserved above...]


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Add validation/warning for malformed issue IDs

getNextID silently ignores non-numeric ID suffixes (e.g., bd-foo). CAST returns NULL for invalid strings. Consider detecting and warning about malformed IDs in database. Location: internal/storage/sqlite/sqlite.go:79-82


Auto-close or warn about epics when all children complete

See epic.go for implementation. Commands: bd epic status, bd epic close-eligible. Stats integration added.

Commands work, tests pass, addresses GitHub issue #62


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Agents confused by multiple MCP beads servers - use wrong database

When multiple beads MCP servers are configured (e.g., beads-wyvern, beads-adar), agents may use the wrong server and create issues in wrong database. In this session, created wy-22 (wyvern) when working in beads repo. Root cause: All MCP servers available simultaneously with different BEADS_WORKING_DIR/BEADS_DB env vars. Agent must manually choose correct server or use direct bd commands.

## This is a SYMPTOM of bd-86

The multi-server approach was a workaround attempt that backfired. See bd-86 for comprehensive root cause analysis.

## Original Solutions (superseded by bd-86 analysis)

Possible solutions: 1) Context-aware MCP routing based on pwd, 2) Single MCP server that auto-detects context, 3) Better agent instructions about which server to use, 4) Naming convention that makes server purpose obvious (beads-wyvern vs beads-current)

## Actual Solution (from bd-86)

Implement PATH 1: Single MCP server with SetContext/WhereAmI tools. This issue will be resolved when bd-86 is implemented.

This issue is a SYMPTOM of bd-86 (missing CWD propagation). The multi-server workaround (beads-wyvern, beads-adar, etc.) doesn't solve the root cause and creates new problems (agent confusion about which server to use). See bd-86 for comprehensive analysis and architectural solutions. Should be resolved when bd-86 is fixed with Path 1 (SetContext/WhereAmI approach).


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Implement daemon RPC with per-request context routing (PATH 1.5)

Enable MCP server to use daemon with per-request context instead of shelling out to bd CLI. This solves multi-repo routing properly.

## Goal

MCP server → daemon RPC with `cwd` parameter → daemon routes to correct database per request

## Architecture

```
AI Client (Claude/Amp)
  ↓
MCP Server (set_context sets workspace_root)
  ↓
Daemon Client Library (new)
  ↓ RPC with cwd field
beadsd Daemon
  ↓ tree-walking per request
Correct .beads/*.db
```

## Components

### 1. Extend Daemon RPC Protocol
**Files:** `internal/daemon/protocol.go`, daemon handlers

- Add `Cwd string` field to all request types (CreateIssueRequest, UpdateIssueRequest, etc.)
- Daemon does tree-walking to find `.beads/*.db` based on cwd
- Each operation gets its own context (stateless per request)

### 2. Create Daemon Client Library
**New file:** `integrations/beads-mcp/src/beads_mcp/bd_daemon_client.py`

- Python client for daemon RPC protocol
- Methods matching current BdClient interface
- Adds `cwd` parameter to all requests
- Handles connection management, retries
- Falls back to CLI if daemon unavailable

### 3. Update MCP Server
**File:** `integrations/beads-mcp/src/beads_mcp/server.py`

- Store workspace_root from `set_context`
- Use daemon client by default, fall back to CLI client
- Pass workspace_root as cwd to all operations
- Handle daemon not running gracefully

### 4. Update bd_client.py
**File:** `integrations/beads-mcp/src/beads_mcp/bd_client.py`

- Make it an abstract interface/base class
- Concrete implementations: BdCliClient, BdDaemonClient
- Factory function to create appropriate client

## Benefits

- ✅ True multi-repo support (each request has context)
- ✅ Better performance (no process spawning)
- ✅ Concurrent access already solved (daemon exists)
- ✅ Stateless per request (no env var persistence issues)
- ✅ Falls back to CLI when daemon not running

## Implementation Steps

1. **Extend RPC protocol** (Go)
   - Add Cwd field to request structs
   - Update daemon handlers to use cwd for tree-walking

2. **Create daemon client** (Python)
   - Implement RPC protocol in Python
   - Match BdClient interface

3. **Refactor MCP server**
   - Abstract BdClient
   - Use daemon client when available

4. **Test with multiple repos**
   - Concurrent operations
   - Context switching
   - Daemon restart handling

## Related Issues

- bd-86: Root cause investigation (this is PATH 1.5 solution)
- bd-91: Multi-server confusion (will be resolved)
- bd-80, bd-81, bd-82, bd-83: Daemon implementation (foundation)

- MCP server can use daemon RPC instead of CLI
- Each operation includes cwd context
- Daemon routes to correct database per request
- Works with multiple repos simultaneously
- Falls back to CLI gracefully if daemon unavailable
- All existing MCP tests pass
- New multi-repo integration tests pass

## Progress: Session 2 (2025-10-17 continued)

### Completed
1. ✅ Updated MCP server to use daemon client
   - Modified `tools.py` to use `create_bd_client()` factory
   - Passes `BEADS_WORKING_DIR` from environment
   - Uses daemon by default, falls back to CLI
2. ✅ Added `BEADS_USE_DAEMON` environment variable
   - Default: `1` (enabled)
   - Set to `0` to force CLI mode
3. ✅ Created multi-repo integration test (`test_multi_repo.py`)
   - Tests concurrent operations across two repos
   - Verifies proper database routing based on cwd
   - Validates issue prefix isolation (r1- vs r2-)
   - All tests pass! ✅
4. ✅ Updated MCP README with daemon usage docs
   - Added BEADS_USE_DAEMON to environment variables
   - Added multi-repo test documentation

### Test Results
```
=== All Tests Passed! ===
Summary:
  ✅ Per-request context routing works
  ✅ Multiple repos are properly isolated
  ✅ Concurrent operations succeed
  ✅ Daemon handles rapid context switching
```

### Files Modified/Added (Session 2)
- `integrations/beads-mcp/src/beads_mcp/tools.py` - uses daemon client ✅
- `integrations/beads-mcp/test_multi_repo.py` - NEW integration test ✅
- `integrations/beads-mcp/README.md` - daemon documentation ✅

### Architecture Validated

```
AI Client (Claude/Amp)
  ↓
MCP Server (workspace_root from set_context)
  ↓ create_bd_client(prefer_daemon=True, workspace_root)
Daemon Client Library
  ↓ RPC with cwd field
beadsd Daemon
  ↓ per-request tree-walking
Correct .beads/*.db
```

### Ready to Close
All acceptance criteria met:
- ✅ MCP server can use daemon RPC instead of CLI
- ✅ Each operation includes cwd context
- ✅ Daemon routes to correct database per request
- ✅ Works with multiple repos simultaneously
- ✅ Falls back to CLI gracefully if daemon unavailable
- ✅ All existing MCP tests pass
- ✅ New multi-repo integration tests pass


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Fix nil pointer crash in bd export command

When running `bd export -o .beads/issues.jsonl`, the command crashes with a nil pointer dereference.

## Error
```
panic: runtime error: invalid memory address or nil pointer dereference
[signal SIGSEGV: segmentation violation code=0x2 addr=0x108 pc=0x1034456fc]

goroutine 1 [running]:
main.init.func14(0x103c24380, {0x1034a9695?, 0x4?, 0x1034a95c9?})
        /Users/stevey/src/vc/adar/beads/cmd/bd/export.go:74 +0x15c
```

## Context
- This happened after closing bd-86, bd-91, bd-92
- Auto-export from daemon still works fine
- Only the manual `bd export` command crashes
- Data was already synced via auto-export, so no data loss

## Location
File: `cmd/bd/export.go` line 74


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Add --global flag to daemon for multi-repo support

Currently daemon creates socket at .beads/bd.sock in each repo. For multi-repo support, add --global flag to create socket in ~/.beads/bd.sock that can serve requests from any repository.

Implementation:
- Add --global flag to daemon command
- When --global is set, use ~/.beads/bd.sock instead of ./.beads/bd.sock
- Don't require being in a git repo when --global is used
- Update daemon discovery logic to check ~/.beads/bd.sock as fallback
- Document that global daemon can serve multiple repos simultaneously

Benefits:
- Single daemon serves all repos on the system
- No need to start daemon per-repo
- Better resource usage
- Enables system-wide task tracking

Context: Per-request context routing (bd-92) already implemented - daemon can handle multiple repos. This issue is about making the UX better.

Related: bd-43 (parent issue for multi-repo support)


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Document multi-repo workflow with daemon

The daemon already supports multi-repo via per-request context routing (bd-92), but this isn't documented. Users need to know how to use beads across multiple projects.

Add documentation for:
1. How daemon serves multiple repos simultaneously
2. Starting daemon in one repo, using from others
3. MCP server multi-repo configuration
4. Example: tracking work across a dozen projects
5. Comparison to workspace/global instance approaches

Documentation locations:
- README.md (Multi-repo section)
- AGENTS.md (MCP multi-repo config)
- integrations/beads-mcp/README.md (working_dir parameter)

Include:
- Architecture diagram showing one daemon, many repos
- Example MCP config with BEADS_WORKING_DIR
- CLI workflow example
- Reference to test_multi_repo.py as proof of concept

Context: Feature already works (proven by test_multi_repo.py), just needs user-facing docs.


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