Compact command fails with daemon - requires --no-daemon workaround

The 'bd compact' command fails with 'Error: compact requires SQLite storage' when used with the daemon (default mode), but works correctly with the '--no-daemon' flag.

The daemon RPC interface doesn't properly expose the compact command, even though the daemon itself uses SQLite storage.

Reproduction:
1. Ensure daemon is running (bd daemon status)
2. Run: bd compact --stats
   Result: Error: compact requires SQLite storage
3. Run: bd compact --stats --no-daemon
   Result: Works correctly, shows statistics

Expected behavior:
The compact command should work through the daemon RPC interface just like other commands (list, create, update, delete, renumber, etc.)

Impact:
Users cannot use compact operations in the normal workflow. They must use --no-daemon which bypasses the daemon entirely.

Suggested fix:
Add compact operation support to the daemon RPC interface, similar to how renumber and other operations are exposed.


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Add customizable time threshold for compact command

Currently compact uses fixed 30-day and 90-day tiers. Add support for custom time thresholds like '--older-than 60h' or '--older-than 2.5d' to allow more flexible compaction policies.

Examples:
  bd compact --all --older-than 60h
  bd compact --all --older-than 2.5d
  bd compact --all --tier 1 --age 48h

This would allow users to set their own compaction schedules based on their workflow needs.


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Add rule-based compaction (e.g., compact children of closed epics)

Support semantic compaction rules beyond just time-based, such as:
- Compact all children of closed epics
- Compact by priority level (e.g., all P3/P4 closed issues)
- Compact by label (e.g., all issues labeled 'archive')
- Compact by type (e.g., all closed chores)

This would allow smarter database size management based on semantic meaning rather than just age.


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Add TestNWayCollision for 5+ clones

## Overview
Add comprehensive tests for N-way (5+) collision resolution to verify the solution scales beyond 3 clones.

## Purpose
While TestThreeCloneCollision validates the basic N-way case, we need to verify:
1. Solution scales to arbitrary N
2. Performance is acceptable with more clones
3. Convergence time is bounded
4. No edge cases in larger collision groups

## Implementation Tasks

### 1. Create TestFiveCloneCollision
File: beads_twoclone_test.go (or new beads_nway_test.go)

```go
func TestFiveCloneCollision(t *testing.T) {
    // Test with 5 clones creating same ID with different content
    // Verify all 5 clones converge after sync rounds

    t.Run("SequentialSync", func(t *testing.T) {
        testNCloneCollision(t, 5, "A", "B", "C", "D", "E")
    })

    t.Run("ReverseSync", func(t *testing.T) {
        testNCloneCollision(t, 5, "E", "D", "C", "B", "A")
    })

    t.Run("RandomSync", func(t *testing.T) {
        testNCloneCollision(t, 5, "C", "A", "E", "B", "D")
    })
}
```

### 2. Implement generalized testNCloneCollision
Generalize the 3-clone test to handle arbitrary N:

```go
func testNCloneCollision(t *testing.T, numClones int, syncOrder ...string) {
    t.Helper()

    if len(syncOrder) != numClones {
        t.Fatalf("syncOrder length (%d) must match numClones (%d)",
            len(syncOrder), numClones)
    }

    tmpDir := t.TempDir()

    // Setup remote and N clones
    remoteDir := setupBareRepo(t, tmpDir)
    cloneDirs := make(map[string]string)

    for i := 0; i < numClones; i++ {
        name := string(rune('A' + i))
        cloneDirs[name] = setupClone(t, tmpDir, remoteDir, name)
    }

    // Each clone creates issue with same ID but different content
    for name, dir := range cloneDirs {
        createIssue(t, dir, fmt.Sprintf("Issue from clone %s", name))
    }

    // Sync in specified order
    for _, name := range syncOrder {
        syncClone(t, cloneDirs[name], name)
    }

    // Final pull for convergence
    for name, dir := range cloneDirs {
        finalPull(t, dir, name)
    }

    // Verify all clones have all N issues
    expectedTitles := make(map[string]bool)
    for i := 0; i < numClones; i++ {
        name := string(rune('A' + i))
        expectedTitles[fmt.Sprintf("Issue from clone %s", name)] = true
    }

    for name, dir := range cloneDirs {
        titles := getTitles(t, dir)
        if !compareTitleSets(titles, expectedTitles) {
            t.Errorf("Clone %s missing issues: expected %v, got %v",
                name, expectedTitles, titles)
        }
    }

    t.Log("✓ All", numClones, "clones converged successfully")
}
```

### 3. Add performance benchmarks
Test convergence time and memory usage:

```go
func BenchmarkNWayCollision(b *testing.B) {
    for _, n := range []int{3, 5, 10, 20} {
        b.Run(fmt.Sprintf("N=%d", n), func(b *testing.B) {
            for i := 0; i < b.N; i++ {
                // Run N-way collision and measure time
                testNCloneCollisionBench(b, n)
            }
        })
    }
}
```

### 4. Add convergence time tests
Verify bounded convergence:

```go
func TestConvergenceTime(t *testing.T) {
    // Test that convergence happens within expected rounds
    // For N clones, should converge in at most N-1 sync rounds

    for n := 3; n <= 10; n++ {
        t.Run(fmt.Sprintf("N=%d", n), func(t *testing.T) {
            rounds := measureConvergenceRounds(t, n)
            maxExpected := n - 1
            if rounds > maxExpected {
                t.Errorf("Convergence took %d rounds, expected ≤ %d",
                    rounds, maxExpected)
            }
        })
    }
}
```

### 5. Add edge case tests
Test boundary conditions:
- All N clones have identical content (dedup works)
- N-1 clones have same content, 1 differs
- All N clones have unique content
- Mix of collisions and non-collisions

## Acceptance Criteria
- TestFiveCloneCollision passes with all sync orders
- All 5 clones converge to identical content
- Performance is acceptable (< 5 seconds for 5 clones)
- Convergence time is bounded (≤ N-1 rounds)
- Edge cases handled correctly
- Benchmarks show scalability to 10+ clones

## Files to Create/Modify
- beads_twoclone_test.go or beads_nway_test.go
- Add helper functions for N-clone setup

## Testing Strategy

### Test Matrix
| N Clones | Sync Orders | Expected Result |
|----------|-------------|-----------------|
| 3        | A→B→C       | Pass            |
| 3        | C→B→A       | Pass            |
| 5        | A→B→C→D→E   | Pass            |
| 5        | E→D→C→B→A   | Pass            |
| 5        | Random      | Pass            |
| 10       | Sequential  | Pass            |

### Performance Targets
- 3 clones: < 2 seconds
- 5 clones: < 5 seconds
- 10 clones: < 15 seconds

## Dependencies
- Requires bd-cbed9619.5, bd-cbed9619.4, bd-0dcea000, bd-4d7fca8a to be completed
- TestThreeCloneCollision must pass first

## Success Metrics
- All tests pass for N ∈ {3, 5, 10}
- Convergence time scales linearly (O(N))
- Memory usage reasonable (< 100MB for 10 clones)
- No data corruption or loss in any scenario


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Add compact --dry-run that shows size savings estimates

When running 'bd compact --dry-run', show estimated database size reduction in KB/MB and percentage, similar to what 'du -h' would show.

Example output:
  Tier 1 candidates: 15 issues
  Current size: 2.4 MB
  After compaction: ~1.7 MB (70% reduction, 0.7 MB saved)

This helps users understand impact before compacting.


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Comment test


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Test description


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Implement storage driver interface for pluggable backends

Create abstraction layer for storage to support multiple backends (SQLite, Postgres, Turso, in-memory testing, etc.).

**Current state:** All storage logic hardcoded to SQLite in internal/storage/sqlite/sqlite.go

**Proposed design:**

```go
// internal/storage/storage.go
type Store interface {
    // Issue CRUD
    CreateIssue(issue *Issue) error
    GetIssue(id string) (*Issue, error)
    UpdateIssue(id string, updates *Issue) error
    DeleteIssue(id string) error
    ListIssues(filter *Filter) ([]*Issue, error)

    // Dependencies
    AddDependency(from, to string, depType DependencyType) error
    RemoveDependency(from, to string, depType DependencyType) error
    GetDependencies(id string) ([]*Dependency, error)

    // Counters, stats
    GetNextID(prefix string) (string, error)
    GetStats() (*Stats, error)

    Close() error
}
```

**Benefits:**
- Better testing (mock/in-memory stores)
- Future flexibility (Postgres, cloud APIs, etc.)
- Clean architecture (business logic decoupled from storage)
- Enable Turso or other backends without refactoring everything

**Implementation steps:**
1. Define Store interface in internal/storage/storage.go
2. Refactor SQLiteStore to implement interface
3. Update all commands to use interface, not concrete type
4. Add MemoryStore for testing
5. Add driver selection via config (storage.driver = sqlite|turso|postgres)
6. Update tests to use interface

**Note:** This is valuable even without adopting Turso. Good architecture practice.

**Context:** From GH issue #2 RFC evaluation. Driver interface is low-cost, high-value regardless of whether we add alternative backends.


Updated Title


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Set up WASM build pipeline

Configure Go→WASM compilation pipeline. Child of epic bd-44d0.

## Tasks
- [ ] Create build-wasm.sh script (GOOS=js GOARCH=wasm)
- [ ] Test basic WASM module loading in Node.js
- [ ] Set up wasm_exec.js wrapper
- [ ] Add WASM build to CI/CD
- [ ] Document build process

## Validation
- bd.wasm compiles successfully
- Can load in Node.js without errors
- Bundle size <10MB


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Create backup and restore procedures

Disaster recovery procedures for Agent Mail data.

Acceptance Criteria:
- Automated daily snapshots (GCP persistent disk)
- SQLite backup script
- Git repository backup
- Restore procedure documentation
- Test restore from backup

File: deployment/agent-mail/backup.sh


Test issue 2


Add transaction helper to replace manual COMMIT/ROLLBACK

Create tx.go with withTx helper that handles transaction lifecycle. Replace manual transaction blocks in create/insert/update paths.

Refactoring complete:
- Created withTx() helper in util.go
- Added ExecInTransaction() as deprecated wrapper for backward compatibility
- Refactored all manual transaction blocks to use withTx():
  - events.go: AddComment
  - dirty.go: MarkIssuesDirty, ClearDirtyIssuesByID
  - labels.go: executeLabelOperation
  - dependencies.go: AddDependency, RemoveDependency
  - compact.go: ApplyCompaction
- All tests pass successfully


Investigate jujutsu integration for beads

Research and document how beads could integrate with jujutsu (jj), the next-generation VCS. Key areas to explore:
- How jj's operation model differs from git (immutable operations, working-copy-as-commit)
- JSONL sync strategy with jj's conflict resolution model
- Daemon compatibility with jj's more frequent rewrites
- Whether auto-import/export needs changes for jj workflows
- Example configurations and documentation updates needed


Implement filesystem shims for WASM

WASM needs JS shims for filesystem access. Child of epic bd-44d0.

## Tasks
- [ ] Implement file read/write shims
- [ ] Map WASM syscalls to Node.js fs API
- [ ] Handle .beads/ directory discovery
- [ ] Test with real JSONL files
- [ ] Support both absolute and relative paths

## Technical Notes
- Use Node.js fs module via syscall/js
- Consider MEMFS for in-memory option


Remove obsolete renumber.go command (hash IDs eliminated need)


Investigate bd export/import sync issue - database and JSONL out of sync

Observed in VC repo: database has 1137 issues but beads.jsonl only has 309. Running 'bd export -o .beads/issues.jsonl' doesn't update the file. Running 'bd import' hangs indefinitely.

Reproduction context:
- VC repo: 1137 issues in DB, 309 in JSONL
- Created 4 new issues with bd create
- bd export didn't write them to JSONL
- bd import hung (possibly daemon lock conflict?)

Need to investigate:
1. Why export doesn't update JSONL when DB has more issues
2. Why import hangs
3. Daemon lock interaction with export/import
4. File path handling (issues.jsonl vs beads.jsonl)

Check export logic for silent failures, file locking, path resolution. Check import for blocking operations, daemon conflicts.

- Root cause of export not updating JSONL identified
- Root cause of import hanging identified
- Fix implemented and verified
- Test coverage for sync scenarios
- Documentation updated if needed

## Root Cause Analysis

The issue was NOT about file path handling or export failing to update JSONL. The actual problem was:

**Import/Export hanging when daemon is running** due to SQLite lock contention:

1. When daemon is connected, `PersistentPreRun` in main.go returns early without initializing the `store` variable
2. Import/Export commands then tried to open the database directly with `sqlite.New(dbPath)`
3. This blocked waiting for the database lock that the daemon already holds → **HANGS INDEFINITELY**

## Solution Implemented

Modified both import.go and export.go to:
1. Detect when `daemonClient` is connected
2. Explicitly close the daemon connection before opening direct SQLite access
3. Added debug logging to help diagnose similar issues

This ensures import/export commands always run in direct mode, avoiding lock contention.

## File Path Handling

The file path confusion (issues.jsonl vs beads.jsonl) was a red herring. The code uses `filepath.Glob("*.jsonl")` which correctly finds ANY `.jsonl` file in `.beads/` directory, so both filenames work.


Extract migration functions to migrations.go

Move migrateDirtyIssuesTable, migrateExternalRefColumn, migrateCompositeIndexes, migrateClosedAtConstraint, migrateCompactionColumns, migrateSnapshotsTable, migrateCompactionConfig, migrateCompactedAtCommitColumn, migrateExportHashesTable, migrateContentHashColumn to a separate migrations.go file


Event-driven daemon architecture

Replace 5-second polling sync loop with event-driven architecture that reacts instantly to changes. Eliminates stale data issues while reducing CPU ~60%. Key components: FileWatcher (fsnotify), Debouncer (500ms), RPC mutation events, optional git hooks. Target latency: <500ms (vs 5000ms). See event_driven_daemon.md for full design.

Production-ready after 3 critical fixes (commit 349b892):
- Skip redundant imports (mtime check prevents self-trigger loops)
- Add server.Stop() in serverErrChan case (clean shutdown)
- Fallback ticker (60s) when watcher unavailable (ensures remote sync)

Ready to make default after integration test (bd-1f4086c5.1) passes.


Integration test: mutation to export latency

Measure time from bd create to JSONL update. Verify <500ms latency. Test with multiple rapid mutations to verify batching.

Test added to daemon_test.go as TestMutationToExportLatency().

Currently skipped with note that it should be enabled once bd-146 (event-driven daemon) is fully implemented and enabled by default.

The test structure is complete:
1. Sets up test environment with fast debounce (500ms)
2. SingleMutationLatency: measures latency from mutation to JSONL update
3. RapidMutationBatching: verifies multiple mutations batch into single export

Once event-driven mode is default, remove the t.Skip() line and the test will validate <500ms latency.


Add comprehensive tests for config.yaml issue-prefix migration

The GH #209 config.yaml migration lacks test coverage:

Missing tests:
- config.SetIssuePrefix() edge cases (empty file, comments, malformed YAML)
- config.GetIssuePrefix() with various config states
- MigrateConfigToYAML() automatic migration logic
- bd init writing to config.yaml instead of DB
- bd migrate DB→config.yaml migration path

Test scenarios needed:
1. SetIssuePrefix with empty config.yaml
2. SetIssuePrefix with existing config.yaml (preserves other settings)
3. SetIssuePrefix with commented issue-prefix line
4. SetIssuePrefix atomic write (temp file cleanup)
5. GetIssuePrefix fallback behavior
6. MigrateConfigToYAML when config.yaml missing prefix but DB has it
7. MigrateConfigToYAML when both missing (detect from issues)
8. MigrateConfigToYAML when config.yaml already has prefix (no-op)
9. Integration test: fresh bd init writes to config.yaml only
10. Integration test: upgrade from v0.21 DB migrates to config.yaml

Priority 1 because this is a user-facing migration affecting all users upgrading to v0.22.


bd-hv01: Storage backend extensibility broken by type assertion

Problem: deletion_tracking.go:69-82 uses type assertion for DeleteIssue which breaks if someone adds a new storage backend.

Fix: Check capability before starting merge or add DeleteIssue to Storage interface.

Files: cmd/bd/deletion_tracking.go:69-82, internal/storage/storage.go


Override test

## Overview

[Describe the high-level goal and scope of this epic]

## Success Criteria

- [ ] Criteria 1
- [ ] Criteria 2
- [ ] Criteria 3

## Background

[Provide context and motivation]

## Scope

**In Scope:**
- Item 1
- Item 2

**Out of Scope:**
- Item 1
- Item 2

## Architecture

[Describe the overall architecture and approach]

## Components

- Component 1: [description]
- Component 2: [description]

## Dependencies

[List external dependencies or constraints]

- [ ] All child issues are completed
- [ ] Integration tests pass
- [ ] Documentation is updated
- [ ] Code review completed


Client self-heal: remove stale pid when lock free + socket missing

When client detects:
- Socket is missing AND
- tryDaemonLock shows lock NOT held

Then automatically:
1. Remove stale daemon.pid file
2. Optionally auto-start daemon (behind BEADS_AUTO_START_DAEMON=1 env var)

This prevents stale artifacts from accumulating after daemon crashes.


Issue 2 to reopen


Proposal: Custom status states via config

Proposal to add 'custom status states' via `bd config`.
Users could define an optional issue status enum (e.g., awaiting_review, review_in_progress) in the config.
This would enable multi-step pipelines to process issues where each step correlates to a specific status.

Examples:
- awaiting_verification
- awaiting_docs
- awaiting_testing


Test FK constraint via close


Add WebSocket support

## Feature Request

[Describe the desired feature]

## Motivation

[Why is this feature needed? What problem does it solve?]

## Use Cases

1. **Use Case 1**: [description]
2. **Use Case 2**: [description]

## Proposed Solution

[High-level approach to implementing this feature]

## Alternatives Considered

- **Alternative 1**: [description and why not chosen]
- **Alternative 2**: [description and why not chosen]

## Technical Design

[Detailed technical approach]

## API Changes

[New commands, flags, or APIs]

## Data Model Changes

[Database schema changes if any]

## Implementation Notes

- Note 1
- Note 2

## Testing Strategy

- Unit tests: [scope]
- Integration tests: [scope]
- Manual testing: [steps]

- [ ] Feature implements all described use cases
- [ ] All tests pass
- [ ] Documentation updated (README, commands)
- [ ] Examples added if applicable
- [ ] No performance regressions


Use -short flag in CI for PR checks

Update CI configuration to use -short flag for PR checks, run full tests nightly.

The slow tests already support testing.Short() and will be skipped.

Expected savings: ~20 seconds for PR checks (fast tests only)

Implementation:
- Update .github/workflows/ci.yml to add -short flag for PR tests
- Create/update nightly workflow for full test runs
- Update README/docs about test strategy

File: .github/workflows/ci.yml:30


Sub-task under A


Investigate auto-export debounce not triggering

Auto-export to JSONL did not trigger automatically after creating bd-33 and bd-17. Had to manually run 'bd export' to sync.

**Expected behavior:** Auto-export should trigger ~5 seconds after CRUD operations (per CLAUDE.md documentation).

**Actual behavior:** Issues bd-33 and bd-17 were created but JSONL was not updated until manual 'bd export' was run.

**Investigation needed:**
1. Check if auto-flush goroutine is running
2. Verify debounce timer is being triggered on CreateIssue()
3. Check for errors/panics in background export
4. Verify auto-flush is enabled by default
5. Check if there's a race condition with shutdown

**Impact:** HIGH - Data loss risk if users create issues and don't realize they haven't synced to Git.

**Testing:**
```bash
# Create issue and wait 10 seconds
bd create "Test" -p 4
sleep 10
grep "Test" .beads/issues.jsonl  # Should find it
```

**Workaround:** Manually run 'bd export' after CRUD operations.

**Context:** Discovered during GH issue #2 RFC evaluation while creating bd-33 and bd-17.


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Build collision resolution tooling for distributed branch workflows

When branches diverge and both create issues, auto-incrementing IDs collide on merge. Build excellent tooling to detect collisions during import, auto-renumber issues with fewer dependencies, update all references in descriptions and dependency links, and provide clear user feedback. Goal: keep beautiful brevity of numeric IDs (bd-210) while handling distributed creation gracefully.


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Add TestNWayCollision for 5+ clones

## Overview
Add comprehensive tests for N-way (5+) collision resolution to verify the solution scales beyond 3 clones.

## Purpose
While TestThreeCloneCollision validates the basic N-way case, we need to verify:
1. Solution scales to arbitrary N
2. Performance is acceptable with more clones
3. Convergence time is bounded
4. No edge cases in larger collision groups

## Implementation Tasks

### 1. Create TestFiveCloneCollision
File: beads_twoclone_test.go (or new beads_nway_test.go)

```go
func TestFiveCloneCollision(t *testing.T) {
    // Test with 5 clones creating same ID with different content
    // Verify all 5 clones converge after sync rounds

    t.Run("SequentialSync", func(t *testing.T) {
        testNCloneCollision(t, 5, "A", "B", "C", "D", "E")
    })

    t.Run("ReverseSync", func(t *testing.T) {
        testNCloneCollision(t, 5, "E", "D", "C", "B", "A")
    })

    t.Run("RandomSync", func(t *testing.T) {
        testNCloneCollision(t, 5, "C", "A", "E", "B", "D")
    })
}
```

### 2. Implement generalized testNCloneCollision
Generalize the 3-clone test to handle arbitrary N:

```go
func testNCloneCollision(t *testing.T, numClones int, syncOrder ...string) {
    t.Helper()

    if len(syncOrder) != numClones {
        t.Fatalf("syncOrder length (%d) must match numClones (%d)",
            len(syncOrder), numClones)
    }

    tmpDir := t.TempDir()

    // Setup remote and N clones
    remoteDir := setupBareRepo(t, tmpDir)
    cloneDirs := make(map[string]string)

    for i := 0; i < numClones; i++ {
        name := string(rune('A' + i))
        cloneDirs[name] = setupClone(t, tmpDir, remoteDir, name)
    }

    // Each clone creates issue with same ID but different content
    for name, dir := range cloneDirs {
        createIssue(t, dir, fmt.Sprintf("Issue from clone %s", name))
    }

    // Sync in specified order
    for _, name := range syncOrder {
        syncClone(t, cloneDirs[name], name)
    }

    // Final pull for convergence
    for name, dir := range cloneDirs {
        finalPull(t, dir, name)
    }

    // Verify all clones have all N issues
    expectedTitles := make(map[string]bool)
    for i := 0; i < numClones; i++ {
        name := string(rune('A' + i))
        expectedTitles[fmt.Sprintf("Issue from clone %s", name)] = true
    }

    for name, dir := range cloneDirs {
        titles := getTitles(t, dir)
        if !compareTitleSets(titles, expectedTitles) {
            t.Errorf("Clone %s missing issues: expected %v, got %v",
                name, expectedTitles, titles)
        }
    }

    t.Log("✓ All", numClones, "clones converged successfully")
}
```

### 3. Add performance benchmarks
Test convergence time and memory usage:

```go
func BenchmarkNWayCollision(b *testing.B) {
    for _, n := range []int{3, 5, 10, 20} {
        b.Run(fmt.Sprintf("N=%d", n), func(b *testing.B) {
            for i := 0; i < b.N; i++ {
                // Run N-way collision and measure time
                testNCloneCollisionBench(b, n)
            }
        })
    }
}
```

### 4. Add convergence time tests
Verify bounded convergence:

```go
func TestConvergenceTime(t *testing.T) {
    // Test that convergence happens within expected rounds
    // For N clones, should converge in at most N-1 sync rounds

    for n := 3; n <= 10; n++ {
        t.Run(fmt.Sprintf("N=%d", n), func(t *testing.T) {
            rounds := measureConvergenceRounds(t, n)
            maxExpected := n - 1
            if rounds > maxExpected {
                t.Errorf("Convergence took %d rounds, expected ≤ %d",
                    rounds, maxExpected)
            }
        })
    }
}
```

### 5. Add edge case tests
Test boundary conditions:
- All N clones have identical content (dedup works)
- N-1 clones have same content, 1 differs
- All N clones have unique content
- Mix of collisions and non-collisions

## Acceptance Criteria
- TestFiveCloneCollision passes with all sync orders
- All 5 clones converge to identical content
- Performance is acceptable (< 5 seconds for 5 clones)
- Convergence time is bounded (≤ N-1 rounds)
- Edge cases handled correctly
- Benchmarks show scalability to 10+ clones

## Files to Create/Modify
- beads_twoclone_test.go or beads_nway_test.go
- Add helper functions for N-clone setup

## Testing Strategy

### Test Matrix
| N Clones | Sync Orders | Expected Result |
|----------|-------------|-----------------|
| 3        | A→B→C       | Pass            |
| 3        | C→B→A       | Pass            |
| 5        | A→B→C→D→E   | Pass            |
| 5        | E→D→C→B→A   | Pass            |
| 5        | Random      | Pass            |
| 10       | Sequential  | Pass            |

### Performance Targets
- 3 clones: < 2 seconds
- 5 clones: < 5 seconds
- 10 clones: < 15 seconds

## Dependencies
- Requires bd-cbed9619.5, bd-cbed9619.4, bd-cbed9619.3, bd-cbed9619.2 to be completed
- TestThreeCloneCollision must pass first

## Success Metrics
- All tests pass for N ∈ {3, 5, 10}
- Convergence time scales linearly (O(N))
- Memory usage reasonable (< 100MB for 10 clones)
- No data corruption or loss in any scenario


Critical bug


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Test simple issue

Testing the new bd comment alias!

Another test with JSON output

Test comment from file


Verify auto-export works


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Version test issue


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Add optional post-merge git hook example for bd sync

Create example git hook that auto-runs bd sync after git pull/merge.

Add to examples/git-hooks/:
- post-merge hook that checks if .beads/issues.jsonl changed
- If changed: run `bd sync` automatically
- Make it optional/documented (not auto-installed)

Benefits:
- Zero-friction sync after git pull
- Complements auto-detection as belt-and-suspenders

Note: post-merge hook already exists for pre-commit/post-merge. Extend it to support sync.


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Sync versions to 0.9.2 across all components

Version mismatch discovered: bd CLI is 0.9.2 but other components still at 0.9.0 or 1.0.0.

Current state:
- bd CLI (cmd/bd/version.go): 0.9.2 ✓
- Plugin (.claude-plugin/plugin.json): 0.9.0 ✗
- MCP Server (integrations/beads-mcp): 1.0.0 ✗
- README.md: 0.9.0 ✗

Files to update:
1. .claude-plugin/plugin.json
2. integrations/beads-mcp/pyproject.toml
3. README.md (all mentions)
4. PLUGIN.md (if any mentions)
5. CHANGELOG.md (add 0.9.1 and 0.9.2 entries)

Root cause: Version bumps only updated version.go, not other components.
Solution needed: Script or process to sync versions across all files.


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Issue with labels

This is a description


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Add EXPLAIN QUERY PLAN tests for ready work query

Verify that the hierarchical blocking query uses proper indexes and doesn't do full table scans.

**Queries to analyze:**
1. The recursive CTE (both base case and recursive case)
2. The final SELECT with NOT EXISTS
3. Impact of various filters (status, priority, assignee)

**Implementation:**
Add test function that:
- Runs EXPLAIN QUERY PLAN on GetReadyWork query
- Parses output to verify no SCAN TABLE operations
- Documents expected query plan in comments
- Fails if query plan degrades

**Benefits:**
- Catch performance regressions in tests
- Document expected query behavior
- Ensure indexes are being used

Related to: bd-52 (composite index on depends_on_id, type)


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Add performance benchmarks document

Document actual performance metrics with hyperfine tests


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Create cmd/bd/daemon_watcher.go (~150 LOC)

Implement FileWatcher using fsnotify to watch JSONL file and git refs. Handle platform differences (inotify/FSEvents/ReadDirectoryChangesW). Include edge case handling for file rename, event storm, watcher failure.


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Improve cmd/bd test coverage from 21% to 40% (multi-session effort)

Current coverage: 21.0% of statements in cmd/bd
Target: 40%
This is a multi-session incremental effort.

Focus areas:
- Command handler tests (create, update, close, list, etc.)
- Flag validation and error cases
- JSON output formatting
- Edge cases and error handling

Track progress with 'go test -cover ./cmd/bd'

Coverage improved from 21% to 27.4% (package) and 42.9% (total function coverage).

Added tests for:
- compact.go test coverage (eligibility checks, dry run scenarios)
- epic.go test coverage (epic status, children tracking, eligibility for closure)

New test files created:
- epic_test.go (3 test functions covering epic functionality)

Enhanced compact_test.go:
- TestRunCompactSingleDryRun
- TestRunCompactAllDryRun

Total function coverage now at 42.9%, exceeding the 40% target.


Debug MCP Agent Mail tool execution errors

**EXTERNAL WORK**: Debug the standalone MCP Agent Mail server (separate from beads integration).

The Agent Mail server runs as an independent service at ~/src/mcp_agent_mail. This is NOT beads code - it's a separate GitHub project we're evaluating for optional coordination features.

Current Issue:
- MCP API endpoint returns errors when calling ensure_project tool
- Error: "Server encountered an unexpected error while executing tool"
- Core HTTP server works, web UI functional, but tool wrapper layer fails

Server Details:
- Location: ~/src/mcp_agent_mail (separate repo)
- Repository: https://github.com/Dicklesworthstone/mcp_agent_mail
- Runs on: http://127.0.0.1:8765
- Bearer token: In .env file

Investigation Steps:
1. Check tool execution logs for full stack trace
2. Verify Git storage initialization at ~/.mcp_agent_mail_git_mailbox_repo
3. Review database setup (storage.sqlite3)
4. Test with simpler MCP tools if available
5. Compare with working test cases in tests/

Why This Matters:
- Blocks [deleted:bd-6hji] (testing file reservations)
- Need working MCP API to validate Agent Mail benefits
- Proof of concept for lightweight beads integration later

Note: The actual beads integration (bd-wfmw) will be lightweight HTTP client code only.


Investigate vector/semantic search for issue discovery

From GH issue #2 RFC discussion: Evaluate if vector/semantic search over issues would provide value for beads.

**Use case:** Find semantically related issues (e.g., 'login broken' finds 'authentication failure', 'session expired').

**Questions to answer:**
1. What workflows would this enable that we can't do now?
2. Is dataset size (typically 50-200 issues) large enough to benefit?
3. Do structured features (deps, tags, types) already provide better relationships?
4. What's the maintenance cost (embeddings, storage, recomputation)?

**Alternatives to consider:**
- Improve 'bd list' filtering with regex/boolean queries
- Add 'bd related <id>' showing deps + mentions + same tags
- Export to JSON and pipe to external AI tools

**Decision:** Only implement if clear use case emerges. Don't add complexity for theoretical benefits.

**Context:** Part of evaluating Turso RFC ideas (GH #2). Vector search was proposed but unclear if needed for typical beads usage.


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Add 'bd status' command for issue database overview

Implement a bd status command that provides a quick snapshot of the issue database state, similar to how git status shows working tree state.

Expected output: Show summary including counts by state (open, in-progress, blocked, closed), recent activity (last 7 days), and quick overview without needing multiple queries.

Example output showing issue counts, recent activity stats, and pointer to bd list for details.

Proposed options: --all (show all issues), --assigned (show issues assigned to current user), --json (JSON format output)

Use cases: Quick project health check, onboarding for new contributors, integration with shell prompts or CI/CD, daily standup reference


Add visual indicators for nodes with multiple parents in dep tree

When a node appears in the dependency tree via multiple paths (diamond dependencies), add a visual indicator like (*) or (multiple parents) to help users understand the graph structure. This would make it clear when deduplication has occurred. Example: 'bd-503: Shared dependency (*) [P1] (open)'


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bd-hv01: No snapshot versioning or timestamps causes stale data usage

Problem: If sync is interrupted (crash, kill -9, power loss), stale snapshots persist indefinitely. Next sync uses stale data leading to incorrect deletions.

Fix: Add metadata to snapshots with timestamp, version, and commit SHA. Validate snapshots are recent (< 1 hour old), from compatible version, and from expected git commit.

Files: cmd/bd/deletion_tracking.go (all snapshot functions)


Update AGENTS.md with event-driven mode

Document BEADS_DAEMON_MODE env var. Explain opt-in during Phase 1. Add troubleshooting for watcher failures.


Refactor cmd/bd/daemon.go for testability and maintainability

## Current Structure Analysis

daemon.go contains:
- Command setup and CLI flag parsing
- Path/config resolution (getGlobalBeadsDir, ensureBeadsDir, getPIDFilePath, etc.)
- Daemon lifecycle (start, stop, status, health, metrics)
- Lock management (setupDaemonLock, acquireDaemonLock)
- RPC server setup (startRPCServer)
- Export/import operations (exportToJSONLWithStore, importToJSONLWithStore)
- Sync orchestration (createExportFunc, createAutoImportFunc, createSyncFunc)
- Event loop (runEventLoop, runDaemonLoop)
- Global daemon mode (runGlobalDaemon)
- Logging setup (setupDaemonLogger)

## Proposed Module Breakdown

1. **daemon_config.go** - Configuration & path resolution
   - getGlobalBeadsDir, ensureBeadsDir
   - getPIDFilePath, getLogFilePath, getSocketPathForPID
   - getEnvInt, getEnvBool
   - boolToFlag helper

2. **daemon_lifecycle.go** - Start/stop/status operations
   - isDaemonRunning, startDaemon, stopDaemon
   - showDaemonStatus, showDaemonHealth, showDaemonMetrics
   - migrateToGlobalDaemon

3. **daemon_sync.go** - Export/import/sync logic
   - exportToJSONLWithStore, importToJSONLWithStore
   - createExportFunc, createAutoImportFunc, createSyncFunc
   - validateDatabaseFingerprint

4. **daemon_server.go** - RPC server setup
   - startRPCServer, runGlobalDaemon

5. **daemon_loop.go** - Event loop & orchestration
   - runEventLoop, runDaemonLoop

6. **daemon_logger.go** - Logging setup
   - setupDaemonLogger, daemonLogger type

Keep daemon.go as Cobra command definition only.


Extract daemon logger functions to daemon_logger.go


Extract daemon server functions to daemon_server.go


Extract daemon sync functions to daemon_sync.go


Extract daemon config functions to daemon_config.go


Add tests for daemon sync module


Add tests for daemon lifecycle module


Add tests for daemon config module


Extract daemon lifecycle functions to daemon_lifecycle.go


Investigate why test issues persist in database

Test issues (bd-0do3, bd-cjxp, bd-phr2, etc.) keep appearing in ready/list output, cluttering real work. These appear to be leftover test data from test runs.

Need to investigate:
1. Why are test issues not being cleaned up after tests?
2. Are tests creating issues in the main database instead of test databases?
3. Should we add better test isolation or cleanup hooks?
4. Can we add a label/prefix to distinguish test issues from real issues?

These test issues have characteristics:
- Empty descriptions
- Generic titles like "Test issue 0", "Bug P0", "Issue to reopen with reason"
- Created around 2025-11-07 19:00-19:07
- Some assigned to test users like "alice", "bob", "testuser"

## Root Cause Analysis

**Problem**: Python MCP integration tests created test issues in production `.beads/beads.db` instead of isolated test databases.

**Evidence**:
- 29 test issues created on Nov 7, 2025 at 19:00-19:07
- Patterns: "Bug P0", "Test issue X", assignees "alice"/"bob"/"testuser"
- Git commit 0e8936b shows test issues committed to .beads/beads.jsonl
- Tests were being fixed for workspace isolation around the same time

**Why It Happened**:
1. Before commit 0e8936b, `test_client_lazy_initialization()` didn't set `BEADS_WORKING_DIR`
2. Tests fell back to discovering `.beads/` in the project root directory
3. Auto-sync committed test issues to production database

**Resolution**:
1. ✅ Closed 29 test pollution issues (bd-0do3, bd-cjxp, etc.)
2. ✅ Added `failIfProductionDatabase()` guard in Go test helpers
3. ✅ Added production pollution checks in RPC test setup
4. ✅ Created `conftest.py` with pytest safety checks for Python tests
5. ✅ Added `BEADS_TEST_MODE` env var to mark test execution
6. ✅ Tests now fail fast if they detect production database usage

**Prevention**:
- All test helper functions now verify database paths are in temp directories
- Python tests fail immediately if BEADS_DB points to production
- BEADS_TEST_MODE flag helps identify test vs production execution
- Clear error messages guide developers to use proper test isolation

**Files Modified**:
- cmd/bd/test_helpers_test.go - Added failIfProductionDatabase()
- internal/rpc/rpc_test.go - Added temp directory verification
- integrations/beads-mcp/tests/conftest.py - New file with pytest safeguards


Update AGENTS.md with Agent Mail workflow

Update agent workflow section to include Agent Mail coordination as optional step.

Acceptance Criteria:
- Add Agent Mail to recommended workflow
- Show both with/without examples
- Update "Multi-Agent Patterns" section
- Cross-reference to AGENT_MAIL.md

File: AGENTS.md (lines 468-475)


Fix silent error handling in RPC response writing

Marshal and write errors silently ignored in writeResponse, can send partial JSON and hang clients.

Location: internal/rpc/server_lifecycle_conn.go:228-232

Problem:
- json.Marshal error ignored - cyclic reference sends corrupt JSON
- Write error ignored - connection closed, no indication to caller
- WriteByte error ignored - client hangs waiting for newline
- Flush error ignored - partial data buffered

Current code:
func (s *Server) writeResponse(writer *bufio.Writer, resp Response) {
    data, _ := json.Marshal(resp)  // Ignored!
    _, _ = writer.Write(data)      // Ignored!
    _ = writer.WriteByte('\n')     // Ignored!
    _ = writer.Flush()             // Ignored!
}

Solution: Return errors, handle in caller, close connection on error

Impact: Client hangs waiting for response; corrupt JSON sent

Effort: 1 hour


Document shared memory test isolation pattern in test_helpers.go

Tests were failing because :memory: creates a shared database across all tests. The fix is to use "file::memory:?mode=memory&cache=private" for test isolation.

Should document this pattern in test_helpers.go and potentially update newTestStore to use private memory by default.


Support --parent flag in daemon mode

Added support for hierarchical child issue creation using --parent flag in daemon mode. Previously only worked in direct mode.


Fix TestTwoCloneCollision timeout


bd-hv01: Silent partial deletion failures cause DB inconsistency

Problem: deletion_tracking.go:76-77 logs deletion errors as warnings but continues. If deletion fails midway (database locked, disk full), some issues delete but others don't. System thinks all deletions succeeded.

Impact: Database diverges from JSONL, silent corruption, issues may resurrect on next sync.

Fix: Collect errors and fail the operation:
var deletionErrors []error
for _, id := range acceptedDeletions {
    if err := d.DeleteIssue(ctx, id); err != nil {
        deletionErrors = append(deletionErrors, fmt.Errorf("issue %s: %w", id, err))
    }
}
if len(deletionErrors) > 0 {
    return false, fmt.Errorf("deletion failures: %v", deletionErrors)
}

Files: cmd/bd/deletion_tracking.go:73-82


Test integration issue

This is a real integration test


Investigate and upgrade to modernc.org/sqlite 1.39.1+

We had to pin modernc.org/sqlite to v1.38.2 due to a FOREIGN KEY constraint regression in v1.39.1 (SQLite 3.50.4).

**Issue:** [deleted:bd-47], GH #144

**Symptom:** CloseIssue fails with "FOREIGN KEY constraint failed (787)" when called via MCP/daemon, but works fine via CLI.

**Root Cause:** Unknown - likely stricter FK enforcement in SQLite 3.50.4 or modernc.org wrapper changes.

**Workaround:** Pinned to v1.38.2 (SQLite 3.49.x)

**TODO:**
1. Monitor modernc.org/sqlite releases for fixes
2. Check SQLite 3.50.5+ changelogs for FK-related fixes
3. Investigate why daemon mode fails but CLI succeeds (connection reuse? transaction isolation?)
4. Consider filing upstream issue with reproducible test case
5. Upgrade when safe


Add cross-type cycle detection warnings to dependency operations

When adding a dependency with 'bd dep add', run DetectCycles() afterwards and warn users if any cycles exist (across all dependency types, not just 'blocks'). This provides visibility into circular dependencies without blocking the operation.

Implementation approach:
1. After successfully adding a dependency in AddDependency, call DetectCycles()
2. If cycles are found, print a warning to stderr showing:
   - The cycle path(s) detected
   - Which dependency types are involved
   - A note that this may cause confusion in dependency visualization
3. Do NOT fail the operation - this is informational only
4. Consider adding a --quiet flag to suppress warnings if needed

The warning should be clear and actionable, e.g.:
WARNING: Circular dependency detected:
  vc-5 (blocks) → vc-13 (parent-child) → vc-5
This may cause confusion in dependency visualization.

- After 'bd dep add' creates a cross-type cycle, a warning is printed to stderr
- Warning includes the full cycle path with dependency types
- Operation still succeeds (warning only, not an error)
- No warning is printed when no cycles exist
- Warning message is clear and actionable

Current behavior: bd PREVENTS cycles (errors out). This issue wants to ALLOW cycles but WARN.

Decision: Current behavior is better. Cycles break the ready work algorithm and dep tree visualization. Prevention is safer than warnings users might ignore.

Code at dep.go:70-92 has cycle detection but it's unreachable - AddDependency errors before that code runs.

Recommend closing as won't-do or changing requirement to match current behavior.


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Multi-repo hydration layer

Build core infrastructure to hydrate database from N repos (N≥1), with smart caching via file mtime tracking and routing writes to correct JSONL based on source_repo metadata.

Components:
- Config schema for repos.additional
- source_repo metadata field (which repo owns each issue)
- Hydration logic (read from N JSONLs)
- Write routing (write to correct JSONL)
- Smart caching (file mtime tracking to avoid re-parsing)
- SQLite DB as cache layer

1. Can configure N repos via config.toml
2. Database hydrates from all configured repos
3. Writes route to correct JSONL via source_repo
4. File mtime caching prevents re-parsing unchanged JSONLs
5. Query performance <100ms even with 5-10 polling interval
6. N=1 (single repo) works unchanged


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Cache compiled regexes in replaceIDReferences for performance

replaceIDReferences() compiles the same regex patterns on every call. With 100 issues and 10 ID mappings, that's 1000 regex compilations. Pre-compile regexes once and reuse. Can use a struct with compiled regex, placeholder, and newID. Located in collision.go:329. Estimated performance improvement: 10-100x for large batches.


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Add BEADS_DAEMON_MODE flag handling

Add environment variable BEADS_DAEMON_MODE (values: poll, events). Default to 'poll' for Phase 1. Wire into daemon startup to select runEventLoop vs runEventDrivenLoop.


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Unit tests for FileWatcher

Test watcher detects JSONL changes. Test git ref changes trigger import. Test debounce integration. Test watcher recovery from file removal/rename.


Optimize reference updates to avoid loading all issues into memory

In updateReferences(), we call SearchIssues with no filter to get ALL issues for updating references. For large databases (10k+ issues), this loads everything into memory. Options: 1) Use batched processing with LIMIT/OFFSET, 2) Use SQL UPDATE with REPLACE() directly, 3) Stream results instead of loading all at once. Located in collision.go:266


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Agent 3 Issue 81

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Fix N-way collision convergence

Epic to fix the N-way collision convergence problem documented in n-way-collision-convergence.md.

## Problem Summary
The current collision resolution implementation works correctly for 2-way collisions but does not converge for 3-way (and by extension N-way) collisions. TestThreeCloneCollision demonstrates this with reproducible failures.

## Root Causes Identified
1. Pairwise resolution doesn't scale - each clone makes local decisions without global context
2. DetectCollisions modifies state during detection (line 83-86 in collision.go)
3. No remapping history - can't track transitive remap chains (test-1 → test-2 → test-3)
4. Import-time resolution is too late - happens after git merge

## Solution Architecture
Replace pairwise resolution with deterministic global N-way resolution using:
- Content-addressable identity (content hashing)
- Global collision resolution (sort all versions by hash)
- Read-only detection phase (separate from modification)
- Idempotent imports (content-first matching)

## Success Criteria
- TestThreeCloneCollision passes without skipping
- All clones converge to identical content after final pull
- No data loss (all issues present in all clones)
- Works for N workers (test with 5+ clones)
- Idempotent imports (importing same JSONL multiple times is safe)

## Implementation Phases
See child issues for detailed breakdown of each phase.


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Auto-configure git merge driver during `bd init`

Enhance `bd init` to optionally set up beads-merge as git merge driver.

**Tasks**:
- Prompt user to install git merge driver
- Configure `.git/config`: `merge.beads.driver "bd merge %A %O %L %R"`
- Create/update `.gitattributes`: `.beads/beads.jsonl merge=beads`
- Add `--skip-merge-driver` flag for non-interactive use
- Update AGENTS.md onboarding section

**Files**:
- `cmd/bd/init.go`
- `.gitattributes` template


Add --strict flag for dependency import failures

Currently dependency import errors are warnings (logged to stderr, execution continues). Missing targets or cycles may indicate JSONL corruption. Add --strict flag to fail on any dependency errors for data integrity validation. Location: cmd/bd/import.go:159-164


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Add merge helper commands (bd sync --merge)

Add commands to merge beads branch back to main.

Tasks:
- Implement bd sync --merge command
- Implement bd sync --status command
- Implement bd sync --auto-merge (optional, for automation)
- Detect merge conflicts and provide guidance
- Show commit diff between branches
- Verify main branch is clean before merge
- Push merged changes to remote

Estimated effort: 2-3 days

- bd sync --merge successfully merges beads branch
- Conflicts detected with helpful error message
- bd sync --status shows clear diff
- Works with protected main (user must have push access)
- Git history is clean (no unnecessary merge commits)


Fix import zero-value field handling

Import uses zero-value checks (Priority != 0) to determine field updates. This prevents setting priority to 0 or clearing string fields. Export/import round-trip not fully idempotent for zero values. Consider JSON presence detection or explicit preserve-existing semantics. Location: cmd/bd/import.go:95-106


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Implement topological sort for import ordering

Refactor upsertIssues() to sort issues by hierarchy depth before batch creation. Ensures parents are created before children, fixing latent bug where parent-child pairs in same batch can fail if ordered wrong. Sort by dot count, create in depth-order batches (0→1→2→3).


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Increase test coverage for auto-flush and auto-import features

Critical features have 0% test coverage despite being core workflow functionality.

**Uncovered areas (0% coverage):**

Auto-flush/Auto-import (dirty tracking):
- MarkIssueDirty / MarkIssuesDirty
- GetDirtyIssues / GetDirtyIssueCount
- ClearDirtyIssues / ClearDirtyIssuesByID
- Auto-flush debouncing logic
- Auto-import hash comparison

Database/file discovery:
- FindDatabasePath (finds .beads/*.db in directory tree)
- FindJSONLPath (finds issues.jsonl)
- findDatabaseInTree helper

Label operations:
- AddLabel / RemoveLabel
- GetLabels / GetIssuesByLabel

Events/Comments:
- AddComment
- GetEvents
- GetStatistics

Metadata storage:
- SetMetadata / GetMetadata (used for import hash tracking)

CLI output formatting:
- outputJSON
- printCollisionReport / printRemappingReport
- createIssuesFromMarkdown

**Priority areas:**
1. Auto-flush/import (highest risk - core workflow)
2. Database discovery (second - affects all operations)
3. Labels/events (lower priority - less commonly used)

**Test approach:**
- Add unit tests for dirty tracking in sqlite package
- Add integration tests for auto-flush timing and debouncing
- Add tests for import hash detection and idempotency
- Add tests for database discovery edge cases (permissions, nested dirs)

**Target:** Get overall coverage from 60% → 75%, focus on cmd/bd (currently 24.1%)

**Note:** These features work well in practice (dogfooding proves it) but edge cases (disk full, permissions, concurrent access, race conditions) are untested.

Added comprehensive tests for CLI output functions (outputJSON, printCollisionReport, printRemappingReport).

Coverage analysis shows:
- outputJSON: 60% coverage (increased from 0%)
- printCollisionReport: 100% coverage (increased from 0%)
- printRemappingReport: 100% coverage (increased from 0%)
- cmd/bd overall: 19.7% (increased from 18.8%)

Other areas already have excellent coverage:
✅ Dirty tracking: TestMarkIssueDirty, TestMarkIssuesDirty, TestGetDirtyIssueCount, TestClearDirtyIssuesByID
✅ Auto-flush: TestAutoFlushDirtyMarking, TestAutoFlushDebounce, TestAutoFlushConcurrency
✅ Auto-import: TestAutoImportIfNewer, TestAutoImportHashUnchanged, TestAutoImportCollisions
✅ Database discovery: TestFindDatabasePathInTree, TestFindJSONLPath
✅ Labels: TestAddLabel, TestRemoveLabel, TestGetLabels, TestGetIssuesByLabel
✅ Metadata: TestSetAndGetMetadata, TestGetMetadataNotFound
✅ Events: TestAddComment, TestAddMultipleComments, TestGetEvents

The remaining low coverage in cmd/bd is primarily Cobra command setup and CLI wiring, which is difficult to unit test and best tested via integration/E2E tests.


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Add label-based filtering to bd ready command

Allow filtering ready work by labels to help organize work by sprint, week, or category.

Example usage:
  bd ready --label week1-2
  bd ready --label frontend,high-priority

This helps teams organize work into batches and makes it easier for agents to focus on specific categories of work.

Implementation notes:
- Add --label flag to ready command
- Support comma-separated labels (AND logic)
- Should work with existing ready work logic (unblocked issues)


Handle missing JSONL directory in findJSONLPath

findJSONLPath() assumes the database directory exists. If someone runs bd init to create a new database but the .beads directory doesn't exist yet, the glob operations might fail silently. Add os.MkdirAll(dbDir, 0755) to ensure directory exists before globbing. Located in cmd/bd/main.go:188-201.


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Add mutation channel to internal/rpc/server.go

Add mutationChan chan MutationEvent to Server struct. Emit events on CreateIssue, UpdateIssue, DeleteIssue, AddComment. Non-blocking send with default case for full channel.


Document bd-wasm installation and usage

Create documentation for bd-wasm:
- Update README with npm installation instructions
- Add troubleshooting section for WASM-specific issues
- Document known limitations vs native bd
- Add examples for Claude Code Web sandbox usage
- Update INSTALLING.md with bd-wasm option


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Enforce daemon singleton per workspace with file locking

Agent in ~/src/wyvern discovered 4 simultaneous daemon processes running, causing infinite directory recursion (.beads/.beads/.beads/...). Each daemon used relative paths and created nested .beads/ directories.

Root cause: No singleton enforcement. Multiple `bd daemon` processes can start in same workspace.

Expected: One daemon per workspace (each workspace = separate .beads/ dir with bd.sock)
Actual: Multiple daemons can run simultaneously in same workspace

Note: Separate git clones = separate workspaces = separate daemons (correct). Git worktrees share .beads/ and have known limitations (documented, use --no-daemon).

Use flock (file locking) on daemon socket or database file to enforce singleton:

1. On daemon start, attempt exclusive lock on .beads/bd.sock or .beads/daemon.lock
2. If lock held by another process, refuse to start (exit with clear error)
3. Hold lock for lifetime of daemon process
4. Release lock on daemon shutdown

Alternative: Use PID file with stale detection (check if PID is still running)

Implementation location: Daemon startup code in cmd/bd/ or internal/daemon/

1. Starting second daemon process in same workspace fails with clear error
2. Test: Start daemon, attempt second start, verify failure
3. Killing daemon releases lock, allowing new daemon to start
4. No infinite .beads/ directory recursion possible
5. Works correctly with auto-start mechanism

## Fix Summary

Successfully prevented the nested .beads/.beads/ recursion bug by implementing two safeguards:

1. **Path Canonicalization in FindDatabasePath()** (beads.go):
   - Added filepath.Abs() + filepath.EvalSymlinks() to normalize all database paths
   - Prevents relative path edge cases that create nested directories
   - Ensures all daemons see the same canonical path

2. **Nested Directory Detection** (daemon_lifecycle.go):
   - Added explicit check for ".beads/.beads" pattern in setupDaemonLock()
   - Fails fast with clear error message if nested structure detected
   - Provides user hints about proper usage

## Root Cause

The daemon lock (added Oct 22, 2025) correctly prevents simultaneous daemons in the SAME workspace. However, when BEADS_DB used a relative path (e.g., ".beads/beads.db") from inside the .beads directory, FindDatabasePath() would resolve it to a nested path creating a separate workspace:
- First daemon: /workspace/.beads/beads.db
- Second daemon from .beads/: /workspace/.beads/.beads/beads.db ← Different lock file!

## Testing

All acceptance criteria passed:
✅ 1. Second daemon start fails with "daemon already running" error
✅ 2. Killing daemon releases lock, new daemon can start
✅ 3. No infinite .beads/ recursion possible (tested nested BEADS_DB path)
✅ 4. Works with auto-start mechanism

The fix addresses the edge case while maintaining the existing lock mechanism's correctness.


Agent 1 Issue 51

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Add visibility for auto-flush failures

flushToJSONL() writes warnings to stderr when flush fails, but calling code has no way to know if flush succeeded or failed. This means a command could return success even though JSONL is now out of sync. Consider maintaining a 'last flush status' variable or counter for failed flushes, and warn user after multiple consecutive failures (e.g., 3+). Located in cmd/bd/main.go:227-307.


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Daemon crashes silently when multiple .db files exist in .beads/

When daemon detects multiple .db files (after filtering out .backup and vc.db files), it writes error details to .beads/daemon-error file before exiting.

The error file is checked when:
1. Daemon discovery fails to connect (internal/daemon/discovery.go)
2. Auto-start fails to yield a running daemon (cmd/bd/main.go)
3. Daemon list shows 'daemon not responding' error

This makes the error immediately visible to users without requiring them to check daemon logs.

File created:  cmd/bd/daemon.go (writes daemon-error on multiple .db detection)
Files modified:
- internal/daemon/discovery.go (reads daemon-error and surfaces in DaemonInfo.Error)
- cmd/bd/main.go (displays daemon-error when auto-start fails)

Testing: Create multiple .db files in .beads/, start daemon, verify error file created and shown in bd daemons list

Root cause: Daemon exits with os.Exit(1) when multiple .db files detected (daemon.go:1381), but error only goes to daemon log file. User sees 'daemon not responding' without knowing why.

Current detection:
- daemon.go filters out .backup and vc.db files
- bd doctor detects multiple databases
- Error message tells user to run 'bd init' or manually remove

Problem: Error is not user-visible unless they check daemon logs.

Proposed fix options:
1. Surface the error in 'bd info' and 'bd daemons list' output
2. Add a hint in error messages to run 'bd doctor' when daemon fails
3. Make daemon write error to a .beads/daemon-error file that gets checked
4. Improve 'bd doctor' to run automatically when daemon is unhealthy


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WASM integration testing

Comprehensive testing of WASM build. Child of epic bd-44d0.

## Tasks
- [ ] Unit tests for WASM module
- [ ] Integration tests with real JSONL files
- [ ] Test all bd commands for parity
- [ ] Performance benchmarks
- [ ] Test in actual Claude Code Web sandbox
- [ ] Document any limitations

## Test Coverage Target
- >90% of bd CLI commands work identically


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Implement `bd setup cursor` for Cursor IDE integration

Create a `bd setup cursor` command that integrates Beads workflow into Cursor IDE via .cursorrules file. Unlike Claude Code (which has hooks), Cursor uses a static rules file to provide context to its AI.

## Implementation

Create `cursor` subcommand in `cmd/bd/setup.go` that manages `.cursorrules` integration:

### Command Interface
```bash
bd setup cursor           # Install/update Cursor integration
bd setup cursor --check   # Verify .cursorrules has bd section
bd setup cursor --remove  # Remove bd section from .cursorrules
```

### Behavior

**If `.cursorrules` doesn't exist:**
- Create new file with complete bd rules template
- Mark sections for easy identification

**If `.cursorrules` exists:**
- Check if bd section already exists (look for marker comments)
- If not exists: append bd section
- If exists: update in place (preserve user customizations outside bd section)
- Backup original with `.cursorrules.backup` suffix

### .cursorrules Template

```markdown
# Beads Issue Tracking
# Auto-generated by 'bd setup cursor' - do not remove these markers
# BEGIN BEADS INTEGRATION

This project uses [Beads (bd)](https://github.com/steveyegge/beads) for issue tracking.

## Core Rules
- Track ALL work in bd (never use markdown TODOs or comment-based task lists)
- Use `bd ready` to find available work
- Use `bd create` to track new issues/tasks/bugs
- Use `bd sync` at end of session to sync with git remote
- Git hooks auto-sync on commit/merge

## Quick Reference
```bash
bd prime                              # Load complete workflow context
bd ready                              # Show issues ready to work (no blockers)
bd list --status=open                 # List all open issues
bd create --title="..." --type=task  # Create new issue
bd update <id> --status=in_progress  # Claim work
bd close <id>                         # Mark complete
bd dep <from> <to>                    # Add dependency (from blocks to)
bd sync                               # Sync with git remote
```

## Workflow
1. Check for ready work: `bd ready`
2. Claim an issue: `bd update <id> --status=in_progress`
3. Do the work
4. Mark complete: `bd close <id>`
5. Sync: `bd sync` (or let git hooks handle it)

## Context Loading
Run `bd prime` to get complete workflow documentation in AI-optimized format (~1-2k tokens).

For detailed docs: see AGENTS.md, QUICKSTART.md, or run `bd --help`

# END BEADS INTEGRATION
```

### Detection Logic

```go
func setupCursor() error {
    cursorRulesPath := ".cursorrules"

    // Check if file exists
    content, err := os.ReadFile(cursorRulesPath)
    if err != nil {
        if os.IsNotExist(err) {
            // Create new file
            return createCursorRules(cursorRulesPath)
        }
        return err
    }

    // Check if bd section exists
    if hasBeadsSection(string(content)) {
        // Update existing section
        return updateBeadsSection(cursorRulesPath, string(content))
    } else {
        // Append new section
        return appendBeadsSection(cursorRulesPath, string(content))
    }
}

func hasBeadsSection(content string) bool {
    return strings.Contains(content, "BEGIN BEADS INTEGRATION")
}
```

## Files
- `cmd/bd/setup.go` - Add cursor subcommand
- `cmd/bd/setup_cursor.go` - Cursor-specific logic
- `cmd/bd/setup_cursor_test.go` - Tests
- Template stored as Go string constant

## Differences from Claude Setup

| Aspect | Claude | Cursor |
|--------|--------|--------|
| **Integration file** | `.claude/commands/`, `.claude/hooks/` | `.cursorrules` |
| **Auto-refresh** | Hooks call `bd prime` | Static rules (manual refresh) |
| **Setup complexity** | Multiple files | Single file |
| **Update frequency** | Dynamic (hooks) | Static (updated via `bd setup cursor`) |

- `bd setup cursor` creates/updates .cursorrules
- Idempotent (safe to run multiple times)
- Preserves non-bd content in .cursorrules
- Backs up existing .cursorrules before modifying
- `bd setup cursor --check` verifies integration
- Markers allow updating bd section without affecting user content
- Unit tests for template insertion/update logic
- Documentation in AGENTS.md mentions Cursor setup


Add topological sort utility functions

Create internal/importer/sort.go with utilities for depth-based sorting of issues. Functions: GetHierarchyDepth(id), SortByDepth(issues), GroupByDepth(issues). Include stable sorting for same-depth issues.


Add test coverage for auto-flush feature

Add comprehensive tests for auto-flush functionality:\n- Test that markDirtyAndScheduleFlush() is called after CRUD operations\n- Test debounce timing (rapid operations result in single flush)\n- Test --no-auto-flush flag disables feature\n- Test flush on program exit\n- Test concurrent operations don't cause races\n- Test error scenarios (disk full, permission denied, etc.)\n- Test import command triggers auto-flush\n\nCurrent implementation has no test coverage for the auto-flush feature. Located in cmd/bd/main_test.go (to be created).


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Audit Current Cache Usage

Understand exactly what code depends on the storage cache

- Document showing all cache dependencies
- Confirmation that removing cache won't break MCP
- List of tests that need updating

Files to examine:
- internal/rpc/server_cache_storage.go (cache implementation)
- internal/rpc/client.go (how req.Cwd is set)
- internal/rpc/server_*.go (all getStorageForRequest calls)
- integrations/beads-mcp/ (MCP multi-repo logic)

Tasks:
- Document all callers of getStorageForRequest()
- Verify req.Cwd is only set by RPC client for database discovery
- Confirm MCP server doesn't rely on multi-repo cache behavior
- Check if any tests assume multi-repo routing
- Review environment variables: BEADS_DAEMON_MAX_CACHE_SIZE, BEADS_DAEMON_CACHE_TTL, BEADS_DAEMON_MEMORY_THRESHOLD_MB


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Add orphan detection migration

Create migration to detect orphaned children in existing databases. Query: SELECT id FROM issues WHERE id LIKE '%.%' AND substr(id, 1, instr(id || '.', '.') - 1) NOT IN (SELECT id FROM issues). Log results, let user decide action (delete orphans or convert to top-level).


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Add migration scripts for GitHub Issues

Create scripts to import from GitHub Issues API or exported JSON


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Add fsnotify dependency to go.mod


Add tests for extracted modules

Create tests for migrations.go, hash_ids.go, batch_ops.go, and validators.go


Implement content-hash based collision resolution for deterministic convergence

The current collision resolution uses creation timestamps to decide which issue to keep vs. remap. This is non-deterministic when two clones create issues at nearly the same time.

Root cause of bd-71107098:
- Clone A creates test-1="Issue from clone A" at T0
- Clone B creates test-1="Issue from clone B" at T0+30ms
- Clone B syncs first, remaps Clone A's to test-2
- Clone A syncs second, sees collision, remaps Clone B's to test-2
- Result: titles are swapped between clones

Solution:
- Use content-based hashing (title + description + priority + type)
- Deterministic winner: always keep issue with lower hash
- Same collision on different clones produces same result (idempotent)

Implementation:
- Modify ScoreCollisions in internal/storage/sqlite/collision.go
- Replace timestamp-based scoring with content hash comparison
- Ensure hash function is stable across platforms


File change test issue


Add circular dependency detection to bd doctor

Added cycle detection as Check #10 in bd doctor command. Uses same recursive CTE query as DetectCycles() to find circular dependencies. Reports error status with count and fix suggestion if cycles found.


Replace getStorageForRequest with Direct Access

Replace all getStorageForRequest(req) calls with s.storage

- No references to getStorageForRequest() in codebase (except in deleted file)
- All handlers use s.storage directly
- Code compiles without errors

Files to update:
- internal/rpc/server_issues_epics.go (~8 calls)
- internal/rpc/server_labels_deps_comments.go (~4 calls)
- internal/rpc/server_compact.go (~2 calls)
- internal/rpc/server_export_import_auto.go (~2 calls)
- internal/rpc/server_routing_validation_diagnostics.go (~1 call)

Pattern: store, err := s.getStorageForRequest(req) → store := s.storage


Add "bd daemons" command for multi-daemon management

Add a new "bd daemons" command with subcommands to manage daemon processes across all beads repositories/worktrees. Should show all running daemons with metadata (version, workspace, uptime, last sync), allow stopping/restarting individual daemons, auto-clean stale processes, view logs, and show exclusive lock status.

Subcommands:
- list: Show all running daemons with metadata (workspace, PID, version, socket path, uptime, last activity, exclusive lock status)
- stop <path|pid>: Gracefully stop a specific daemon
- restart <path|pid>: Stop and restart daemon
- killall: Emergency stop all daemons
- health: Verify each daemon responds to ping
- logs <path>: View daemon logs

Features:
- Auto-clean stale sockets/dead processes
- Discovery: Scan for .beads/bd.sock files + running processes
- Communication: Use existing socket protocol, add GET /status endpoint for metadata


Add concurrent import race condition tests

Currently no tests verify behavior when multiple clones import simultaneously with external_ref matching.

Scenarios to test:
1. Two clones import same external_ref update at same time
2. Clone A imports while Clone B updates same issue
3. Verify transaction isolation prevents corruption
4. Document expected behavior (last-write-wins vs timestamp-based)

Related: bd-1022
Files: internal/importer/external_ref_test.go


Improve internal/daemon test coverage (currently 22.5%)

Daemon functionality needs better coverage:
- Auto-start behavior
- Lock file management
- Discovery mechanisms
- Connection handling
- Error recovery

Current coverage: 58.3% (improved from 22.5% as of Nov 2025)


Benchmark Helper Functions

Extend existing benchmark helpers in internal/storage/sqlite/bench_helpers_test.go (or create if organizing separately).

Existing helper (in compact_bench_test.go):
- setupBenchDB(tb) - Creates temp SQLite database with basic config
  * Used by compact and cycle benchmarks
  * Returns (*SQLiteStorage, cleanup func())

New helpers to add:
- setupLargeBenchDB(b *testing.B) storage.Storage
  * Creates 10K issue database using LargeSQLite fixture
  * Returns configured storage instance

- setupXLargeBenchDB(b *testing.B) storage.Storage
  * Creates 20K issue database using XLargeSQLite fixture
  * Returns configured storage instance

Implementation options:
1. Add to existing compact_bench_test.go (co-located with setupBenchDB)
2. Create new bench_helpers_test.go for organization

Both approaches:
- Build tag: //go:build bench
- Uses fixture generator from internal/testutil/fixtures
- Follows existing setupBenchDB() pattern
- Handles database cleanup

These helpers reduce duplication across new benchmark functions and provide consistent large-scale database setup.


Add godoc comments for auto-flush functions

Add comprehensive godoc comments for findJSONLPath(), markDirtyAndScheduleFlush(), and flushToJSONL() explaining behavior, concurrency considerations, and error handling. Include notes about debouncing behavior (timer resets on each write, flush occurs 5s after LAST operation) and flush-on-exit guarantees. Located in cmd/bd/main.go:188-307.


Document hierarchical blocking behavior in README

The fix for bd-50 changes user-visible behavior: children of blocked epics are now automatically blocked.

**What needs documenting:**
1. README.md dependency section should explain blocking propagation
2. Clarify that 'blocks' + 'parent-child' together create transitive blocking
3. Note that 'related' and 'discovered-from' do NOT propagate blocking
4. Add example showing epic → child blocking propagation

**Example to add:**
```bash
# If epic is blocked, children are too
bd create "Epic 1" -t epic -p 1
bd create "Task 1" -t task -p 1
bd dep add task-1 epic-1 --type parent-child

# Block the epic
bd create "Blocker" -t task -p 0
bd dep add epic-1 blocker-1 --type blocks

# Now both epic-1 AND task-1 are blocked
bd ready  # Neither will show up
```


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bd doctor should check for multiple DBs, multiple JSONLs, daemon health

Currently bd doctor only checks:
- .beads/ directory exists
- Database version vs CLI version
- ID format (hash vs sequential)
- CLI version vs latest GitHub release

It should ALSO check for operational issues that cause silent failures:

1. **Multiple database files** (*.db excluding backups and vc.db)
   - Warn if multiple *.db files found (ambiguous which to use)
   - Suggest running 'bd migrate' or manually removing old DBs

2. **Multiple JSONL files**
   - Check for both issues.jsonl and beads.jsonl
   - Warn about ambiguity, suggest standardizing on one

3. **Daemon health** (integrate bd daemons health)
   - Check if daemon running for this workspace
   - Detect version mismatches between daemon and CLI
   - Detect zombie daemons (running but unresponsive)
   - Detect stale daemon.pid files

4. **Database-JSONL sync issues**
   - Check if JSONL is newer than last import
   - Warn if they're out of sync

5. **Permissions issues**
   - Check if .beads/ directory is writable
   - Check if database file is readable/writable

Implementation approach:
- Add new check functions to doctor.go
- Reuse logic from bd daemons health
- Keep checks fast (< 1 second total)
- Output actionable fixes for each issue


Document versioning and release strategy

Create comprehensive versioning strategy for beads ecosystem.

Components to document:
1. bd CLI (Go binary) - main version number
2. Plugin (Claude Code) - tracks CLI version
3. MCP server (Python) - bundled with plugin
4. Release workflow - how to sync all three

Decisions to make:
- Should plugin.json auto-update from bd CLI version?
- Should we have a VERSION file at repo root?
- How to handle breaking changes across components?
- What's the update notification strategy?

References:
- plugin.json engines field now requires bd >=0.9.0
- /bd-version command added for checking compatibility
- PLUGIN.md now documents update workflow


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Create version bump script

Create scripts/bump-version.sh to automate version syncing across all components.

The script should:
1. Take a version number as argument (e.g., ./scripts/bump-version.sh 0.9.3)
2. Update all version files:
   - cmd/bd/version.go (Version constant)
   - .claude-plugin/plugin.json (version field)
   - .claude-plugin/marketplace.json (plugins[].version)
   - integrations/beads-mcp/pyproject.toml (version field)
   - README.md (Alpha version mention)
   - PLUGIN.md (version requirements)
3. Validate semantic versioning format
4. Show diff preview before applying
5. Optionally create git commit with standard message

This prevents the version mismatch issue that occurred when only version.go was updated.

Related: bd-43 (version sync issue)


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Add system-wide/multi-repo support for beads

GitHub issue #4 requests ability to use beads across multiple projects and for system-wide task tracking.

Current limitation: beads is per-repository isolated. Each project has its own .beads/ directory and issues cannot reference issues in other projects.

Potential approaches:
1. Global beads instance in ~/.beads/global.db for cross-project work
2. Project references - allow issues to link across repos
3. Multi-project workspace support - one beads instance managing multiple repos
4. Integration with existing MCP server to provide remote multi-project access

Use cases:
- System administrators tracking work across multiple machines/repos
- Developers working on a dozen+ projects simultaneously
- Cross-cutting concerns that span multiple repositories
- Global todo list with project-specific subtasks

Related:
- GitHub issue #4: https://github.com/steveyegge/beads/issues/4
- Comparison to membank MCP which already supports multi-project via centralized server
- MCP server at integrations/beads-mcp/ could be extended for this

See also: Testing framework for plugins (also from GH #4)

Multi-repo support status update:

✅ **COMPLETED (P1 - Core functionality):**
- bd-98: --global daemon flag ✅
- bd-99: Multi-repo documentation ✅
- bd-92: Per-request context routing ✅

**REMAINING (Optional enhancements):**
- bd-100 (P2): 'bd repos' command - nice-to-have for UX
- bd-101 (P2): Daemon auto-start - convenience feature
- bd-102 (P3): Workspace config - alternative approach
- bd-103 (P4): Cross-repo references - future feature

**Decision:** Core multi-repo support is COMPLETE and working. Remaining items are independent enhancements, not blockers.

Recommend closing bd-43 as complete. Open new issues for specific enhancements if needed.


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Add coverage threshold to CI pipeline

Current CI runs tests with coverage but doesn't enforce minimum threshold. Add step to fail if coverage drops below target.

Current coverage: 60%
Recommended thresholds:
- Warn: 55%
- Fail: 50%

This prevents coverage regression while allowing gradual improvement toward 80% target for 1.0.

Implementation:
1. Add coverage check step after test run
2. Use 'go tool cover -func=coverage.out' to get total
3. Parse percentage and compare to threshold
4. Optionally: Use codecov's built-in threshold features

Related to test coverage improvement work (upcoming issue).


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Test basic bd commands in WASM (init, create, list)

Compile and verify basic bd functionality works in WASM:
- Test bd init --quiet
- Test bd create with simple issue
- Test bd list --json output
- Verify SQLite database creation and queries work
- Document any runtime issues or workarounds needed


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WASM port of bd for Claude Code Web sandboxes

Enable beads to work in Claude Code Web sandboxes by compiling bd to WebAssembly.

## Problem
Claude Code Web sandboxes cannot install bd CLI due to network restrictions:
- GitHub releases return 403
- go install fails with DNS errors
- Binary cannot be downloaded

## Solution
Compile bd Go codebase to WASM, publish to npm as drop-in replacement.

## Technical Approach
- Use GOOS=js GOARCH=wasm to compile bd
- modernc.org/sqlite already supports js/wasm target
- Publish to npm as bd-wasm package
- Full feature parity with bd CLI

## Success Criteria
- bd-wasm installs via npm in web sandbox
- All core bd commands work identically
- JSONL output matches native bd
- Performance within 2x of native

WASM port abandoned - Claude Code Web has full VMs not browser restrictions. Better: npm + native binary