Fix cross-worktree sync losing status changes (GH#865)

Left snapshot protection during sync ignores timestamps, causing newer remote changes to be skipped. Need to make protection timestamp-aware: only protect if local is newer than incoming. See issue for detailed analysis and fix options.


wish: list & ready show issues as hierarchy tree

`bd ready` and `bd list` just show a flat list, and it's up to the reader to parse which ones are dependent or sub-issues of others. It would be much easier to understand if they were shown in a tree format


Release v{{version}}

SUPERSEDED by bd-7bs4. Use the new proto for releases.


Tests for messaging and graph links

Comprehensive test coverage for all new features.

Test files:
- cmd/bd/mail_test.go - mail command tests
- internal/storage/sqlite/graph_links_test.go - graph link tests
- internal/hooks/hooks_test.go - hook execution tests

Test cases:
- Mail send/inbox/read/ack lifecycle
- Thread creation and traversal (replies_to)
- Bidirectional relates_to
- Duplicate marking and queries
- Supersedes chains
- Ephemeral cleanup
- Identity resolution priority
- Hook execution (mock hooks)
- Schema migration preserves data

Target: >80% coverage on new code


gt done --phase-complete: gastown changes for phase handoff

The gt done --phase-complete flag and Witness handling changes need to be
applied to the gastown project. These changes are already written and tested
in the mayor/rig but need to be properly committed through a gastown worktree.

Files changed:
- internal/cmd/done.go: Add --phase-complete and --gate flags
- internal/beads/beads.go: Add AddGateWaiter method
- internal/witness/protocol.go: Add Gate field to PolecatDonePayload
- internal/witness/handlers.go: Handle PHASE_COMPLETE exit type

This is a dependency for bd-quw1 (polecat phase handoff).

The beads changes (bd gate add-waiter, bd gate show) are committed in bd-quw1.


Merge: opal-1767142018955

branch: polecat/opal-1767142018955
target: main
source_issue: opal-1767142018955
rig: beads


Code smell: 20+ global variables in main.go

main.go lines 63-103 have over 20 global variables managing command-line state, daemon connection, auto-flush, auto-import, and error handling.

**Globals include:**
dbPath, actor, store, jsonOutput, daemonStatus, daemonClient, noDaemon, rootCtx, rootCancel, autoFlushEnabled, flushMutex, storeMutex, storeActive, flushFailureCount, lastFlushError, flushManager, hookRunner, skipFinalFlush, autoImportEnabled, versionUpgradeDetected, previousVersion, upgradeAcknowledged

**Problem:**
- Global state makes testing difficult
- Race conditions possible between goroutines
- Hard to track which functions modify which globals

**Acceptance Criteria:**
- [ ] Create CommandContext struct to hold runtime state
- [ ] Pass context through command execution
- [ ] Reduce global count to essential minimum
- [ ] Tests pass


Fix --as flag: uses title instead of ID in mol bond

In bondProtoProto, the --as flag is documented as 'Custom ID for compound proto' but the implementation uses it as the title, not the issue ID.

**Current behavior (mol.go:637-638):**
```go
if customID != '' {
    compoundTitle = customID  // Used as title, not ID
}
```

**Options:**
1. Change flag description to say 'Custom title' (documentation fix)
2. Actually use it as a custom ID prefix or full ID (feature change)
3. Add separate --title flag and make --as actually set ID

Recommend option 1 for simplest fix - change 'Custom ID' to 'Custom title' in the flag description.


Add covering index (label, issue_id) for label queries

GetIssuesByLabel joins labels table but requires table lookup after using idx_labels_label.

**Query (labels.go:165):**
```sql
SELECT ... FROM issues i
JOIN labels l ON i.id = l.issue_id
WHERE l.label = ?
```

**Problem:** Current idx_labels_label index doesn't cover issue_id, requiring row lookup.

**Solution:** Add migration:
```sql
CREATE INDEX IF NOT EXISTS idx_labels_label_issue ON labels(label, issue_id);
```

This is a covering index - query can be satisfied entirely from the index without touching the labels table rows.


Test agent bead

Testing new agent type


Add pre-sync validation hook

Future: Hook integration to run bd lint before sync, respecting config settings.


Merge: obsidian-1767142004753

branch: polecat/obsidian-1767142004753
target: main
source_issue: obsidian-1767142004753
rig: beads


Merge: onyx-1767138516448

branch: polecat/onyx-1767138516448
target: main
source_issue: onyx-1767138516448
rig: beads


Wait for CI

Monitor GitHub Actions for release completion.

https://github.com/steveyegge/beads/actions

Expected time: 5-10 minutes

Watch for:
- Build artifacts (all platforms)
- Test suite pass
- npm publish
- PyPI publish


Distinct prefixes for protos, molecules, wisps

Template/workflow entities should have visually distinct prefixes from regular issues.

**Problem:**
- Protos (bd-7bs4) look like regular issues - invites squashing
- Molecules (poured instances) also use bd- prefix
- Wisps are in separate DB but still use bd- when referenced

**Proposed Prefixes:**
- `proto-` for templates (e.g., proto-release, proto-review)
- `mol-` for active molecules (poured from protos)
- `wisp-` for ephemeral wisps (vapor phase)

**Benefits:**
- Instant visual recognition of entity type
- Prevents accidental modification of templates
- Clear lifecycle: proto → mol → wisp → digest

**Implementation options:**
1. Separate databases with different prefixes
2. Issue type determines prefix generation
3. Naming convention enforced by bd pour/wisp commands


Ephemeral issue cleanup and history compaction

## Problem

Beads history grows without bound. Every message, handoff, work assignment
stays in issues.jsonl forever. Enterprise users will balk at "git as database."

## Solution: Two-Tier Cleanup

### Tier 1: Ephemeral Cleanup (v1)

bd cleanup --ephemeral --closed

- Deletes closed issues where ephemeral=true from issues.jsonl
- Safe: only removes explicitly marked ephemeral + closed
- Preserves git history (commits still exist)
- Run after swarm completion

### Tier 2: History Compaction (v2)

bd compact --squash

- Rewrites issues.jsonl to remove tombstones
- Optionally squashes git history (interactive rebase equivalent)
- Preserves Merkle proofs for deleted items
- Advanced: cold storage tiering

## HOP Context

| Layer | HOP Role | Persistence |
|-------|----------|-------------|
| Execution trace | None | Ephemeral |
| Work scaffolding | None | Summarizable |
| Work outcome | CV entry | Permanent |
| Validation record | Stake proof | Permanent |

"Execution is ephemeral. Outcomes are permanent. You can't squash your CV."

## Success Criteria

- After cleanup --ephemeral: issues.jsonl only contains persistent work
- Work outcomes preserved (CV entries)
- Validation records preserved (stake proofs)
- Execution scaffolding removed (transient coordination)

## Implementation Plan (REVISED after code review)

See history/EPHEMERAL_MOLECULES_DESIGN.md for comprehensive design + review.

## Key Simplification

After code review, Tier 1 is MUCH simpler than originally designed:

- **Original**: Separate ephemeral repo with routing.ephemeral config
- **Revised**: Just set Wisp: true in cloneSubgraph()

The wisp field and bd cleanup --wisp already exist\!

## Child Tasks (in dependency order)

1. **bd-2vh3.2**: Tier 1 - Ephemeral spawning (SIMPLIFIED) [READY]
   - Just add Wisp: true to template.go:474
   - Add --persistent flag to opt out
2. **bd-2vh3.3**: Tier 2 - Basic bd mol squash command
3. **bd-2vh3.4**: Tier 3 - AI-powered squash summarization
4. **bd-2vh3.5**: Tier 4 - Auto-squash on molecule completion
5. **bd-2vh3.6**: Tier 5 - JSONL archive rotation (DEFERRED: post-1.0)

## What Already Exists

| Component | Location |
|-----------|----------|
| Ephemeral field | internal/types/types.go:45 |
| bd cleanup --wisp | cmd/bd/cleanup.go:72 |
| cloneSubgraph() | cmd/bd/template.go:456 |
| loadTemplateSubgraph() | cmd/bd/template.go |

## HOP Alignment

'Execution is ephemeral. Outcomes are permanent. You can't squash your CV.'


Verify release artifacts

Check GitHub releases page - binaries for darwin/linux/windows should be available


bd mol reset: Reset molecule to initial state for looping

Implement bd mol reset for patrol loop behavior.

## Command

```bash
bd mol reset <mol-id>
```

## Behavior

1. Load molecule state from .beads/molecules/<mol-id>.state.yaml
2. Reset all step states to pending
3. Clear current_step (or set to first step)
4. Preserve: bonded_at, bonded_by, variables
5. Update: reset_count++, last_reset_at

## Use Case: Deacon Patrol Loop

```
inbox-check → spawn-work → self-inspect → mol-reset → (loop)
```

The Deacon runs its patrol, then resets the molecule to start fresh.
No gt handoff needed unless context is high.

## State After Reset

```yaml
id: mol-deacon-patrol
status: running
current_step: inbox-check  # Back to first
reset_count: 5
last_reset_at: 2025-12-24T...
steps:
  inbox-check: pending      # All reset
  spawn-work: pending
  self-inspect: pending
```

## Files

- cmd/bd/mol_reset.go
- internal/mol/state.go (add Reset method)


Add gate checking to Deacon patrol loop

Integrate gate checking into Deacon's patrol cycle.

## Patrol Integration
```go
func (d *Deacon) checkGates(ctx context.Context) {
    gates, _ := d.store.ListOpenGates(ctx)

    for _, gate := range gates {
        // Check timeout
        if time.Since(gate.CreatedAt) > gate.Timeout {
            d.notifyWaiters(gate, "timeout")
            d.closeGate(gate, "timed out")
            continue
        }

        // Check condition
        if d.checkCondition(gate.AwaitType, gate.AwaitID) {
            d.notifyWaiters(gate, "cleared")
            d.closeGate(gate, "condition met")
        }
    }
}
```

## Note
This task is in Gas Town (gt), not beads. May need to be moved there.


Test refile v2

Testing improved refile


Verify GitHub release

Check the GitHub releases page.

https://github.com/steveyegge/beads/releases/tag/v0.39.0

Verify:
- Release created
- Binaries attached (linux, darwin, windows)
- Checksums present


beads-release

Beads release workflow - from version bump to verified release.

This formula orchestrates a complete release cycle:
1. Preflight checks (clean git, up to date)
2. Documentation updates (CHANGELOG, info.go)
3. Version bump (all components)
4. Git operations (commit, tag, push)
5. CI verification (GitHub Actions)
6. Artifact verification (GitHub, npm, PyPI)
7. Local installation update
8. Daemon restart

## Usage

```bash
bd wisp create beads-release --var version=0.37.0
```

Or assign to a polecat:
```bash
gt sling beads/polecats/p1 --formula beads-release --var version=0.37.0
```


Merge: obsidian-mk04ca9j

branch: polecat/obsidian-mk04ca9j
target: main
source_issue: obsidian-mk04ca9j
rig: beads
agent_bead: bd-beads-polecat-obsidian
retry_count: 0
last_conflict_sha: null
conflict_task_id: null


Fix daemon/direct mode inconsistency in relate and duplicate commands

The relate.go and duplicate.go commands have inconsistent daemon/direct mode handling:

When daemonClient is connected, they resolve IDs via RPC but then perform updates directly via store.UpdateIssue(), bypassing the daemon.

Affected locations:
- relate.go:125-139 (runRelate update)
- relate.go:235-246 (runUnrelate update)
- duplicate.go:120 (runDuplicate update)
- duplicate.go:207 (runSupersede update)

Should either use RPC for updates when daemon is running, or document why direct access is intentional.


Optimize GetReadyWork performance - 752ms on 10K database (target: <50ms)

# Performance Analysis (10K Issue Database)

Analyzed using CPU profiles from benchmark suite on Apple M2 Pro.

## Operation Performance

| Operation                        | Time    | Allocations | Memory |
|----------------------------------|---------|-------------|--------|
| bd ready (GetReadyWork)          | ~752ms  | 167,466     | 16MB   |
| bd list (SearchIssues no filter) | ~11.6ms | 89,214      | 5.8MB  |
| bd list (SearchIssues filtered)  | ~9.2ms  | 62,365      | 3.5MB  |
| bd create (CreateIssue)          | ~2.6ms  | 146         | 8.6KB  |
| bd update (UpdateIssue)          | ~0.32ms | 364         | 15KB   |
| bd close (UpdateIssue)           | ~0.32ms | 364         | 15KB   |

**Target: <50ms for all operations on 10K database**

**Current issue: GetReadyWork is 15x over target (752ms vs 50ms)**

## Root Cause

GetReadyWork (internal/storage/sqlite/ready.go:90-128) uses recursive CTE to propagate blocking:
- 65x slower than SearchIssues
- Recalculates entire blocked issue tree on every call
- Algorithm:
  1. Find directly blocked issues via 'blocks' dependencies
  2. Recursively propagate blockage to descendants (max depth: 50)
  3. Exclude all blocked issues from results

## CPU Profile Analysis

- Database syscalls (pthread_cond_signal, syscall6): ~75%
- SQLite engine overhead: inherent to recursive CTE
- Application code (query construction): <1%

**Bottleneck is the recursive CTE query execution, not application code.**

## Optimization Recommendations

### High Impact (Likely to achieve <50ms target)

1. **Cache blocked issue calculation**
   - Add `blocked_issues` table updated on dependency changes
   - Trade write complexity for read speed (ready called >> dependency changes)
   - Eliminates recursive CTE on every read

2. **Add/verify database indexes**
   ```sql
   CREATE INDEX IF NOT EXISTS idx_dependencies_blocked
     ON dependencies(issue_id, type, depends_on_id);
   CREATE INDEX IF NOT EXISTS idx_issues_status
     ON issues(status);
   ```

### Medium Impact

3. **Reduce allocations** (167K allocations for GetReadyWork)
   - Profile `scanIssues()` for object pooling opportunities
   - Reuse slice capacity for repeated calls

### Low Impact (Not recommended)
- Query optimization for CRUD operations (already <3ms)
- Connection pooling tuning (not showing in profiles)

## Verification

Run benchmarks to validate optimization:
```bash
make bench-quick
go tool pprof -http=:8080 internal/storage/sqlite/bench-cpu-*.prof
```

Profile files automatically generated in `internal/storage/sqlite/`.


Add versionChanges to info.go

Add entry at TOP of versionChanges in cmd/bd/info.go


GHI #891: close_reason field dropped during merge/sync

GitHub Issue #891: close_reason field dropped during merge/sync

https://github.com/steveyegge/beads/issues/891


bd mol publish: Push formula to GitHub repo

Publish a formula to a GitHub repository for sharing.

## Usage
```bash
# Create new repo and publish
bd mol publish mol-my-workflow --repo github.com/myorg/mol-my-workflow

# Update existing repo
bd mol publish mol-my-workflow --repo github.com/myorg/mol-my-workflow --tag v1.1.0
```

## Implementation
1. Export proto to formula.json (if not already a file)
2. Validate formula structure
3. Create GitHub repo if --create flag (uses `gh repo create`)
4. Copy formula.json to repo
5. Generate README.md from formula description
6. Commit and push
7. Create git tag if --tag specified
8. Add mol-formula topic to repo

## Flags
- `--repo <url>` - Target GitHub repo (required)
- `--tag <version>` - Create version tag
- `--create` - Create repo if doesn't exist
- `--private` - Create as private repo

## Workflow
```bash
# Full publish flow
bd mol distill my-epic --name my-workflow
bd mol promote bd-proto-xxx --as my-workflow
bd mol publish mol-my-workflow --repo github.com/me/mol-my-workflow --create --tag v1.0.0
```


Implement backup functionality for reset

Add backup capability that can be used by reset command.

## Functionality
- Copy .beads/ to .beads-backup-{timestamp}/
- Timestamp format: YYYYMMDD-HHMMSS
- Preserve file permissions
- Return backup path for user feedback

## Location
`internal/reset/backup.go` - keep with reset package for now (YAGNI)

## Interface
```go
func CreateBackup(beadsDir string) (backupPath string, err error)
```

## Notes
- Simple recursive file copy, no compression needed
- Error if backup dir already exists (unlikely with timestamp)
- Backup directories SHOULD be gitignored
- Add `.beads-backup-*/` pattern to .beads/.gitignore template in doctor package
- Consider: ListBackups() for future `bd backup list` command (not for this PR)


Code smell: Incomplete TODOs in formula/types.go

internal/formula/types.go has multiple TODO items for features that are defined in the schema but not implemented:

- Line 170: Expand field not implemented in bd cook
- Line 174: ExpandVars field not implemented
- Line 179: Gate integration pending (bd-udsi gates)
- Line 186: Condition evaluation not implemented
- Line 210: Additional expansion features

**Problem:**
- Schema defines features that aren't implemented
- Can confuse users who try to use these fields
- Creates maintenance burden of unused code paths

**Acceptance Criteria:**
- [ ] Either implement the features OR
- [ ] Remove unimplemented fields from schema OR
- [ ] Document clearly which fields are future-only
- [ ] Update related beads issues if they exist


bd agent state fails when agent bead doesn't exist

## Bug

`bd agent state <agent> <state>` fails if the agent doesn't already exist as a bead.

## Reproduction

```
gt sling gt-nrpiq gastown
...
Warning: couldn't update agent gt-gastown-polecat-toast hook to gt-nrpiq:
  updating agent state: bd agent state gt-gastown-polecat-toast running:
  Error: failed to resolve agent gt-gastown-polecat-toast:
  no issue found matching "gt-gastown-polecat-toast"
```

## Context from HOP Design

From **docs/hop/CONTEXT.md**:
> "Each polecat should have a chain: What work have they done? What's their success rate? What skills have they demonstrated?"

From **docs/PRIMING.md**:
> "Polecats are ephemeral executors. Like K8s pods. They have names (for debugging, logs) but no persistent identity."

**Resolution**: Polecat *sessions* are ephemeral, but polecat *names* (toast, nux, furiosa, etc.) are recycled and SHOULD have persistent identity beads. The name is the identity - sessions come and go.

Think of it like K8s:
- **Pod** = polecat session (ephemeral, killed after task)
- **ServiceAccount** = polecat identity bead (persistent, accumulates history)

## Solution

`bd agent state` should **auto-create** the agent bead on first use:

```go
// If agent bead doesn't exist, create it
if errors.Is(err, ErrNotFound) {
    // Create identity bead for this agent
    _, err = CreateIssue(Issue{
        Title:    fmt.Sprintf("Agent: %s", agentName),
        Type:     "agent",
        Status:   state,
        Metadata: map[string]string{
            "role": parseRole(agentName),  // polecat, witness, etc.
            "rig":  parseRig(agentName),   // gastown, beads, etc.
        },
    })
}
```

This enables:
1. Work history accumulation per polecat name
2. Skill/success tracking over time
3. CV chain for the polecat identity
4. `bd list --type=agent` to see all agents

## Non-goals

- Session tracking (ephemeral, don't persist)
- Work attribution to polecat (credits human owner)
- Agent scheduling (Gas Town handles that)


Merge: onyx-mk04d5pr

branch: polecat/onyx-mk04d5pr
target: main
source_issue: onyx-mk04d5pr
rig: beads
agent_bead: bd-beads-polecat-onyx
retry_count: 0
last_conflict_sha: null
conflict_task_id: null


Push to main

Push the release commit to origin.

```bash
git push origin main
```

If rejected, someone else pushed. Pull, rebase, try again.


HANDOFF: Version 0.30.7 release in progress

## Context
Doing a 0.30.7 patch release with bug fixes.

## What's done
- Fixed #657: bd graph nil pointer crash (graph.go:102)
- Fixed #652: Windows npm installer file lock (postinstall.js)
- Updated CHANGELOG.md and info.go
- Pushed to main, CI running (run 20390861825)
- Created version-bump molecule template (bd-6s61) and instantiated for 0.30.7 (bd-8pyn)

## In progress
Molecule bd-8pyn has 3 remaining tasks:
  - bd-dxo7: Wait for CI to pass
  - bd-7l70: Verify release artifacts
  - bd-5c91: Update local installation

## Check CI
  gh run list --repo steveyegge/beads --limit 1
  gh run view 20390861825 --repo steveyegge/beads

## New feature filed
bd-n777: Timer beads for scheduled agent callbacks
Design for Deacon-managed timers that can interrupt agents via tmux

## Resume commands
  bd --no-daemon show bd-8pyn
  gh run list --repo steveyegge/beads --limit 1


Create bd admin parent command and nest cleanup/compact/reset

## Task
Create new `bd admin` parent command and move:
- `bd cleanup` → `bd admin cleanup`
- `bd compact` → `bd admin compact`
- `bd reset` → `bd admin reset`

## Implementation

### 1. Create admin.go
New file with parent command:
```go
var adminCmd = &cobra.Command{
    Use:   "admin",
    Short: "Administrative commands for database maintenance",
    Long: `Administrative commands for beads database maintenance.

These commands are for advanced users and should be used carefully:
  cleanup   Delete closed issues and prune expired tombstones
  compact   Compact old closed issues to save space
  reset     Remove all beads data and configuration

For routine operations, prefer 'bd doctor --fix'.`,
}

func init() {
    rootCmd.AddCommand(adminCmd)
    adminCmd.AddCommand(cleanupCmd)
    adminCmd.AddCommand(compactCmd)
    adminCmd.AddCommand(resetCmd)
}
```

### 2. Update cleanup.go, compact.go, reset.go
- Remove `rootCmd.AddCommand()` from each init()
- Keep all existing functionality

### 3. Create hidden aliases for backwards compatibility
Top-level hidden commands that forward to admin subcommands.

### 4. Update docs (major updates)
- docs/CLI_REFERENCE.md - cleanup, compact references
- docs/QUICKSTART.md - compact, cleanup references
- docs/FAQ.md - compact references
- docs/TROUBLESHOOTING.md - compact references
- docs/DELETIONS.md - compact reference
- docs/CONFIG.md - compact reference
- skills/beads/SKILL.md - compact reference
- commands/compact.md - update all examples
- examples/compaction/README.md - update examples

## Files to create
- cmd/bd/admin.go

## Files to modify
- cmd/bd/cleanup.go
- cmd/bd/compact.go
- cmd/bd/reset.go
- cmd/bd/main.go (aliases)
- Multiple docs (see list above)


Update CHANGELOG.md for 0.30.4

1. Change `## [Unreleased]` to `## [0.30.4] - 2025-12-17`
2. Add new empty `## [Unreleased]` section at top
3. Ensure all changes since 0.30.3 are documented


bd create --rig flag for cross-rig issue filing

## Problem

To create an issue in a different rig, you must cd to that rig's directory. This is clunky when coordinating across rigs.

## Proposed Solution

Add a --rig flag to bd create that leverages existing routes.jsonl:

```bash
# From anywhere in town
bd create --rig beads --title="bug report" --type=bug

# Equivalent to:
cd ~/gt/beads/mayor/rig && bd create --title="..."
```

## How it works

1. Parse --rig flag (rig name, not prefix)
2. Look up rig in routes.jsonl to find beads location
3. Determine prefix from rig config
4. Create issue in that location with auto-generated ID

## Why elegant

- Leverages existing routing infrastructure
- Rig names are human-memorable (not cryptic prefixes)
- Works from anywhere in town
- Prefix auto-determined from rig config
- Reads naturally: "create in beads"

## Alternative

Also consider --prefix for power users who know prefixes:
```bash
bd create --prefix bd "Title here"
```


Update docs for import bug fix

Update AGENTS.md, README.md, TROUBLESHOOTING.md with import.orphan_handling config documentation. Document resurrection behavior, tombstones, config modes. Add troubleshooting section for import failures with deleted parents.


Integrate detect-pollution into bd doctor

## Task
Move `bd detect-pollution` → `bd doctor --check=pollution`

## Current state
- detect-pollution already shows deprecation hint pointing to doctor
- Doctor command exists with multiple checks

## Implementation

### 1. Update doctor.go
- Add pollution check to the doctor checks
- Add `--check=pollution` flag option
- Integrate detect-pollution logic

### 2. Update detect_pollution.go
- Mark as hidden (deprecated)
- Forward to doctor --check=pollution
- Keep for one release cycle

### 3. Update docs
- Remove detect-pollution from any command lists
- Update doctor docs to include pollution check

## Files to modify
- cmd/bd/doctor.go
- cmd/bd/detect_pollution.go


Merge: amber-1767146829144

branch: polecat/amber-1767146829144
target: main
source_issue: amber-1767146829144
rig: beads


Update local installation

Update local bd to the new version.

Option 1 - Homebrew:
```bash
brew upgrade bd
```

Option 2 - Install script:
```bash
curl -fsSL https://raw.githubusercontent.com/steveyegge/beads/main/scripts/install.sh | bash
```

Verify:
```bash
bd --version
```

Should show 0.99.0-test.


Investigate Claude Code crash logging improvements

## Problem

Claude Code doesn't leave useful crash logs when it terminates unexpectedly. Investigation of a crash on 2025-12-26 showed:

- Debug logs in ~/.claude/debug/ just stop mid-stream with no error/exit message
- No signal handlers appear to log SIGTERM/SIGKILL/SIGINT
- No dedicated crash log file exists
- When Node.js crashes hard or gets killed, there's no record of why

## What we found

- Session debug log (02080b1a-...) stopped at 22:58:40 UTC mid-operation
- No 'exit', 'error', 'crash', 'signal' entries at end of file
- macOS DiagnosticReports showed Chrome crashes but no Node crashes
- System logs showed no relevant kill/OOM events

## Desired improvements

1. Exit handlers that log graceful shutdown
2. Signal handlers that log SIGTERM/SIGINT before exiting
3. A dedicated crash log or at least a 'last known state' file
4. Possibly CLI flags to enable verbose crash debugging

## Investigation paths

- Check if Claude Code has --debug or similar flags
- Look at Node.js crash handling best practices
- Consider if we can wrap claude invocations to capture crashes

## Related

This came up while investigating why a crew worker session crashed at end of a code review task.


Commit and push release

git add -A && git commit && git push to trigger CI


Add --pretty flag to bd ready

bd list has --pretty but bd ready doesn't. Should support same tree format with status/priority symbols for consistency.


Technical debt: Scattered TODOs should be tracked as issues

Multiple TODO comments exist in the codebase that should be tracked as proper issues:

1. cmd/bd/migrate_hash_ids.go:24 - 'Consider integrating into bd doctor migration detection'
2. cmd/bd/migrate_tombstones.go:72 - Same
3. cmd/bd/migrate_sync.go:16 - Same
4. cmd/bd/migrate_issues.go:15 - Same
5. cmd/bd/create.go:164 - 'Switch to target repo for multi-repo support'
6. cmd/bd/create.go:208 - 'Add RPC method to get config in daemon mode'
7. cmd/bd/daemon_logger.go:131 - 'Remove this once all callers are updated'
8. cmd/bd/mol_stale.go:67 - 'Add RPC endpoint for stale check'
9. cmd/bd/sync_test.go:444 - 'Refactor to use direct import logic'
10. cmd/bd/jira.go:633 - 'In a full implementation, fetch Jira issue and compare timestamps'
11. internal/formula/types.go:170,174,179,186,210 - Multiple 'Not yet implemented' TODOs
12. internal/importer/importer_test.go:1010 - 'Test hangs due to database deadlock'

Consider:
1. Running 'grep -r TODO' periodically to find new ones
2. Adding a lint rule to discourage inline TODOs
3. Converting each to a bd issue with proper tracking

Location: Various files across codebase


Implement conditional bond type for mol bond

The mol bond command accepts 'conditional' as a bond type but doesn't implement any conditional-specific behavior. It currently behaves identically to 'parallel'.

**Expected behavior:**
Conditional bonds should mean 'B runs only if A fails' per the help text (mol.go:318).

**Implementation needed:**
- Add failure-condition dependency handling
- Possibly new dependency type or status-based blocking
- Update bondProtoProto, bondProtoMol, bondMolMol to handle conditional

**Alternative:**
Remove 'conditional' from valid bond types until implemented.

This is new functionality, not a regression.


Remove deprecated daemon logger function

In cmd/bd/daemon_logger.go:131, there's a TODO to remove a deprecated function once all callers are updated to use the new signature. Need to audit callers and clean up.

File: cmd/bd/daemon_logger.go:131


Merge: opal-1767138520240

branch: polecat/opal-1767138520240
target: main
source_issue: opal-1767138520240
rig: beads


bd close lacks cross-rig routing support

The `bd close` command doesn't support cross-rig routing like `bd show` does.

**Reproduction:**
```
# From gastown directory
bd show bd-xyz    # Works (routes to beads)
bd close bd-xyz   # Fails with 'no issue found matching'
```

**Root cause:**
- `show.go` uses `needsRouting()` and `resolveAndGetIssueWithRouting()`
- `close.go` only uses `utils.ResolvePartialIDs()` without routing

**Other affected commands (likely):**
- reopen
- dep
- comments
- label
- duplicate
- defer/undefer

**Fix:**
Add routing support to `close.go` similar to `show.go` lines 44-147.


Polymorphic bond command: bd mol bond A B

Implement proto-to-proto bonding to create compound protos.

COMMAND: bd mol bond proto-feature proto-testing [--as proto-feature-tested] [--type sequential]

BEHAVIOR:
- Load both proto subgraphs
- Create new compound proto with combined structure
- B's root becomes child of A's root (sequential) or sibling (parallel)
- Wire dependencies: B depends on A's leaf nodes (sequential) or runs parallel
- Store bonded_from metadata for lineage tracking

FLAGS:
- --as NAME: Custom ID for compound proto (default: generates hash)
- --type: sequential (default) or parallel
- --dry-run: Preview compound structure

OUTPUT:
- New compound proto in catalog
- Shows combined variable requirements

UPDATE: bond is now polymorphic - handles proto+proto, proto+mol, and mol+mol based on operand types. Separate 'attach' command eliminated.


Audit and standardize JSON output across all commands

Ensure consistent JSON format and error handling when --json flag is used.

**Scope:**
1. Verify all commands respect --json flag
2. Standardize success response format
3. Standardize error response format
4. Document JSON schemas

**Commands to audit:**
- Core CRUD: create, update, delete, show, list, search ✓
- Queries: ready, blocked, stale, count, stats, status
- Deps: dep add/remove/tree/cycles
- Labels: label commands
- Comments: comments add/list/delete
- Epics: epic status/close-eligible
- Export/import: already support --json ✓

**Testing:**
- Success cases return valid JSON
- Error cases return valid JSON (not plain text)
- Consistent field naming (snake_case vs camelCase)
- Array vs object wrapping consistency

## Audit Complete (2025-12-25)

### Findings

**✓ All commands support --json flag**
- Query commands: ready, blocked, stale, count, stats, status
- Dep commands: add, remove, tree, cycles
- Label commands: add, remove, list, list-all
- Comments: list, add
- Epic: status, close-eligible

**✓ Field naming is consistent**
- All fields use snake_case: created_at, issue_type, dependency_count, etc.

**✗ Error output is INCONSISTENT**
- Only bd show uses FatalErrorRespectJSON (returns JSON errors)
- All other commands use fmt.Fprintf(os.Stderr, ...) (returns plain text)

### Files needing fixes

| File | stderr writes | Commands |
|------|---------------|----------|
| show.go | 51 | update, close, edit |
| dep.go | 41 | dep add/remove/tree/cycles |
| label.go | 19 | label add/remove/list |
| comments.go | ~10 | comments add/list |
| epic.go | ~5 | epic status/close-eligible |

### Follow-up

Created epic bd-28sq to track fixing all error handlers.


Add git operations for --hard reset

Implement git integration for hard reset mode.

## Operations Needed
1. `git rm -rf .beads/*.jsonl` - remove data files from index
2. `git commit -m 'beads: reset to clean state'` - commit removal
3. After re-init: `git add .beads/` and commit fresh state

## Edge Cases to Handle
- Uncommitted changes in .beads/ - warn or error
- Detached HEAD state - warn, maybe block
- Git not initialized - skip git ops, warn
- Git operations fail mid-way - clear error messaging

## Interface
```go
type GitState struct {
    IsRepo       bool
    IsDirty      bool   // uncommitted changes in .beads/
    IsDetached   bool   // detached HEAD
    Branch       string // current branch name
}

func CheckGitState(beadsDir string) (*GitState, error)
func GitRemoveBeads(beadsDir string) error
func GitCommitReset(message string) error
func GitAddAndCommit(beadsDir, message string) error
```

## Location
`internal/reset/git.go` - keep with reset package for now

Note: Codebase has no central git package. internal/compact/git.go is compact-specific.
Future refactoring could extract shared git utilities, but YAGNI for now.


Add --hard flag to bd cleanup to permanently cull tombstones before cutoff date

Currently tombstones persist for 30 days before cleanup prunes them. Need an official way to force-cull tombstones earlier than the default TTL, for scenarios like cleaning house after extended absence where resurrection from old clones is not a concern. Proposed: bd cleanup --hard --older-than N to bypass the 30-day tombstone TTL.


Fix JSON errors in show.go (update/close/edit commands)

Replace ~51 direct stderr writes with FatalErrorRespectJSON() in show.go.

Commands affected:
- updateCmd (~10 error handlers)
- closeCmd (~15 error handlers)
- editCmd (~10 error handlers)
- showCmd (already uses FatalErrorRespectJSON in some places)

Key error paths:
- ID resolution errors (lines 565, 570, 579)
- Validation errors (lines 474, 515, 524, 545)
- RPC/daemon errors (line 639+)
- Store operation errors


Code Review: Beads Refactoring Sprint

Epic for code smell fixes identified during Beads code review.

## Scope
11 issues covering:
- P2: Duplicated code in cook.go (2 issues)
- P3: Long functions and God Objects (5 issues)
- P4: Technical debt and cleanup (4 issues)

## Approach
Swarm with polecats, each taking 1-2 issues. All changes should:
1. Pass existing tests
2. Not change external behavior
3. Improve code maintainability

## Success Criteria
All 11 child issues closed with passing CI.


Code smell: Issue struct still has ~100 fields - consider composition

internal/types/types.go Issue struct (lines 14-100) still has approximately 100 fields across many categories despite prior cleanup:

- Core identification (ID, ContentHash)
- Content (Title, Description, Design)
- Status & Workflow
- Assignment, Timestamps
- External integration
- Compaction metadata
- Relational data (Labels, Dependencies, Comments)
- Tombstone, Messaging, Context markers
- Bonding, HOP, Gate, Source tracing, Agent identity fields

**Problem:**
- Very large struct is difficult to understand
- Hard to identify required vs optional fields
- High change risk

**Acceptance Criteria:**
- [ ] Group related fields into embedded structs (IssueMetadata, IssueCompaction, IssueAgent, etc.)
- [ ] Use composition instead of single flat struct
- [ ] Maintain backward compatibility for serialization
- [ ] Tests pass


bd ship command for publishing capabilities

Add `bd ship <capability>` command that:

1. Finds issue with `export:<capability>` label
2. Validates issue is closed (or --force to override)
3. Adds `provides:<capability>` label
4. Protects `provides:*` namespace (only bd ship can add these labels)

Example:
```bash
bd ship mol-run-assignee
# Output: Shipped mol-run-assignee (bd-xyz)
```

Part of cross-project dependency system.
See: gastown/docs/cross-project-deps.md


Merge: bd-t4sb

branch: polecat/capable
target: main
source_issue: bd-t4sb
rig: beads


refinery Handoff


Implement bd close --continue flag

Auto-advance to next step in molecule when closing an issue. Referenced by gt-um6q, gt-lz13. Needed for molecule navigation workflow.


bd repair: Limit verbose output for large orphan counts

When there are thousands of orphaned references, bd repair prints them all, flooding the terminal.

Fix: Add --verbose flag; default to summary only (e.g., 'Found 1,234 orphaned dependencies'). Only print individual items with --verbose or when count is small (<20).


Add integration tests for bd reset command

End-to-end integration tests for the reset command.

## Test Scenarios

### Basic reset
1. Init beads, create some issues
2. Run bd reset --force
3. Verify .beads/ is fresh, issues gone

### Hard reset
1. Init beads, create issues, commit
2. Run bd reset --hard --force
3. Verify git history has reset commits

### Backup functionality
1. Init beads, create issues
2. Run bd reset --backup --force
3. Verify backup exists with correct contents
4. Verify main .beads/ is reset

### Dry run
1. Init beads, create issues
2. Run bd reset --dry-run
3. Verify nothing changed

### Confirmation prompt
1. Init beads
2. Run bd reset (no --force)
3. Verify prompts for confirmation
4. Test both y and n responses

## Location
tests/integration/reset_test.go or similar


Support daemon.auto_commit and daemon.auto_push in config.yaml (GH#871)

Allow team-wide auto-sync settings via config.yaml instead of SQLite. This enables teams to share auto-commit/auto-push settings through version control.


Test event


Thread Test

Testing the thread feature


Improve test coverage for internal/daemon (27.3% → 60%)

The daemon package has only 27.3% test coverage. The daemon is critical for background operations and reliability.

Key areas needing tests:
- Daemon autostart logic
- Socket handling
- PID file management
- Health checks

Current coverage: 27.3%
Target coverage: 60%


Add integration tests for RPC server and event loops

After adding basic unit tests for daemon utilities, the complex daemon functions still need integration tests:

Core daemon lifecycle:
- startRPCServer: Initializes and starts RPC server with proper error handling
- runEventLoop: Polling-based sync loop with parent monitoring and signal handling
- runDaemonLoop: Main daemon initialization and setup

Health checking:
- isDaemonHealthy: Checks daemon responsiveness and health metrics
- checkDaemonHealth: Periodic health verification

These require more complex test infrastructure (mock RPC, test contexts, signal handling) and should be tackled after the unit test foundation is in place.


Fix sync.remote config not being respected (GH#872)

bd config set sync.remote <name> sets the value but bd sync still tries to use 'origin'. Need to check where the sync code reads the remote name and ensure it uses the configured value.


Add bd reset command for clean slate restart

Implement a command to reset beads to a clean starting state.

**Context:** GitHub issue #479 - users sometimes get beads into an invalid state after updates, and there's no clean way to start fresh. The git backup/restore mechanism that protects against accidental deletion also makes it hard to intentionally reset.

**Current workaround** (from maphew):
```bash
bd daemons killall
git rm .beads/*.jsonl
git commit -m 'remove old issues'
rm .beads/*
bd init
bd onboard
```

**Desired:** A proper `bd reset` command that handles this cleanly and safely.


Version Bump: 0.30.7

Release checklist for version 0.30.7. This molecule ensures all release steps are completed properly.


bd doctor: detect issues referenced in commits but still open

Add a doctor check that finds 'orphaned' issues - ones referenced in git commit messages (e.g., 'fix bug (bd-xxx)') but still marked as open in beads.

**Detection logic:**
1. Get all open issue IDs from beads
2. Parse git log for issue ID references matching pattern \(prefix-[a-z0-9.]+\)
3. Report issues that appear in commits but are still open

**Output:**
⚠ Warning: N issues referenced in commits but still open
  bd-xxx: 'Issue title' (commit abc123)
  bd-yyy: 'Issue title' (commit def456)

  These may be implemented but not closed. Run 'bd show <id>' to check.

**Implementation:**
- Add check to doctor/checks.go
- Use git log parsing (already have git utilities)
- Match against configured issue_prefix


Show pin indicator in bd list output

Add a visual indicator (e.g., pin emoji or [P] marker) for pinned issues in bd list output so users can easily identify them.


Implement global N-way collision resolution algorithm

**Summary:** Replaced pairwise collision resolution with a global N-way algorithm that deterministically resolves issue ID conflicts across multiple clones. The new approach groups collisions, deduplicates by content hash, and assigns sequential IDs to ensure consistent synchronization.

**Key Decisions:**
- Use content hash for global, stable sorting
- Group collisions by base ID
- Assign sequential IDs based on sorted unique versions
- Eliminate order-dependent remapping logic

**Resolution:** Implemented ResolveNWayCollisions function that guarantees deterministic issue ID assignment across multiple synchronization scenarios, solving the core challenge of maintaining consistency in distributed systems with potential conflicts.


Crew worker emma in beads - human-managed persistent workspace.

role_type: crew
rig: beads
agent_state: idle
hook_bead: null
role_bead: gt-crew-role
cleanup_status: null


RemoveDependency fails on external deps - FK violation in dirty_issues

In dependencies.go:225, RemoveDependency marks BOTH issueID and dependsOnID as dirty. For external refs (e.g., external:project:capability), dependsOnID doesn't exist in the issues table. This causes FK violation since dirty_issues.issue_id has FK constraint to issues.id.

Fix: Check if dependsOnID starts with 'external:' and only mark source issue as dirty, matching the logic in AddDependency (lines 162-170).

Repro: bd dep rm <issue> external:project:capability


HOP-compatible schema additions

Add optional fields to Beads schema to enable future HOP integration.
All fields are backwards-compatible (optional, omitted if empty).

## Reference
See ~/gt/docs/hop/BEADS-SCHEMA-CHANGES.md for full specification.

## P1 Changes (Must Have Before Launch)

### 1. EntityRef type
Structured entity reference that can become HOP URI:
```go
type EntityRef struct {
    Name     string // "polecat/Nux"
    Platform string // "gastown"
    Org      string // "steveyegge"
    ID       string // "polecat-nux"
}
```

### 2. creator field
Every issue tracks who created it (EntityRef).

### 3. assignee_ref field
Structured form alongside existing string assignee.

### 4. validations array
Track who validated work completion:
```go
type Validation struct {
    Validator *EntityRef
    Outcome   string    // accepted, rejected, revision_requested
    Timestamp time.Time
    Score     *float32  // Future
}
```

## P2 Changes (Should Have)

### 5. work_type field
"mutex" (default) or "open_competition"

### 6. crystallizes field
Boolean - does this work compound (true) or evaporate (false)?

### 7. cross_refs field
Array of URIs to beads in other repos:
- "beads://github/anthropics/claude-code/bd-xyz"

## P3 Changes (Nice to Have)

### 8. skill_vector placeholder
Reserved for future embeddings: []float32

## Implementation Notes
- All fields optional in JSONL serialization
- Empty/null fields omit from output
- No migration needed for existing data
- CLI additions: --creator, --validated-by filters

Scope reduced after review. P1 only: EntityRef type, creator field, validations array. Deferred: assignee_ref, work_type, crystallizes, cross_refs, skill_vector (YAGNI - semantics unclear, can add later when needed).


Improve test coverage for internal/beads (48.1% → 70%)

Improve test coverage for internal/beads package from 48% to 70%.

## Current State
- Coverage: 48.4%
- Files: beads.go, fingerprint.go
- Tests: beads_test.go (moderate coverage)

## Functions Needing Tests

### beads.go (database discovery)
- [ ] followRedirect - needs redirect file tests
- [ ] findDatabaseInBeadsDir - needs various dir structures
- [x] NewSQLiteStorage - likely covered
- [ ] FindDatabasePath - needs BEADS_DB env var tests
- [ ] hasBeadsProjectFiles - needs file existence tests
- [ ] FindBeadsDir - needs directory traversal tests
- [ ] FindJSONLPath - needs path derivation tests
- [ ] findGitRoot - needs git repo tests
- [ ] findDatabaseInTree - needs nested directory tests
- [ ] FindAllDatabases - needs multi-database tests
- [ ] FindWispDir - needs wisp directory tests
- [ ] FindWispDatabasePath - needs wisp path tests
- [ ] NewWispStorage - needs wisp storage tests
- [ ] EnsureWispGitignore - needs gitignore creation tests
- [ ] IsWispDatabase - needs path classification tests

### fingerprint.go (repo identification)
- [ ] ComputeRepoID - needs various remote URL tests
- [ ] canonicalizeGitURL - needs URL normalization tests
- [ ] GetCloneID - needs clone identification tests

## Implementation Guide

1. **Use temp directories:**
   ```go
   func TestFindBeadsDir(t *testing.T) {
       tmpDir := t.TempDir()
       beadsDir := filepath.Join(tmpDir, ".beads")
       os.MkdirAll(beadsDir, 0755)

       // Create test files
       os.WriteFile(filepath.Join(beadsDir, "beads.db"), []byte{}, 0644)

       // Change to tmpDir and test
       oldWd, _ := os.Getwd()
       os.Chdir(tmpDir)
       defer os.Chdir(oldWd)

       result := FindBeadsDir()
       assert.Equal(t, beadsDir, result)
   }
   ```

2. **Test scenarios:**
   - BEADS_DB environment variable set
   - .beads/ in current directory
   - .beads/ in parent directory
   - Redirect file pointing elsewhere
   - No beads directory found
   - Wisp directory alongside main beads

3. **Git remote URL tests:**
   ```go
   tests := []struct{
       input    string
       expected string
   }{
       {"git@github.com:user/repo.git", "github.com/user/repo"},
       {"https://github.com/user/repo", "github.com/user/repo"},
       {"ssh://git@github.com/user/repo.git", "github.com/user/repo"},
   }
   ```

## Success Criteria
- Coverage ≥ 70%
- All FindXxx functions have tests
- Environment variable handling tested
- Edge cases (missing dirs, redirects) covered

## Run Tests
```bash
go test -v -cover ./internal/beads
go test -race ./internal/beads
```


Parallel step detection in molecules

Detect and flag parallelizable steps in molecules.

## Detection Rules
Steps can run in parallel when:
1. No Needs dependencies between them
2. Not in same sequential chain
3. Across dynamic arms (arm-ace and arm-nux can parallelize)

## Output in bd mol show
```
patrol-x7k (mol-witness-patrol)
├── inbox-check [completed]
├── survey-workers [completed]
│   ├── arm-ace [parallel group A]
│   │   ├── capture [can parallelize]
│   │   ├── assess [needs: capture]
│   │   └── execute [needs: assess]
│   └── arm-nux [parallel group A]
│       ├── capture [can parallelize]
│       └── ...
├── aggregate [gate: waits for all-children]
```

## Flags
- `bd mol show <id> --parallel` - Highlight parallel opportunities
- `bd ready --mol <id>` - List all steps that can run now

## Future: Parallel Execution Hints
For agents using Task tool subagents:
- Identify independent arms that can run simultaneously
- Suggest parallelization strategy


Test role bead


Review PR #834: Add Windows ARM64 build support

Review and potentially merge PR #834 from ramarivera adding native Windows ARM64 (aarch64) build support.

Key changes:
- GoReleaser: Added bd-windows-arm64 build configuration
- CI Workflow: Installed gcc-mingw-w64-aarch64 toolchain
- WinGet Manifest: Added ARM64 installer entry
- Release Notes: Updated to mention Windows ARM64 support

Fixes #833. No code changes - purely build configuration.


Swarm: 13 beads backlog issues for polecat execution

## Swarm Overview

13 issues prepared for parallel polecat execution. All issues have been enhanced with concrete implementation guidance, file lists, and success criteria.

## Issue List

### Bug (1) - HIGH PRIORITY
| ID | Priority | Title |
|----|----------|-------|
| bd-phtv | P1 | Pinned field overwritten by subsequent commands |

### Test Coverage (3)
| ID | Package | Target |
|----|---------|--------|
| bd-io8c | internal/syncbranch | 27% → 70% |
| bd-thgk | internal/compact | 17% → 70% |
| bd-tvu3 | internal/beads | 48% → 70% |

### Code Quality (3)
| ID | Task |
|----|------|
| bd-qioh | FatalError pattern standardization |
| bd-rgyd | Split queries.go (1704 lines → 5 files) |
| bd-u2sc.3 | Split cmd/bd files (sync/init/show/compact) |

### Features (4)
| ID | Task |
|----|------|
| bd-au0.5 | Search date/priority filters |
| bd-ykd9 | Doctor --fix auto-repair |
| bd-g4b4 | Close hooks system |
| bd-likt | Gate daemon RPC |

### Polish (2)
| ID | Task |
|----|------|
| bd-4qfb | Doctor output formatting |
| bd-u2sc.4 | slog structured logging |

## Issue Details

All issues have been enhanced with:
- Concrete file lists to modify
- Code snippets and patterns
- Success criteria
- Test commands

Run `bd show <id>` for full details on any issue.

## Execution Notes

- All issues are independent (no blockers between them)
- bd-phtv (P1 bug) should get priority - affects bd pin functionality
- Test coverage tasks are straightforward but time-consuming
- File split tasks (bd-rgyd, bd-u2sc.3) are mechanical but important

## Completed During Prep

- bd-ucgz (P2 bug) - Fixed inline: external deps orphan check (commit f2db0a1d)
- Moved 5 gastown issues out of beads backlog (gt-dh65, gt-ng6g, gt-fqcz, gt-gswn, gt-rw2z)
- Deferred 4 premature/post-1.0 issues
- Closed bd-udsi epic (core implementation complete)


Fix G304 potential file inclusion in cmd/bd/tips.go:259

Linting issue: G304: Potential file inclusion via variable (gosec) at cmd/bd/tips.go:259:18. Error: if data, err := os.ReadFile(settingsPath); err == nil {


Merge: bd-dtl8

branch: polecat/dag
target: main
source_issue: bd-dtl8
rig: beads


Remove legacy autoflush code paths

## Problem

The autoflush system has dual code paths - an old timer-based approach and a new FlushManager. Both are actively used based on whether flushManager is nil.

## Locations

- main.go:78-81: isDirty, needsFullExport, flushTimer marked 'used by legacy code'
- autoflush.go:291-369: Functions with 'Legacy path for backward compatibility with tests'

## Current Behavior

```go
// In markDirtyAndScheduleFlush():
if flushManager != nil {
    flushManager.MarkDirty(false)
    return
}
// Legacy path for backward compatibility with tests
```

## Proposed Fix

1. Ensure flushManager is always initialized (even in tests)
2. Remove the legacy timer-based code paths
3. Remove isDirty, needsFullExport, flushTimer globals
4. Update tests to use FlushManager

## Risk

Low - the FlushManager is the production path. Legacy code only runs when flushManager is nil (test scenarios).


bd dep add: Auto-resolve cross-rig IDs using routes.jsonl

Currently, adding a dependency to an issue in another rig requires verbose external reference syntax:

```bash
# This fails - can't resolve bd-* from gastown context
bd dep add gt-xyz bd-abc

# This works but is verbose
bd dep add gt-xyz external:beads:bd-abc
```

The town-level routing (~/gt/.beads/routes.jsonl) already knows how to map prefixes to rigs:
```json
{"prefix": "gt-", "path": "gastown/mayor/rig"}
{"prefix": "bd-", "path": "beads/mayor/rig"}
```

Enhancement: When `bd dep add` encounters an ID with a foreign prefix, it should:
1. Check routes.jsonl for the prefix mapping
2. Auto-resolve to external:<project>:<id> internally
3. Allow the simpler `bd dep add gt-xyz bd-abc` syntax

This would make cross-rig dependencies much more ergonomic.


Merge: jasper-1767142011373

branch: polecat/jasper-1767142011373
target: main
source_issue: jasper-1767142011373
rig: beads


GH#519: bd sync fails when sync.branch is currently checked-out branch


Add {{version}} to versionChanges in info.go

Add new entry at the TOP of versionChanges array in cmd/bd/info.go:

```go
{
    Version: "{{version}}",
    Date:    "{{date}}",
    Changes: []string{
        // Add notable changes here
    },
},
```

Copy changes from CHANGELOG.md [Unreleased] section.


activity --follow: Silent error handling

In activity.go:175-179, when the daemon is down or errors occur during polling in --follow mode, errors are silently ignored:

```go
newEvents, err := fetchMutations(lastPoll)
if err != nil {
    // Daemon might be down, continue trying
    continue
}
```

This means:
- Users won't know if the daemon is unreachable
- Could appear frozen when actually failing
- No indication of lost events

Should at least show a warning after N consecutive failures, or show '...' indicator to show polling status.

Discovered during code review of bd-xo1o implementation.


Tier 1: Ephemeral repo routing

Simplified: Make mol spawn set ephemeral=true on spawned issues.

## The Fix

Modify cloneSubgraph() in template.go to set Ephemeral: true:

```go
// template.go:474
newIssue := &types.Issue{
    Title:      substituteVariables(oldIssue.Title, vars),
    // ... existing fields ...
    Ephemeral:  true,  // ADD THIS LINE
}
```

## Optional: Add --persistent flag

Add flag to bd mol spawn for when you want spawned issues to persist:

```bash
bd mol spawn mol-code-review --var pr=123  # ephemeral (default)
bd mol spawn mol-code-review --var pr=123 --persistent  # not ephemeral
```

## Why This Is Simpler Than Original Design

Original design proposed separate ephemeral repo routing. After code review:

- Ephemeral field already exists in schema
- bd cleanup --ephemeral already works
- No new config needed
- No multi-repo complexity

## Acceptance Criteria

- bd mol spawn creates issues with ephemeral=true
- bd cleanup --ephemeral -f deletes them after closing
- --persistent flag opts out of ephemeral
- Existing molecules continue to work


Merge: bd-u2sc.3

branch: polecat/Modular
target: main
source_issue: bd-u2sc.3
rig: beads


Edge Schema Consolidation: Unify all edges in dependencies table

Consolidate all edge types into the dependency table per decision 004.

## Changes
- Add metadata column to dependencies table
- Add thread_id column for conversation grouping
- Remove redundant Issue fields: replies_to, relates_to, duplicate_of, superseded_by
- Update all code to use dependencies API
- Migration script for existing data
- JSONL format change (breaking)

Reference: ~/gt/hop/decisions/004-edge-schema-consolidation.md


Simplify bd onboard to minimal AGENTS.md snippet pointing to bd prime

## Context
GH#604 raised concerns about bd onboard bloating AGENTS.md with ~100+ lines of static instructions that:
- Load every session whether beads is being used or not
- Get stale when bd upgrades
- Waste tokens

## Solution
Simplify `bd onboard` to output a minimal snippet (~2 lines) that points to `bd prime`:

```markdown
## Issue Tracking
This project uses beads (`bd`) for issue tracking.
Run `bd prime` for workflow context, or hooks auto-inject it.
```

## Rationale
- `bd prime` is dynamic, concise (~80 lines), and always matches installed bd version
- Hooks already auto-inject `bd prime` at session start when .beads/ detected
- AGENTS.md only needs to mention beads exists, not contain full instructions

## Implementation
1. Update `cmd/bd/onboard.go` to output minimal snippet
2. Keep `--output` flag for BD_GUIDE.md generation (may still be useful)
3. Update help text to explain the new approach


Formula versioning: Version field and git tag integration

Add versioning support to formulas for tracking updates.

## Formula Version Field
```json
{
  "formula": "mol-code-review",
  "version": "1.2.0",
  "min_bd_version": "0.25.0",
  ...
}
```

## Version Semantics
- Use semver: MAJOR.MINOR.PATCH
- MAJOR: Breaking changes to step structure
- MINOR: New optional steps or variables
- PATCH: Documentation, bug fixes

## Git Tag Integration
- `bd mol install repo@v1.2.0` fetches that tag
- `bd mol install repo` fetches latest tag (or main if no tags)
- `bd mol publish --tag v1.2.0` creates tag

## Proto Version Tracking
Local proto should store:
```
source_repo: github.com/anthropics/mol-code-review
source_version: v1.2.0
installed_at: 2025-12-25T12:00:00Z
```

This enables `bd mol update` to check for newer versions.


Crew worker dave in beads - human-managed persistent workspace.

role_type: crew
rig: beads
agent_state: idle
hook_bead: null
role_bead: gt-crew-role
cleanup_status: null


Explore wiki-style documentation structure

Our docs are growing into a book. Evaluate options for wiki-like structure:

**Options to evaluate:**
- GitHub Wiki (built-in, limited features)
- mdBook (Rust, CLI-friendly, produces HTML/PDF/ePub)
- MkDocs / Material for MkDocs (Python, beautiful themes)
- Docusaurus (React, powerful but complex)
- Plain markdown with good structure (current approach)

**Requirements:**
- Git-backed (version control)
- Markdown-native (agents can edit)
- Table of contents / navigation
- Cross-linking between pages
- Searchable
- Can be hosted on GitHub Pages

**Deliverables:**
- Recommendation with pros/cons
- If switching: migration plan
- If staying with markdown: structure guidelines for wiki-like organization

References:
- https://squidfunk.github.io/mkdocs-material/alternatives/
- https://www.archbee.com/blog/gitbook-alternatives


Molecule bonding: composable workflow templates

Vision: Molecules should be composable like LEGO bricks or Mad Max war rig sections. Bonding lets you attach molecules together to create compound workflows.

THREE BONDING CONTEXTS:
1. Template-time: bd mol bond A B → Create reusable compound proto
2. Spawn-time: bd mol spawn A --attach B → Attach modules when instantiating
3. Runtime: bd mol attach epic B → Add to running workflow

BOND TYPES:
- Sequential: B after A completes (feature → deploy)
- Parallel: B runs alongside A (feature + docs)
- Conditional: B only if A fails (feature → hotfix)

BOND POINTS (Attachment Sites):
- Default: B depends on A root epic completion
- Explicit: --after issue-id for specific attachment
- Future: Named bond points in proto definitions

VARIABLE FLOW:
- Shared namespace between bonded molecules
- Warn on variable name conflicts
- Future: explicit mapping with --map

DATA MODEL: Issues track bonded_from to preserve compound lineage.

SUCCESS CRITERIA:
- Can bond two protos into a compound proto
- Can spawn with --attach for on-the-fly composition
- Can attach molecules to running workflows
- Compound structure visible in bd mol show
- Variables flow correctly between bonded molecules


Agent bead prefix mismatch: gt- vs bd- for beads polecat agents

When spawning polecats in beads rig, gt sling tries to create agent beads with gt-beads-polecat-* prefix, but beads requires bd- prefix. Warning: 'issue ID gt-beads-polecat-obsidian does not match configured prefix bd'. Agent beads should use the rig's configured prefix.


Phase 2.4: Git merge driver optimization for TOON format

Optimize git 3-way merge for TOON line-oriented format.

## Overview
TOON is line-oriented (unlike binary formats), enabling smarter git merge strategies. Implement custom merge driver to handle TOON-specific merge patterns.

## Required Work

### 2.4.1 TOON Merge Driver
- [ ] Create .git/info/attributes entry for *.toon files
- [ ] Implement custom merge driver script/command
- [ ] Handle tabular format row merges (line-based 3-way)
- [ ] Handle YAML-style format merges
- [ ] Conflict markers for unsolvable conflicts

### 2.4.2 Merge Patterns
- [ ] Row addition: both branches add different rows → union
- [ ] Row deletion: one branch deletes, other modifies → conflict (manual review)
- [ ] Row modification: concurrent field changes → intelligent merge or conflict
- [ ] Field ordering changes: ignore (TOON format resilient to order)

### 2.4.3 Testing & Documentation
- [ ] Unit tests for merge scenarios (3-way merge logic)
- [ ] Integration tests with actual git merges
- [ ] Conflict scenario testing
- [ ] Documentation of merge strategy

## Success Criteria
- Git merge handles TOON conflicts intelligently
- Fewer manual merge conflicts than JSONL
- Round-trip preserved through merges
- All 70+ tests still passing
- Git history stays clean (minimal conflict markers)


Split internal/storage/sqlite/queries.go (1586 lines)

Split internal/storage/sqlite/queries.go (1704 lines) into logical modules.

## Current State
queries.go is 1704 lines with mixed responsibilities:
- Issue CRUD operations
- Search/filter operations
- Delete operations (complex cascade logic)
- Helper functions (parsing, formatting)

## Proposed Split

### 1. queries.go (keep ~400 lines) - Core CRUD
```go
// Core issue operations
func (s *SQLiteStorage) CreateIssue(...)
func (s *SQLiteStorage) GetIssue(...)
func (s *SQLiteStorage) UpdateIssue(...)
func (s *SQLiteStorage) CloseIssue(...)
```

### 2. queries_search.go (~300 lines) - Search/Filter
```go
// Search and filtering
func (s *SQLiteStorage) SearchIssues(...)
func (s *SQLiteStorage) GetIssueByExternalRef(...)
func (s *SQLiteStorage) GetCloseReason(...)
func (s *SQLiteStorage) GetCloseReasonsForIssues(...)
```

### 3. queries_delete.go (~400 lines) - Delete Operations
```go
// Delete operations with cascade logic
func (s *SQLiteStorage) CreateTombstone(...)
func (s *SQLiteStorage) DeleteIssue(...)
func (s *SQLiteStorage) DeleteIssues(...)
func (s *SQLiteStorage) resolveDeleteSet(...)
func (s *SQLiteStorage) expandWithDependents(...)
func (s *SQLiteStorage) validateNoDependents(...)
func (s *SQLiteStorage) checkSingleIssueValidation(...)
func (s *SQLiteStorage) trackOrphanedIssues(...)
func (s *SQLiteStorage) collectOrphansForID(...)
func (s *SQLiteStorage) populateDeleteStats(...)
func (s *SQLiteStorage) executeDelete(...)
func (s *SQLiteStorage) findAllDependentsRecursive(...)
```

### 4. queries_helpers.go (~100 lines) - Utilities
```go
// Helper functions (already at top of file)
func parseNullableTimeString(...)
func parseJSONStringArray(...)
func formatJSONStringArray(...)
```

### 5. queries_rename.go (~100 lines) - ID/Prefix Operations
```go
// ID and prefix management
func (s *SQLiteStorage) UpdateIssueID(...)
func (s *SQLiteStorage) RenameDependencyPrefix(...)
func (s *SQLiteStorage) RenameCounterPrefix(...)
func (s *SQLiteStorage) ResetCounter(...)
```

## Implementation Steps

1. **Create new files** with package declaration:
   ```go
   // queries_delete.go
   package sqlite

   import (...)
   ```

2. **Move functions** - cut/paste, maintaining order within each file

3. **Update imports** - each file needs its own imports

4. **Run tests** after each file split:
   ```bash
   go test ./internal/storage/sqlite/...
   ```

5. **Run linter** to catch any issues:
   ```bash
   golangci-lint run ./internal/storage/sqlite/...
   ```

## File Organization
```
internal/storage/sqlite/
├── queries.go          # Core CRUD (~400 lines)
├── queries_search.go   # Search/filter (~300 lines)
├── queries_delete.go   # Delete cascade (~400 lines)
├── queries_helpers.go  # Utilities (~100 lines)
└── queries_rename.go   # ID operations (~100 lines)
```

## Success Criteria
- No file > 500 lines
- All tests pass
- No functionality changes
- Clear separation of concerns


Molecule execution state management

Implement molecule execution state tracking.

## State Location

```
.beads/molecules/<mol-id>.state.yaml
```

## State Schema

```yaml
id: mol-deacon-patrol
formula: mol-deacon-patrol  # Source formula
bonded_at: ISO timestamp
bonded_by: entity who created it

# Execution state
status: running | paused | completed | failed
current_step: step-id
started_at: ISO timestamp
completed_at: ISO timestamp (if done)

# Loop tracking
reset_count: 0
last_reset_at: null

# Per-step state
steps:
  inbox-check:
    status: completed | in_progress | pending
    started_at: ...
    completed_at: ...
  spawn-work:
    status: pending
  self-inspect:
    status: pending

# Variables (from formula instantiation)
variables:
  rig: gastown
  issue_id: gt-xxx
```

## Operations

- CreateState(molID, formula, variables) - Initialize state
- LoadState(molID) - Read current state
- SaveState(molID, state) - Write state
- AdvanceStep(molID) - Mark current complete, find next
- ResetState(molID) - Reset all steps to pending

## Files

- internal/mol/state.go
- internal/mol/types.go


Merge: bd-g4b4

branch: polecat/Hooker
target: main
source_issue: bd-g4b4
rig: beads


Dead code: fetchAndRebaseInWorktree() marked DEPRECATED but still exists

attached_args: Remove dead code fetchAndRebaseInWorktree

The function fetchAndRebaseInWorktree() in internal/syncbranch/worktree.go (lines 811-830) is marked as DEPRECATED with a comment:

```go
// fetchAndRebaseInWorktree is DEPRECATED - kept for reference only.
// Use contentMergeRecovery instead to avoid tombstone resurrection.
```

Since contentMergeRecovery() is the replacement and is being used, this dead code should be removed to reduce maintenance burden.

Location: internal/syncbranch/worktree.go:811-830


Work on beads-ocs: Thin shim hooks to eliminate version d...

Work on beads-ocs: Thin shim hooks to eliminate version drift (GH#615). Replace full hook scripts with thin shims that call bd hooks run. When done, submit MR (not PR) to integration branch for Refinery.


bd mol bond: Dynamic bond with variable substitution

Implement dynamic molecule bonding with runtime variable substitution.

## Command
```bash
bd mol bond <proto-id> <parent-wisp-id> --var key=value --var key2=value2
```

## Behavior
1. Parse proto molecule template
2. Substitute {{key}} placeholders with provided values
3. Create wisp children under the parent molecule
4. Child IDs follow pattern: parent-id.child-ref (e.g., patrol-x7k.arm-ace)
5. Nested children: parent-id.child-ref.step-ref (e.g., patrol-x7k.arm-ace.capture)

## Variable Substitution
- In step titles: "Inspect {{polecat_name}}" -> "Inspect ace"
- In descriptions: Full template substitution
- In Needs directives: Allow referencing parent steps

## Output
```
✓ Bonded mol-polecat-arm to patrol-x7k
  Created: patrol-x7k.arm-ace (5 steps)
```


Merge: bd-ao0s

branch: polecat/rictus
target: main
source_issue: bd-ao0s
rig: beads


Test prefix bd


Remove redundant edge fields from Issue struct

Remove from Issue struct:
- RepliesTo -> dependency with type replies-to
- RelatesTo -> dependencies with type relates-to
- DuplicateOf -> dependency with type duplicates
- SupersededBy -> dependency with type supersedes

Keep: Sender, Ephemeral (these are attributes, not relationships)


Crew worker wolf in beads - human-managed persistent workspace.

role_type: crew
rig: beads
agent_state: idle
hook_bead: null
role_bead: gt-crew-role
cleanup_status: null


Add GetWorkerStatus RPC endpoint

New RPC endpoint to get all workers and their current molecule/step in one call. Returns: assignee, moleculeID, moleculeTitle, currentStep, totalSteps, stepTitle, lastActivity, status. Enables activity feed TUI to show worker state without multiple round trips.


Wait for CI to pass

Monitor GitHub Actions - all checks must pass before release artifacts are built


Crew worker grip in beads - human-managed persistent workspace.

role_type: crew
rig: beads
agent_state: idle
hook_bead: null
role_bead: gt-crew-role
cleanup_status: null


Add tests for import/export functionality

Import/export functions like ImportIssues, exportToJSONLWithStore, and AutoImportIfNewer have low coverage. These are critical for data integrity and multi-repo synchronization.


Beads commands operate on stale database without warning

All beads read operations should validate database is in sync with JSONL before proceeding.

**Current Behavior:**
- Commands can query/read from stale database
- Only mutation operations (like 'bd sync') check if JSONL is newer
- User gets incorrect results without realizing database is out of sync

**Expected Behavior:**
- All beads commands should have pre-flight check for database freshness
- If JSONL is newer than database, refuse to operate with error: "Database out of sync. Run 'bd import' first."
- Same safety check that exists for 'bd sync' should apply to ALL operations

**Impact:**
- Users make decisions based on incomplete/outdated data
- Silent failures lead to confusion (e.g., thinking issues don't exist when they do)
- Similar to running git commands on stale repo without being warned to pull

**Example:**
- Searched for bd-g9eu issue file: not found
- Issue exists in .beads/issues.jsonl (in git)
- Database was stale, but no warning was given
- Led to incorrect conclusion that issue was already closed/deleted

## Implementation Complete

**Phase 1: Created staleness check (cmd/bd/staleness.go)**
- ensureDatabaseFresh() function checks JSONL mtime vs last_import_time
- Returns error with helpful message when database is stale
- Auto-skips in daemon mode (daemon has auto-import)

**Phase 2: Added to all read commands**
- list, show, ready, status, stale, info, duplicates, validate
- Check runs before database queries in direct mode
- Daemon mode already protected via checkAndAutoImportIfStale()

**Phase 3: Code Review Findings**
See follow-up issues:
- bd-XXXX: Add warning when staleness check errors
- bd-YYYY: Improve CheckStaleness error handling
- bd-ZZZZ: Refactor redundant daemon checks (low priority)

**Testing:**
- Build successful: go build ./cmd/bd
- Binary works: ./bd --version
- Ready for manual testing

**Next Steps:**
1. Test with stale database scenario
2. Implement review improvements
3. Close issue when tests pass


Add creator field to Issue struct

Add Creator *EntityRef field to Issue. Tracks who created the issue. Optional, omitted if nil in JSONL. This enables CV chain tracking - every piece of work is attributed to its creator.


Wisp storage: ephemeral molecule tracking

Implement ephemeral molecule storage for patrol cycles.

## Architecture

Wisps are ephemeral molecules stored in `.beads-wisps/` (gitignored).
When squashed, they create digests in permanent `.beads/`.

**Storage is per-rig, not per-role**: Witness and Refinery share mayor/rig's
`.beads-wisps/` since they execute from that context.

## Design Doc
See: gastown/mayor/rig/docs/wisp-architecture.md

## Key Requirements

1. **Ephemeral storage**: `.beads-wisps/` directory, gitignored
2. **Bond with --wisp**: Creates in wisps instead of permanent
3. **Squash**: Deletes wisp, creates digest in permanent beads
4. **Burn**: Deletes wisp, no digest
5. **Wisp commands**: `bd wisp list`, `bd wisp gc`

## Storage Locations

| Context | Location |
|---------|----------|
| Rig (Deacon, Witness, Refinery) | mayor/rig/.beads-wisps/ |
| Polecat (if used) | polecats/<name>/.beads-wisps/ |

## Children (to be created)
- bd mol bond --wisp flag
- .beads-wisps/ storage backend
- bd mol squash handles wisp to permanent
- bd wisp list command
- bd wisp gc command (orphan cleanup)


Fix JSON errors in epic.go

Replace direct stderr writes with FatalErrorRespectJSON() in epic.go.

Commands affected:
- epicStatusCmd
- epicCloseEligibleCmd


Code smell: ComputeContentHash() is 100+ lines of repetitive code

attached_args: Refactor ComputeContentHash repetitive code

The ComputeContentHash() method in internal/types/types.go (lines 87-190) is over 100 lines of repetitive code:

```go
h.Write([]byte(i.Title))
h.Write([]byte{0}) // separator
h.Write([]byte(i.Description))
h.Write([]byte{0})
h.Write([]byte(i.Design))
// ... repeated 40+ times
```

Consider:
1. Using reflection to iterate over struct fields tagged for hashing
2. Creating a helper function that takes field name and value
3. Using a slice of fields to hash and iterating over it
4. At minimum, extracting the repetitive pattern into a helper

Location: internal/types/types.go:87-190


Test Agent


Add close_reason field to CLI schema and documentation

PR #551 persists close_reason, but the CLI documentation may not mention this field as part of the issue schema.

## Current State
- close_reason is now persisted in database
- `bd show --json` will return close_reason in JSON output
- Documentation may not reflect this new field

## What's Missing
- CLI reference documentation for close_reason field
- Schema documentation showing close_reason is a top-level issue field
- Example output showing close_reason in bd show --json
- bd close command documentation should mention close_reason parameter is optional

## Suggested Action
1. Update README.md or CLI reference docs to list close_reason as an issue field
2. Add example to bd close documentation
3. Update any type definitions or schema specs
4. Consider adding close_reason to verbose list output (bd list --verbose)


Consider using types.Status in merge package for type safety

The merge package uses string for status comparison (e.g., result.Status == closed, issue.Status == StatusTombstone). The types package defines Status as a type alias with validation. While the merge package needs its own Issue struct for JSONL flexibility, it could import and use types.Status for constants to get compile-time type checking. Current code: if left == closed || right == closed. Could be: if left == string(types.StatusClosed). This is low priority since string comparison works correctly. Files: internal/merge/merge.go:44, 488, 501-521


Install 0.30.4 MCP server locally

Upgrade the MCP server (after PyPI publish):
```bash
pip install --upgrade beads-mcp
# OR if using uv:
uv tool upgrade beads-mcp
```

Verify:
```bash
pip show beads-mcp | grep Version
```

```verify
pip show beads-mcp 2>/dev/null | grep -q 'Version: 0.30.4'
```


Add bd setup gemini for Gemini CLI integration

## Summary

Add `bd setup gemini` command to install beads hooks for Gemini CLI, similar to existing `bd setup claude`.

Ref: GitHub #845

## Research Findings

### Gemini CLI Has Compatible Hooks

Gemini CLI (https://geminicli.com/docs/hooks/) supports nearly identical hook events:

| Gemini CLI Event | Claude Code Equivalent | Purpose |
|------------------|----------------------|---------|
| **SessionStart** | SessionStart | Initialize resources, load context |
| **SessionEnd** | - | Clean up, save state |
| **PreCompress** | PreCompact | Before context compression |
| **BeforeAgent** | - | Add context before planning |

Configuration format is almost identical to Claude:
```json
{
  "hooks": {
    "SessionStart": [{
      "matcher": "",
      "hooks": [{
        "type": "command",
        "command": "bd prime"
      }]
    }]
  }
}
```

### GEMINI.md Support

- Hierarchical loading: ~/.gemini/GEMINI.md → project root → subdirectories
- Concatenated into system prompt automatically
- Gemini CLI also reads AGENTS.md (already supported via `bd setup factory`)

### Antigravity

Google's IDE-based agentic platform (released Nov 2025):
- Uses Gemini 3 with 1M token context
- Has "knowledge base" for saved context
- Less documented - may share Gemini CLI infrastructure
- Needs separate research for dedicated support

## Implementation Plan

### Phase 1: Core Gemini CLI Support

1. **Create `cmd/bd/setup/gemini.go`**
   - Mirror structure from `claude.go`
   - Target: `~/.gemini/settings.json`
   - Install SessionStart and PreCompress hooks
   - Support --project flag for local settings
   - Support --stealth flag

2. **Add doctor check in `cmd/bd/doctor/gemini.go`**
   - Check if hooks installed
   - Verify settings.json structure

3. **Update `cmd/bd/setup.go`**
   - Add gemini subcommand
   - Wire up to setup/gemini.go

### Phase 2: Optional Enhancements

4. **GEMINI.md generation** (optional)
   - Could generate project-level GEMINI.md
   - Or document that AGENTS.md already works

5. **Antigravity support** (separate issue)
   - Needs research on Antigravity's configuration system
   - May be able to share Gemini CLI hooks
   - May need IDE-specific integration

## Open Questions

1. Where does Gemini CLI store settings? Need to verify `~/.gemini/settings.json` path
2. Does Gemini CLI use same JSON structure as Claude for hooks?
3. Can one implementation cover both Gemini CLI and Antigravity?
4. Should we generate GEMINI.md or rely on AGENTS.md?

## Acceptance Criteria

- [ ] `bd setup gemini` installs hooks to Gemini CLI settings
- [ ] `bd setup gemini --check` verifies installation
- [ ] `bd doctor` reports Gemini CLI integration status
- [ ] Documentation updated in docs/SETUP.md


Test refile command

Testing bd refile


Update .claude-plugin/marketplace.json to 0.30.4

Update version field in .claude-plugin/marketplace.json:
```json
"version": "0.30.4"
```

```verify
jq -e '.plugins[0].version == "0.30.4"' .claude-plugin/marketplace.json
```


No logging/debugging for tombstone resurrection events

Per the design document bd-zvg Open Question 1: Should resurrection log a warning? Recommendation was Yes. Currently, when an expired tombstone loses to a live issue (resurrection), there is no logging or debugging output. This makes it hard to understand why an issue reappeared. Recommendation: Add optional debug logging when resurrection occurs, e.g., Issue bd-abc resurrected (tombstone expired). Files: internal/merge/merge.go:359-366, 371-378, 400-405, 410-415


Respond to GitHub issue #479 with solution

Once bd reset is implemented and released, respond to GitHub issue #479.

## Response should include
- Announce the new bd reset command
- Show basic usage examples
- Link to any documentation
- Thank the user for the feedback

## Example response
```
Thanks for raising this! We've added a `bd reset` command to handle this case.

Usage:
- `bd reset` - Reset to clean state (prompts for confirmation)
- `bd reset --backup` - Create backup first
- `bd reset --hard` - Also clean up git history

This is available in version X.Y.Z.
```

## Notes
- Wait until feature is merged and released
- Consider if issue should be closed or left for user confirmation


Swarm: Test coordinator display

Swarm molecule orchestrating epic bd-2rkr.

Epic: bd-2rkr
Coordinator:


Commit release

git add -A && git commit -m 'release: v{{version}}'


Merge: bd-l13p

branch: polecat/nux
target: main
source_issue: bd-l13p
rig: beads


Update Homebrew formula

Update the Homebrew tap with new version:

```bash
./scripts/update-homebrew.sh 0.33.2
```

This script waits for GitHub Actions to complete (~5 min), then updates the formula with new SHA256 hashes.


Restart daemon with {{version}}

Restart the bd daemon to pick up new version:

```bash
bd daemon --stop
bd daemon --start
bd daemon --health  # Verify Version: {{version}}
```


bd mol squash handles wisp→digest

Update bd mol squash to handle ephemeral molecules.

## Behavior for Ephemeral Molecules
1. Delete wisp from .beads-ephemeral/
2. Create digest issue in .beads/ (permanent)
3. Digest has type:digest and squashed_from field

## Digest Format
```json
{
  "id": "<parent>.digest-NNN",
  "type": "digest",
  "title": "<proto> cycle @ <timestamp>",
  "description": "<summary from --summary flag>",
  "parent": "<proto-id>",
  "squashed_from": "<wisp-id>"
}
```

## Implementation
- Detect if molecule is ephemeral (check storage location or flag)
- Delete from ephemeral store
- Create digest in permanent store
- Return digest ID

## Testing
- Test squash of ephemeral mol creates digest
- Test wisp is deleted after squash
- Test digest is queryable


Merge: obsidian-mjxeci6l

branch: polecat/obsidian-mjxeci6l
target: main
source_issue: obsidian-mjxeci6l
rig: beads
agent_bead: bd-beads-polecat-obsidian


Code review: bd mol bond --ref and bd activity (bd-xo1o work)

Review dave's recent commits for bd-xo1o (Dynamic Molecule Bonding):

## Commits to Review
- ee04b1ea: feat: add dynamic molecule bonding with --ref flag (bd-xo1o.1)
- be520d90: feat: add bd activity command for real-time state feed (bd-xo1o.3)

## Review Focus
1. Code quality and correctness
2. Error handling
3. Edge cases
4. Test coverage
5. Documentation

## Deliverables
- File beads for any issues found
- Note any concerns or suggestions
- Verify the implementation matches the bd-xo1o epic requirements


Document BEADS_DIR pattern for multi-agent workspaces (Gas Town)

Gas Town and similar multi-agent systems need to configure separate beads databases per workspace/rig, distinct from any project-level beads.

## Use Case

In Gas Town:
- Each 'rig' (managed project) has multiple agents (polecats, refinery, witness)
- All agents in a rig should share a single beads database at the rig level
- This should be separate from any .beads/ the project itself uses
- The BEADS_DIR env var enables this

## Documentation Needed

1. Add a section to docs explaining BEADS_DIR for multi-agent setups
2. Example: setting BEADS_DIR in agent startup scripts/hooks
3. Clarify interaction with project-level .beads/ (BEADS_DIR takes precedence)

## Current Support

Already implemented in internal/beads/beads.go:FindDatabasePath():
- BEADS_DIR env var is checked first (preferred)
- BEADS_DB env var still supported (deprecated)
- Falls back to .beads/ search in tree

Just needs documentation for the multi-agent workspace pattern.


Code smell: Duplicated IssueDetails struct in show.go (4 definitions)

The IssueDetails struct is defined 4 times within show.go at lines 109, 159, 190, and 372 with identical structure but slightly different JSON tag configurations.

**Problem:**
- Violates DRY principle
- Makes maintenance harder - changes must be applied to multiple locations
- Increases risk of inconsistency between definitions
- Takes up ~50 lines of duplicated code

**Acceptance Criteria:**
- [ ] Extract IssueDetails to a single package-level type
- [ ] Update all 4 locations to use the shared type
- [ ] Ensure JSON output remains consistent
- [ ] Tests pass


Issue lifecycle hooks (on-close, on-complete)

Add hooks that fire on issue state transitions, enabling automation like closing linked GitHub issues.

## Problem

We have `external_ref` to link beads issues to external systems (GitHub, Linear, Jira), but no mechanism to trigger actions when issues close. Currently:

```
bd-u2sc (external_ref: gh-692) closes → nothing happens
```

## Proposed Solution

### Phase 1: Shell Hooks

Add `.beads-hooks/on-close.sh` (and similar lifecycle hooks):

```bash
# .beads-hooks/on-close.sh
# Called by bd close with issue JSON on stdin
#\!/bin/bash
issue=$(cat)
external_ref=$(echo "$issue" | jq -r '.external_ref // empty')
if [[ "$external_ref" == gh-* ]]; then
    number="${external_ref#gh-}"
    gh issue close "$number" --repo steveyegge/beads \
      --comment "Completed via beads epic $(echo $issue | jq -r .id)"
fi
```

### Lifecycle Events

| Event | Trigger | Use Cases |
|-------|---------|-----------|
| `on-close` | Issue closed | Close external refs, notify, archive |
| `on-complete` | Epic children all done | Roll-up completion, close parent refs |
| `on-status-change` | Any status transition | Sync to external systems |

### Phase 2: Molecule Completion Handlers

Molecules could define completion actions:

```yaml
name: github-issue-tracker
on_complete:
  - action: shell
    command: gh issue close {{external_ref}} --repo {{repo}}
  - action: mail
    to: mayor/
    subject: "Epic {{id}} completed"
```

### Phase 3: Gas Town Integration

For full Gas Town deployments:
- Witness observes closures via beads events
- Routes to integration agents via mail
- Agents handle external system interactions

## Implementation Notes

- Hooks should be async (don't block bd close)
- Pass full issue JSON to hook via stdin
- Support hook timeout and failure handling
- Consider `--no-hooks` flag for bulk operations

## Related

- `external_ref` field already exists (GH#142)
- Cross-project deps: bd-h807, bd-d9mu
- Git hooks: .beads-hooks/ pattern established

## Use Cases

1. **GitHub integration**: Close GH issues when beads epic completes
2. **Linear sync**: Update Linear status when beads status changes
3. **Notifications**: Send mail/Slack when high-priority issues close
4. **Audit**: Log all closures to external system


Consolidate migrate-* commands into migrate subcommands

Move migrate-hash-ids, migrate-issues, migrate-sync, migrate-tombstones under 'migrate' as subcommands. Reduces 5 top-level commands to 1.


Implement subgraph cloning with variable substitution

Core implementation of template instantiation:

1. Add `bd template instantiate <template-id> [--var key=value]...` command
2. Implement subgraph loading:
   - Load template epic
   - Recursively load all children (and their children)
   - Load all dependencies between issues in the subgraph
3. Implement variable substitution:
   - Scan titles and descriptions for `{{name}}` patterns
   - Replace with provided values
   - Error on missing required variables (or prompt interactively)
4. Implement cloning:
   - Generate new IDs for all issues
   - Create cloned issues with substituted text
   - Remap and create dependencies
5. Return the new epic ID

Consider adding `--dry-run` flag to preview what would be created.


Read operations should not modify database file

Read-only operations (bd list, bd ready, bd show) modify the database file. Every open sets WAL pragma, runs schema/migrations, and checkpoints on close. Need sqlite.NewReadOnly() that opens with mode=ro, skips WAL/schema/migrations, and skips checkpoint. See GH#804.


Refinery Patrol

Merge queue processor patrol loop with verification gates.


Polecats get stuck on interactive shell prompts (cp/mv/rm -i)

During swarm operations, polecats frequently get stuck waiting for interactive prompts from shell commands like:
- cp prompting 'overwrite file? (y/n)'
- mv prompting 'overwrite file? (y/n)'
- rm prompting 'remove file?'

This happens because macOS aliases or shell configs may have -i flags set by default.

Root cause: Claude Code runs commands that trigger interactive confirmation prompts, but cannot respond to them, causing the agent to hang indefinitely.

Observed in: Multiple polecats during GH issues swarm (Dec 2024)
- Derrick, Roustabout, Prospector, Warboy all got stuck on y/n prompts

Suggested fixes:
1. AGENTS.md should instruct agents to always use -f flag with cp/mv/rm
2. Polecat startup could set shell aliases to use non-interactive versions
3. bd prime hook could include guidance about non-interactive commands
4. Consider detecting stuck prompts and auto-recovering


Add composite index (issue_id, type) on dependencies table

GetBlockedIssues uses EXISTS clauses that filter by issue_id AND type together.

**Query pattern (ready.go:427-429):**
```sql
EXISTS (
  SELECT 1 FROM dependencies d2
  WHERE d2.issue_id = i.id AND d2.type = 'blocks'
)
```

**Problem:** Only idx_dependencies_issue exists. SQLite must filter type after index lookup.

**Solution:** Add migration:
```sql
CREATE INDEX IF NOT EXISTS idx_dependencies_issue_type ON dependencies(issue_id, type);
```

**Note:** This complements the existing idx_dependencies_depends_on_type for the reverse direction.


mol-beads-release

attached_args: Release v0.38.0 - execute each step in order, verify before proceeding to next

Release checklist for beads version 0.38.0.

This molecule ensures all release steps are completed properly.
Variable: 0.38.0 - target version (e.g., 0.35.0)

## Step: update-release-notes
Update cmd/bd/info.go with release notes for 0.38.0.

Add a new VersionChange entry at the top of versionChanges slice:
```go
{
    Version: "0.38.0",
    Date:    "YYYY-MM-DD",
    Changes: []string{
        "NEW: Feature description",
        "FIX: Bug fix description",
        "IMPROVED: Enhancement description",
    },
},
```

Run `git log --oneline v<previous>..HEAD` to see what changed.

## Step: update-changelog
Update CHANGELOG.md with detailed release notes.

Add a new section after [Unreleased]:
```markdown
## [0.38.0] - YYYY-MM-DD

### Added
- **Feature name** (issue-id) - Description

### Changed
- **Change description** (issue-id)

### Fixed
- **Bug fix** (issue-id) - Description
```

Sort by importance, not chronologically.
Needs: update-release-notes

## Step: bump-version
Run the version bump script.

```bash
./scripts/bump-version.sh 0.38.0
```

This updates version in all files:
- cmd/bd/version.go
- .claude-plugin/*.json
- integrations/beads-mcp/pyproject.toml
- npm-package/package.json
- Hook templates

Needs: update-changelog

## Step: run-tests
Run tests and verify lint passes.

```bash
go test -short ./...
```

CI will run full lint, but fix any obvious issues first.
Needs: bump-version

## Step: commit-release
Commit the release changes.

```bash
git add -A
git commit -m "chore: bump version to v0.38.0"
```

Needs: run-tests

## Step: push-and-tag
Push commit and create release tag.

```bash
git push origin main
git tag v0.38.0
git push origin v0.38.0
```

This triggers GitHub Actions release workflow.
Needs: commit-release

## Step: wait-for-ci
Wait for GitHub Actions to complete.

Monitor: https://github.com/steveyegge/beads/actions

CI will:
- Build binaries via GoReleaser
- Create GitHub Release with assets
- Publish to npm (@beads/bd)
- Publish to PyPI (beads-mcp)
- Update Homebrew tap

Wait until all jobs succeed (~5-10 min).
Needs: push-and-tag

## Step: verify-release
Verify the release is complete.

```bash
# Check GitHub release
gh release view v0.38.0

# Check Homebrew
brew update && brew info steveyegge/beads/bd

# Check npm
npm view @beads/bd version

# Check PyPI
pip index versions beads-mcp
```

Needs: wait-for-ci

## Step: update-local
Update local installations.

```bash
# Upgrade Homebrew
brew upgrade steveyegge/beads/bd

# Or install from source
./scripts/bump-version.sh 0.38.0 --install

# Install MCP locally
pip install -e integrations/beads-mcp

# Restart daemons
pkill -f "bd daemon" || true
```

Verify: `bd --version` shows 0.38.0
Needs: verify-release

## Step: manual-publish
(Optional) Manual publish if CI failed.

```bash
# npm (requires npm login)
./scripts/bump-version.sh 0.38.0 --publish-npm

# PyPI (requires TWINE credentials)
./scripts/bump-version.sh 0.38.0 --publish-pypi

# Or both
./scripts/bump-version.sh 0.38.0 --publish-all
```

Only needed if CI publishing failed.
Needs: wait-for-ci


Merge: onyx-mjw4oxsi

branch: polecat/onyx-mjw4oxsi
target: main
source_issue: onyx-mjw4oxsi
rig: beads
agent_bead: gt-beads-polecat-onyx


Test cross-rig issue creation

Testing --rig flag from town root


Implement content-first idempotent import

**Summary:** Refactored issue import to be content-first and idempotent, ensuring consistent data synchronization across multiple import rounds by prioritizing content hash matching over ID-based updates.

**Key Decisions:**
- Implement content hash as primary matching mechanism
- Create global collision resolution algorithm
- Ensure importing same data multiple times results in no-op

**Resolution:** The new import strategy guarantees predictable convergence across distributed systems, solving rename detection and collision handling while maintaining data integrity during multi-stage imports.


Gate await fields cleared by --no-daemon CLI access (not multi-repo)


Implement bd gate create/show/list/close/wait commands

Implement the gate CLI commands.

## Commands
```bash
# Create gate (returns gate ID)
bd gate create --await <type>:<id> --timeout <duration> --notify <addr>

# Check gate status
bd gate show <id>

# List open gates
bd gate list

# Close gate (usually done by Deacon)
bd gate close <id> --reason "completed"

# Add waiter to existing gate
bd gate wait <id> --notify <addr>
```

## Implementation
- Add cmd/bd/gate.go with subcommands
- Gate create creates wisp issue of type gate
- Gate list filters for open gates
- Gate wait adds to waiters[] array
- All support --json output


GHI #889: postinstall fails on Windows - zip being used by another process

GitHub Issue #889: postinstall fails on Windows: zip 'being used by another process'

https://github.com/steveyegge/beads/issues/889


Update local installation

Run install script or brew upgrade to get new version locally: curl -fsSL .../install.sh | bash


Test prefix beads


Fix TestFallbackToDirectModeEnablesFlush deadlock causing 10min test timeout

## Problem

TestFallbackToDirectModeEnablesFlush in direct_mode_test.go deadlocks for 9m59s before timing out, causing the entire test suite to take 10+ minutes instead of <10 seconds.

## Root Cause

Database lock contention between test cleanup and flushToJSONL():
- Test cleanup (line 36) tries to close DB via defer
- flushToJSONL() (line 132) is still accessing DB
- Results in deadlock: database/sql.(*DB).Close() waits for mutex while GetJSONLFileHash() holds it

## Stack Trace Evidence

```
goroutine 512 [sync.Mutex.Lock, 9 minutes]:
database/sql.(*DB).Close(0x14000643790)
  .../database/sql/sql.go:927 +0x84
github.com/steveyegge/beads/cmd/bd.TestFallbackToDirectModeEnablesFlush.func1()
  .../direct_mode_test.go:36 +0xf4

While goroutine running flushToJSONL() holds DB connection via GetJSONLFileHash()
```

## Impact

- Test suite: 10+ minutes → should be <10 seconds
- ALL other tests pass in ~4 seconds
- This ONE test accounts for 99.9% of test runtime

## Related

This is the EXACT same issue documented in MAIN_TEST_REFACTOR_NOTES.md for why main_test.go refactoring was deferred - global state manipulation + DB cleanup = deadlock.

## Fix Approaches

1. **Add proper cleanup sequencing** - stop flush goroutines BEFORE closing DB
2. **Use test-specific DB lifecycle** - ensure flush completes before cleanup
3. **Mock the flush mechanism** - avoid real DB for testing this code path
4. **Add explicit timeout handling** - fail fast with clear error instead of hanging

## Files

- cmd/bd/direct_mode_test.go:36-132
- cmd/bd/autoflush.go:353 (validateJSONLIntegrity)
- cmd/bd/autoflush.go:508 (flushToJSONLWithState)

## Acceptance

- Test passes without timeout
- Test suite completes in <10 seconds
- No deadlock between cleanup and flush operations


Full event test


bd init UX Improvements

bd init leaves users with incomplete setup, requiring manual bd doctor --fix. Issues found: (1) git hooks not installed if user declines prompt, (2) no auto-migration when CLI is upgraded, (3) stale merge driver configs from old versions. Fix by making bd init more robust with better defaults and auto-migration.


Phase 1.1: TOON Library Integration - Add gotoon dependency

Add gotoon (github.com/alpkeskin/gotoon) to go.mod and create internal/toon wrapper package for TOON encoding/decoding. This enables bdtoon to encode Issue structs to TOON format and decode TOON back to issues.

## Subtasks
1. Add gotoon dependency: go get github.com/alpkeskin/gotoon
2. Create internal/toon package with wrapper functions
3. Write encode tests for Issue struct round-trip conversion
4. Write decode tests for TOON to Issue conversion
5. Add gotoon API options to wrapper (indent, delimiter, length markers)

## Success Criteria
- go.mod includes gotoon dependency
- internal/toon/encode.go exports EncodeTOON(issues) ([]byte, error)
- internal/toon/decode.go exports DecodeTOON(data []byte) ([]Issue, error)
- Round-trip tests verify Issue → TOON → Issue produces identical data
- Tests pass with: go test ./internal/toon -v


bd wisp gc command

Add bd wisp gc command to garbage collect orphaned wisps.

## Usage
```bash
bd wisp gc                # Clean orphaned wisps
bd wisp gc --dry-run      # Show what would be cleaned
bd wisp gc --age 1h       # Custom orphan threshold (default: 1h)
```

## Orphan Detection
A wisp is orphaned if:
- process_id field exists AND process is dead
- OR updated_at older than threshold AND not complete
- AND molecule status is not complete/abandoned

## Behavior
- Delete orphaned wisps (no digest created)
- Report count of cleaned wisps
- --dry-run shows candidates without deleting

## Implementation
- Add 'gc' subcommand to wisp group
- Process detection via os.FindProcess or /proc
- Configurable age threshold


Update cmd/bd/version.go to 0.30.4

Update the Version constant in cmd/bd/version.go:
```go
Version = "0.30.4"
```

```verify
grep -q 'Version = "0.30.4"' cmd/bd/version.go
```


Add global verbosity flags (--verbose, --quiet)

Add consistent verbosity controls across all commands.

**Current state:**
- bd init has --quiet flag
- No other commands have verbosity controls
- Debug output controlled by BD_VERBOSE env var

**Proposal:**
Add persistent flags:
- --verbose / -v: Enable debug output
- --quiet / -q: Suppress non-essential output

**Implementation:**
- Add to rootCmd.PersistentFlags()
- Replace BD_VERBOSE checks with flag checks
- Standardize output levels:
  * Quiet: Errors only
  * Normal: Errors + success messages
  * Verbose: Errors + success + debug info

**Files to modify:**
- cmd/bd/main.go (add flags)
- internal/debug/debug.go (respect flags)
- Update all commands to respect quiet mode

**Testing:**
- Verify --verbose shows debug output
- Verify --quiet suppresses normal output
- Ensure errors always show regardless of mode


Improve test coverage for cmd/bd/doctor/fix (23.9% → 50%)

The doctor/fix package has only 23.9% test coverage. The doctor fix functionality is important for troubleshooting.

Current coverage: 23.9%
Target coverage: 50%


Add display guards for large molecules in bd mol current

When molecule has >100 steps, show summary instead of list.

Changes:
1. Count children first
2. If count > 100: show summary + pointer to bd mol progress
3. Add --range flag for viewing specific step ranges
4. Add --limit flag for capping output


Update CHANGELOG.md

Write the [Unreleased] section with all changes for 0.39.0.

Format: Keep a Changelog (https://keepachangelog.com)

Sections:
- ### Added
- ### Changed
- ### Fixed
- ### Documentation

The bump script will stamp the date automatically.


dave Handoff


Add empty tasks validation in workflow create

workflow.go:321 will panic if wf.Tasks is empty. Add validation that len(wf.Tasks) > 0 before accessing wf.Tasks[0].


hq- prefix routing fails: '.' resolves relative to cwd, not town root

## Problem
The hq- prefix in routes.jsonl maps to '.' which is interpreted relative to the current working directory, not the town root.

## Reproduction
```bash
cd ~/gt && bd show hq-2cchm    # Works
cd ~/gt/beads/crew/emma && bd show hq-2cchm  # Fails: 'no issue found'
```

## Root Cause
routes.jsonl has: {"prefix": "hq-", "path": "."}

The '.' is resolved relative to cwd, so from crew/emma it looks for ~/gt/beads/crew/emma/.beads/ instead of ~/gt/.beads/

## Fix
The routing logic should resolve '.' as the town root, or the route should use an absolute path or a sentinel like 'TOWN_ROOT'.


Verify version consistency

Confirm all versions match 0.99.0-test.

```bash
grep 'Version = ' cmd/bd/version.go
jq -r '.version' .claude-plugin/plugin.json
jq -r '.version' npm-package/package.json
grep 'version = ' integrations/beads-mcp/pyproject.toml
```

All should show 0.99.0-test.


🤝 HANDOFF: Review remaining beads PRs

## Current State
Just merged PR #653 (doctor refactor) and added tests to restore coverage.

## Remaining Open PRs to Review
Run `gh pr list --repo steveyegge/beads` to see current list. As of handoff:

1. #655 - feat: Linear Integration (jblwilliams)
2. #651 - feat(audit): agent audit trail (dchichkov)
3. #648 - Stop init creating redundant @AGENTS.md (maphew)
4. #646 - fix(unix): handle Statfs field types (jordanhubbard)
5. #645 - feat: /plan-to-beads Claude Code command (petebytes)
6. #642, #641, #640 - sync branch fixes (cpdata)

## Review Checklist
- Check CI status with `gh pr checks <num> --repo steveyegge/beads`
- Verify no .beads/ data leaking (we have a hook now)
- Review code quality
- Merge good ones, request changes on problematic ones

## Notes
- User wants us to be proactive about merging good PRs
- Can add tests ourselves if coverage drops


Consolidate daemon/daemons commands

Merge daemons functionality into daemon command with subcommands. Currently have both 'daemon' and 'daemons' at top level.