Add gate timeout tracking and notification

Implement timeout and notification logic for gates.

## Timeout Behavior
1. Gate created with timeout (e.g., 30m)
2. Deacon tracks elapsed time during patrol
3. If timeout reached:
   - Notify all waiters: "Gate timed out"
   - Close gate with timeout reason
   - Waiter can retry, escalate, or fail gracefully

## Notification
- Use gt mail send to notify waiters
- Include gate ID, await type, and reason in message
- Support multiple waiters notification

## Escalation Path
- Witness sees stuck worker, nudges them
- Worker can escalate to human if needed


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


bd list --parent: filter by parent issue

Add --parent flag to bd list to filter issues by parent.

Example:
```bash
bd list --parent=gt-h5n --status=open
```

Would show all open children of gt-h5n.

Useful for:
- Checking epic progress
- Finding swarmable work within an epic
- Molecule step listing

Implemented --parent flag for bd list. Filters children by parent issue using parent-child dependencies.


Merge: bd-d28c

branch: polecat/testcat
target: main
source_issue: bd-d28c
rig: beads


Witness Patrol

Per-rig worker monitor patrol loop with progressive nudging.


dave Handoff


Code Review: PR #551 - Persist close_reason to issues table

Code review of PR #551 which fixes close_reason persistence bug.

## Summary
The PR correctly fixes a bug where close_reason was only stored in the events table, not in the issues.close_reason column. This caused `bd show --json` to return empty close_reason.

## What Was Fixed
- ✅ CloseIssue now updates both close_reason and closed_at
- ✅ ReOpenIssue clears both close_reason and closed_at
- ✅ Comprehensive tests added for both storage and CLI layers
- ✅ Clear documentation in queries.go about dual storage strategy

## Quality Assessment
✅ Tests cover both storage layer and CLI JSON output
✅ Handles reopen case (clearing close_reason)
✅ Good comments explaining dual-storage design
✅ No known issues

## Potential Followups
See linked issues for suggestions.


bd delete --from-file should add deleted issues to deletions manifest

When using bd delete --from-file to bulk delete issues, the deleted issue IDs are not being added to the deletions.jsonl manifest.

This causes those issues to be resurrected during bd sync when git history scanning finds them in old commits.

Expected: All deleted issues should be added to deletions.jsonl so they wont be reimported from git history.

Workaround: Manually add deletion records to deletions.jsonl.


Add --pinned and --no-pinned flags to bd list

Add filtering flags to bd list: --pinned shows only pinned issues, --no-pinned excludes pinned issues. Default behavior shows all issues with a pin indicator.

Already implemented - --pinned and --no-pinned flags exist in bd list


bd mail uses git user.name for sender instead of BEADS_AGENT_NAME

When sending mail via `bd mail send`, the sender field in the stored issue uses git config user.name instead of the BEADS_AGENT_NAME environment variable.

Reproduction:
1. Set BEADS_AGENT_NAME=gastown-alpha
2. Run: bd mail send mayor/ -s 'Test' -m 'Body'
3. Check the issue.jsonl: sender is 'Steve Yegge' (git user.name) not 'gastown-alpha'

Expected: The sender field should use BEADS_AGENT_NAME when set.

This breaks the mail system for multi-agent workflows where agents need to identify themselves by their role (polecat, refinery, etc.) rather than the human user's git identity.

Related: gt mail routing integration with Gas Town

Not applicable - filed against stale bd v0.30.6


gt polecat done should auto-stop running session

Currently 'gt polecat done' fails if session is running, requiring a separate 'gt session stop' first. This is unnecessary friction - done should just stop the session automatically since that's always what you want.

Moving to gastown - this is a gt issue not bd


GH#409: bd init uses issues.jsonl but docs say beads.jsonl

bd init creates config referencing issues.jsonl but README/docs reference beads.jsonl as canonical. Standardize naming. See GitHub issue #409.


bd ready resolves external dependencies

Extend bd ready to check external blocked_by references:

1. Parse external:<project>:<capability> from blocked_by
2. Look up project path from external_projects config
3. Check if target project has provides:<capability> label on a closed issue
4. If not satisfied, issue is blocked

Example output:
```bash
bd ready
# gt-xyz: blocked by external:beads:mol-run-assignee (not provided)
# gt-abc: ready
```

Depends on: bd-om4a (external: prefix), bd-66w1 (config)

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

Implemented external dep resolution in GetReadyWork - filters issues with unsatisfied external:project:capability deps


Deferred HOP schema additions (P2/P3)

Deferred from bd-7pwh after review. Add when semantics are clearer and actually needed:

- assignee_ref: Structured EntityRef alongside string assignee
- work_type: 'mutex' vs 'open_competition' (everything is mutex in v0.1)
- crystallizes: bool for work that compounds vs evaporates (can derive from issue_type)
- cross_refs: URIs to beads in other repos (needs federation first)
- skill_vector: []float32 embeddings placeholder (YAGNI)

These can be added later without breaking changes (all optional fields).


Investigate incremental blocked_issues_cache updates at scale

Current blocked_issues_cache strategy does full DELETE + INSERT on every dependency/status change.

**Problem at scale:**
- 10K issues: ~50ms rebuild (acceptable)
- 100K issues: ~500ms rebuild (noticeable)
- 1M issues: multi-second rebuilds (problematic)

**Current implementation (blocked_cache.go:104-154):**
- DELETE FROM blocked_issues_cache
- INSERT with recursive CTE

**Potential optimizations:**
1. **Incremental updates:** Only add/remove affected issue IDs instead of full rebuild
2. **Dirty tracking:** Skip rebuild if cache is already valid
3. **Async rebuild:** Rebuild in background, serve stale cache briefly
4. **Partial invalidation:** Only invalidate affected subtree

**Decision needed:** Is this premature optimization? Current target is <100K issues.

**Benchmark:** Add benchmark for cache rebuild at 100K scale to measure actual impact.


Run bd doctor at end of bd init to verify setup

Run bd doctor diagnostics at end of bd init (after line 398 in init.go). If issues found, warn user immediately: '⚠ Setup incomplete. Run bd doctor --fix to complete setup.' Catches configuration problems before user encounters them in normal workflow.

Already implemented in commits ec4117d0 and 3a36d0b9 - hooks/merge driver install by default, doctor runs at end of init


Support wisps in nodb mode for lightweight Gas Town rigs

Enable proper wisp support in --no-db mode to allow lightweight Gas Town rigs (including HQ/Mayor) to run without SQLite overhead.

## Motivation
Gas Town HQ and simple rigs could benefit from nodb mode's simplicity. Currently wisps don't work properly in nodb mode.

## Proposed Design

### Phase 1: Session-scoped wisps
- Memory storage already has Wisp field on Issue
- Wisps exist only for the session lifetime
- Acceptable for patrol cycles that complete within a session
- Depends on: bd-9avq (fix the leak)

### Phase 2: Optional wisp persistence
- Add `.beads/wisps.jsonl` for wisp storage (gitignored)
- Load wisps from this file on nodb startup
- Save wisps to this file on nodb exit
- Wisps persist across restarts but don't sync via git

### Phase 3: Verify mol commands
- Test mol squash, burn, bond work with memory storage
- These currently check for SQLite storage type
- May need interface-based approach instead of type assertions

## Files affected
- cmd/bd/nodb.go - wisp filtering and optional persistence
- internal/storage/memory/ - verify wisp field handling
- cmd/bd/mol_*.go - verify memory storage compatibility
- .beads/.gitignore - add wisps.jsonl

Simplified scope: just fix the leak (bd-9avq). Session-scoped wisps are acceptable - they're ephemeral by design. Persistence can be added later if needed.