Release v0.34.0

Minor version release for beads v0.34.0. This bead serves as my persistent work assignment; the actual release steps are tracked in an attached wisp.


Time-dependent tests may be flaky near TTL boundary

Several tombstone merge tests use time.Now() to create test data: time.Now().Add(-24 * time.Hour), time.Now().Add(-60 * 24 * time.Hour), etc. While these work reliably in practice (24h vs 30d TTL has large margin), they could theoretically be flaky if: 1) Tests run slowly, 2) System clock changes during test, 3) TTL constants change. Recommendation: Consider using a fixed reference time or time injection for deterministic tests. Lower priority since current margin is large. Files: internal/merge/merge_test.go:1337-1338, 1352-1353, 1548-1549, 1590-1591


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.


GH#540: Add silent quick-capture mode (bd q)

Add bd q alias for quick capture that outputs only issue ID. Useful for piping/scripting. See GitHub issue #540.


Graph Link: duplicates for deduplication

Implement duplicates link type for marking issues as duplicates.

New command:
- bd duplicate <id> --of <canonical> - marks id as duplicate of canonical
- Auto-closes the duplicate issue

Query support:
- bd show <id> shows 'Duplicate of: <canonical>'
- bd list --duplicates shows all duplicate pairs

Storage:
- duplicates column pointing to canonical issue ID

Essential for large issue databases with many similar reports.


Restart running daemons

Kill and restart any running bd daemons to pick up new version: pkill -f 'bd daemon' && bd daemon --start


Review SQLite indexes and scaling bottlenecks

Audit the beads SQLite schema for:

## Index Review
- Are all frequently-queried columns indexed?
- Are compound indexes needed for common query patterns?
- Any missing indexes on foreign keys or filter columns?

## Scaling Bottlenecks
- How does performance degrade with 10k, 100k, 1M issues?
- Full table scans in hot paths?
- JSONL export/import performance at scale
- Transaction contention in multi-agent scenarios

## Common Query Patterns to Optimize
- bd ready (status + blocked_by resolution)
- bd list with filters (status, type, priority, labels)
- bd show with dependency graph traversal
- bd sync import/export

## Deliverables
- Document current indexes
- Identify missing indexes
- Benchmark key operations at scale
- Recommend schema improvements


Add date and priority filters to bd search for parity with bd list.

## Current State
bd search supports: --status, --type, --assignee, --label, --limit
bd list supports: all of the above PLUS date ranges and priority filters

## Filters to Add

### Priority Filters
```bash
bd search "query" --priority 1           # Exact priority
bd search "query" --priority-min 0       # P0 and above (higher priority)
bd search "query" --priority-max 2       # P2 and below (lower priority)
```

### Date Filters
```bash
bd search "query" --created-after 2025-01-01
bd search "query" --created-before 2025-12-31
bd search "query" --updated-after 2025-01-01
bd search "query" --closed-after 2025-01-01
```

### Content Filters
```bash
bd search "query" --desc-contains "bug"
bd search "query" --notes-contains "todo"
bd search "query" --empty-description    # Issues with no description
bd search "query" --no-assignee          # Unassigned issues
bd search "query" --no-labels            # Issues without labels
```

## Files to Modify

### 1. cmd/bd/search.go
Add flag definitions in init():
```go
searchCmd.Flags().IntP("priority", "p", -1, "Filter by exact priority (0-4)")
searchCmd.Flags().Int("priority-min", -1, "Filter by minimum priority")
searchCmd.Flags().Int("priority-max", -1, "Filter by maximum priority")
searchCmd.Flags().String("created-after", "", "Filter by creation date (YYYY-MM-DD)")
searchCmd.Flags().String("created-before", "", "Filter by creation date")
searchCmd.Flags().String("updated-after", "", "Filter by update date")
searchCmd.Flags().String("updated-before", "", "Filter by update date")
searchCmd.Flags().String("closed-after", "", "Filter by close date")
searchCmd.Flags().String("closed-before", "", "Filter by close date")
searchCmd.Flags().String("desc-contains", "", "Filter by description content")
searchCmd.Flags().String("notes-contains", "", "Filter by notes content")
searchCmd.Flags().Bool("empty-description", false, "Filter issues with empty description")
searchCmd.Flags().Bool("no-assignee", false, "Filter unassigned issues")
searchCmd.Flags().Bool("no-labels", false, "Filter issues without labels")
```

### 2. internal/rpc/protocol.go
Update SearchArgs struct:
```go
type SearchArgs struct {
    Query             string
    Filter            types.IssueFilter
    // Already has most fields via IssueFilter
}
```

Note: types.IssueFilter already has these fields - just need to wire them up!

### 3. cmd/bd/search.go Run function
Parse flags and populate filter:
```go
if priority, _ := cmd.Flags().GetInt("priority"); priority >= 0 {
    filter.Priority = &priority
}
if createdAfter, _ := cmd.Flags().GetString("created-after"); createdAfter != "" {
    t, err := time.Parse("2006-01-02", createdAfter)
    if err != nil {
        FatalError("invalid date format for --created-after: %v", err)
    }
    filter.CreatedAfter = &t
}
// ... similar for other flags
```

## Implementation Steps

1. **Check types.IssueFilter** - verify all needed fields exist
2. **Add flags to search.go** init()
3. **Parse flags** in Run function
4. **Pass to SearchIssues** via filter
5. **Test all combinations**

## Testing
```bash
# Create test issues
bd create "Test P1" -p 1
bd create "Test P2" -p 2 --description "Has description"

# Test filters
bd search "" --priority 1
bd search "" --priority-min 0 --priority-max 1
bd search "" --empty-description
bd search "" --desc-contains "description"
```

## Success Criteria
- All filters work in both direct and daemon mode
- Date parsing handles YYYY-MM-DD format
- --json output includes filtered results
- Help text documents all new flags


gt mq list shows empty when MRs exist


gt handoff deadlock at handoff.go:125

When running 'gt handoff -m "message"' after successful MR submit, go panics with 'fatal error: all goroutines are asleep - deadlock\!' at handoff.go:125. The shutdown request still appears to be sent successfully but the command crashes. Stack trace shows issue is in runHandoff select statement.


Test body-file

This is a test description from a file.

It has multiple lines.


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.


Review PR #512: clarify bd ready docs

Review and merge PR #512 from aspiers. This PR clarifies what bd ready does after git pull in README.md. Simple 1-line change. URL: https://github.com/anthropics/beads/pull/512


Fix TestRunSync_Timeout failing on macOS

The hooks timeout test fails because exec.CommandContext doesn't properly terminate child processes of shell scripts on macOS. The test creates a hook that runs 'sleep 60' with a 500ms timeout, but it waits the full 60 seconds.

Options to fix:
- Use SysProcAttr{Setpgid: true} to create process group and kill the group
- Skip test on darwin with build tag
- Use a different approach for timeout testing

Location: internal/hooks/hooks_test.go:220-253


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).


Support external: prefix in blocked_by field

Allow blocked_by to include external project references:

```bash
bd update gt-xyz --blocked-by="external:beads:mol-run-assignee"
```

Syntax: `external:<project>:<capability>`
- project: name from external_projects config
- capability: matches provides:<capability> label in target project

Storage: Store as-is in blocked_by array. Resolution happens at query time.

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


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.


dave Handoff

attached_molecule: bd-ifuw
attached_at: 2025-12-23T12:49:44Z


Split large cmd/bd files: doctor.go (2948 lines), sync.go (2121 lines)

Code health review found several oversized files:

1. doctor.go - 2948 lines, 48 functions mixed together
   - Should split into doctor/checks/*.go for individual diagnostics
   - applyFixes() and previewFixes() are nearly identical

2. sync.go - 2121 lines
   - ZFC (Zero Flush Check) logic embedded inline (lines 213-247)
   - Multiple mode handlers should be extracted

3. init.go - 1732 lines
4. compact.go - 1097 lines
5. show.go - 1069 lines

Recommendation: Extract into focused sub-packages or split into logical files.


Async Gates for Agent Coordination

Agents need an async primitive for waiting on external events (CI completion, API responses, human approval). Gates are wisp issues that block until external conditions are met, managed by the Deacon.

## Core Concepts

**Gate** = wisp issue that blocks until external condition is met
- Type: gate
- Phase: wisp (never synced, ephemeral)
- Assignee: deacon/ (Deacon monitors it)
- Fields: await_type, await_id, timeout, waiters[]

**Await Types:**
- gh:run:<id> - GitHub Actions run completion
- gh:pr:<id> - PR merged/closed
- timer:<duration> - Simple delay
- human:<prompt> - Human approval required
- mail:<pattern> - Wait for mail matching pattern

## Open Questions
- Should gates live in wisp storage or main storage with wisp flag?
- Do we need a gate catalog (like molecule catalog)?
- Should waits-for dep type work with gates?


Monitor PyPI publish

Watch the PyPI publish action:
https://github.com/steveyegge/beads/actions/workflows/pypi-publish.yml

Verify at: https://pypi.org/project/beads-mcp/0.30.4/

Check:
```bash
pip index versions beads-mcp 2>/dev/null | grep -q '0.30.4'
```

```verify
pip index versions beads-mcp 2>/dev/null | grep -q '0.30.4' || curl -s https://pypi.org/pypi/beads-mcp/json | jq -e '.releases["0.30.4"]'
```


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


Merge: bd-49kw

branch: polecat/nux
target: main
source_issue: bd-49kw
rig: beads


Add bd update --parent flag to change issue parent

Allow changing an issue's parent with bd update --parent <new-parent-id>. Useful for reorganizing tasks under different epics or moving issues between hierarchies. Should update the parent-child dependency relationship.


GH#518: Document bd setup command

bd setup is undiscoverable. Add to README/docs. Currently only findable by grepping source. See GitHub issue #518.


Push release v0.33.2 to remote

Push the commit and tag:

```bash
git push && git push --tags
```

Verify on GitHub that the tag appears in releases.


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.


Create git tag v0.33.2

Create the release tag:

```bash
git tag v0.33.2
```

Verify: `git tag | grep 0.33.2`


Cross-project dependency support

Enable tracking dependencies across project boundaries.

## Mechanism
- Producer: `bd ship <capability>` adds `provides:<capability>` label
- Consumer: `blocked_by: external:<project>:<capability>`
- Resolution: `bd ready` checks external deps via config

## Design Doc
See: gastown/docs/cross-project-deps.md

## Children
- bd-eijl: bd ship command
- bd-om4a: external: prefix in blocked_by
- bd-66w1: external_projects config
- bd-zmmy: bd ready resolution


Test message

Hello world


Rename 'bond' to 'spawn' for instantiation

Rename the bd mol bond command to bd mol spawn for instantiating protos.

- Rename molBondCmd to molSpawnCmd
- Update command Use/Short/Long descriptions
- Keep 'bond' available for the new bonding feature
- Update all documentation references
- Add 'protomolecule' as easter egg alias for 'proto'


Test stdin 2

Description from stdin test


Remove legacy MCP Agent Mail integration

## Summary

Remove the legacy MCP Agent Mail system that requires an external HTTP server. Keep the native `bd mail` system which stores messages as git-synced issues.

## Background

Two mail systems exist in the codebase:
1. **Legacy Agent Mail** (`bd message`) - External server dependency, complex setup
2. **Native bd mail** (`bd mail`) - Built-in, git-synced, no dependencies

The legacy system causes confusion and is no longer needed. Gas Town's Town Mail will use the native `bd mail` system.

## Files to Delete

### CLI Command
- [ ] `cmd/bd/message.go` - The `bd message` command implementation

### MCP Integration
- [ ] `integrations/beads-mcp/src/beads_mcp/mail.py` - HTTP wrapper for Agent Mail server
- [ ] `integrations/beads-mcp/src/beads_mcp/mail_tools.py` - MCP tool definitions
- [ ] `integrations/beads-mcp/tests/test_mail.py` - Tests for legacy mail

### Documentation
- [ ] `docs/AGENT_MAIL.md`
- [ ] `docs/AGENT_MAIL_QUICKSTART.md`
- [ ] `docs/AGENT_MAIL_DEPLOYMENT.md`
- [ ] `docs/AGENT_MAIL_MULTI_WORKSPACE_SETUP.md`
- [ ] `docs/adr/002-agent-mail-integration.md`

## Code to Update

- [ ] Remove `message` command registration from `cmd/bd/main.go`
- [ ] Remove mail tool imports/registration from MCP server `__init__.py` or `server.py`
- [ ] Check for any other references to Agent Mail in the codebase

## Verification

- [ ] `bd message` command no longer exists
- [ ] `bd mail` command still works
- [ ] MCP server starts without errors
- [ ] Tests pass


Test Thread

Initial message for threading test


Replace map[string]interface{} with typed JSON response structs

Many CLI commands use map[string]interface{} for JSON output which loses type safety and compile-time error detection.

Files with map[string]interface{}:
- cmd/bd/compact.go (10+ instances)
- cmd/bd/cleanup.go
- cmd/bd/daemons.go
- cmd/bd/daemon_lifecycle.go

Example fix:
```go
// Before
result := map[string]interface{}{
    "status": "ok",
    "count": 42,
}

// After
type CompactResponse struct {
    Status string `json:"status"`
    Count  int    `json:"count"`
}
result := CompactResponse{Status: "ok", Count: 42}
```

Benefits:
- Compile-time type checking
- IDE autocompletion
- Easier refactoring
- Self-documenting API


Widespread double JSON encoding bug in daemon mode RPC calls

Multiple CLI commands had the same double JSON encoding bug found in bd-1048. All commands that called ResolveID via RPC used string(resp.Data) instead of properly unmarshaling the JSON response. This caused IDs to retain JSON quotes ("bd-1048" instead of bd-1048), which then got double-encoded when passed to subsequent RPC calls.

Affected commands:
- bd show (3 instances)
- bd dep add/remove/tree (5 instances)
- bd label add/remove/list (3 instances)
- bd reopen (1 instance)

Root cause: resp.Data is json.RawMessage (already JSON-encoded), so string() conversion preserves quotes.

Fix: Replace all string(resp.Data) with json.Unmarshal(resp.Data, &id) for proper deserialization.

All commands now tested and working correctly with daemon mode.


Standardize error handling: replace direct fmt.Fprintf+os.Exit with FatalError

Standardize error handling in cmd/bd/ using FatalError pattern.

## Current State
~200+ instances of direct `fmt.Fprintf(os.Stderr, ...) + os.Exit(1)` pattern scattered across cmd/bd/*.go files.

## Target Pattern

Use existing FatalError helper (or create if missing):

```go
// In cmd/bd/helpers.go or similar
func FatalError(format string, args ...interface{}) {
    fmt.Fprintf(os.Stderr, "Error: "+format+"\n", args...)
    os.Exit(1)
}

func FatalErrorf(err error, context string) {
    fmt.Fprintf(os.Stderr, "Error: %s: %v\n", context, err)
    os.Exit(1)
}
```

## Transformation

```go
// Before
fmt.Fprintf(os.Stderr, "Error: %v\n", err)
os.Exit(1)

// After
FatalError("%v", err)

// Before
fmt.Fprintf(os.Stderr, "Error: invalid --since duration: %v\n", err)
os.Exit(1)

// After
FatalError("invalid --since duration: %v", err)
```

## Files to Update (by occurrence count)
Run: `grep -c "os.Exit(1)" cmd/bd/*.go | sort -t: -k2 -rn | head -20`

Priority files (highest occurrence):
- close.go
- show.go
- sync.go
- init.go
- list.go
- create.go
- update.go

## Implementation Steps

1. **Check if FatalError exists** in cmd/bd/helpers.go or create it
2. **Create migration script** or use sed:
   ```bash
   # Find patterns to replace
   grep -rn "fmt.Fprintf(os.Stderr.*Error.*\n.*os.Exit(1)" cmd/bd/
   ```
3. **Replace systematically** file by file
4. **Run tests** after each file to verify behavior unchanged
5. **Run linter** to catch any missed patterns

## Verification
```bash
# Count remaining direct exits (should be near zero)
grep -c "os.Exit(1)" cmd/bd/*.go | awk -F: "{sum+=\$2} END {print sum}"

# Run tests
go test -short ./cmd/bd/...
```

## Success Criteria
- All error exits use FatalError/FatalErrorf
- Consistent "Error: " prefix on all error messages
- Tests pass
- No behavior changes (exit codes remain 1)

## Progress (Dec 2025)

Standardized error handling in 3 major files:
- compact.go: All 48 os.Exit(1) calls converted to FatalError
- sync.go: All error patterns converted (kept 1 valid summary exit)
- migrate.go: 4 patterns converted

## Remaining Work
~326 fmt.Fprintf(os.Stderr, "Error:") patterns remain across ~30 files.
High-count files remaining: show.go (16), dep.go (14), gate.go (28), init.go (11).

## Verification
- Build compiles successfully
- Tests pass


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.


Push version bump to GitHub

git push origin main - triggers CI but no release yet.


Update info.go versionChanges

Add entry to versionChanges in cmd/bd/info.go with agent-actionable changes for test-squash


Verify MCP Server Compatibility

Ensure MCP server works with cache-free daemon