Install and test MCP Agent Mail locally

Install MCP Agent Mail on a single development machine and verify basic functionality.

Acceptance Criteria:
- Server installed via one-line installer
- Server running on port 8765
- Can register a project via HTTP
- Can register an agent identity
- Web UI accessible at /mail

Tested local installation. Server runs on port 8765, web UI works. MCP API tool execution has errors - needs debugging. See /tmp/bd-muls-report.md for details.


Deletions not propagated across multi-workspace sync

## Problem

When working with multiple beads workspaces (clones) sharing the same git remote, deleted issues keep coming back.

## Reproduction

1. Clone A deletes issue `bd-xyz` via `bd delete bd-xyz --force`
2. Clone A daemon syncs and pushes to GitHub
3. Clone B still has `bd-xyz` in its database
4. Clone B daemon exports and pushes its JSONL
5. Clone A pulls and imports → `bd-xyz` comes back!

## Root Cause

**No deletion tracking mechanism.** The system has no way to distinguish between:
- "Issue doesn't exist in JSONL because it was deleted"
- "Issue doesn't exist in JSONL because the export is stale"

Import treats missing issues as "not in this export" rather than "explicitly deleted."

## Solution Options

1. **Tombstone records** - Keep deleted issues in JSONL with `"status":"deleted"` or `"deleted_at"` field
2. **Deletion log** - Separate `.beads/deletions.jsonl` file tracking all deleted IDs
3. **Three-way merge** - Import compares: DB state, old JSONL, new JSONL
4. **Manual conflict resolution** - Detect resurrection and prompt user

## Related

- Similar to resurrection logic for orphaned children (bd-cc4f)
- beads-merge tool handles this better with 3-way merge


Test update


Implement `bd setup claude` command for Claude Code integration

Create a `bd setup claude` command that installs Claude Code integration files (slash commands and hooks). This is idempotent and safe to run multiple times.


Bug P0


Add integration tests for CompactedResult in MCP server

The CompactedResult model is used for list operations when results exceed COMPACTION_THRESHOLD (20 items), but there are no integration tests verifying the actual MCP server behavior with large result sets.

## What's Missing
- Integration test that mocks a large result set (>20 issues) and verifies CompactedResult is returned
- Verification that preview_count matches PREVIEW_COUNT (5)
- Verification that total_count reflects actual result size
- Test that compaction threshold is configurable (currently hardcoded COMPACTION_THRESHOLD=20)

## Why This Matters
The compaction logic is critical for preventing context overflow with large lists. Without integration tests, we can't verify it works correctly with the actual MCP protocol.

## Suggested Implementation
Create test_mcp_compaction.py with:
1. test_list_with_large_result_set_returns_compacted_result()
2. test_ready_work_respects_compaction_threshold()
3. test_compacted_result_structure_is_valid()


bd doctor: detect and fix stale beads-sync branch

## Problem

When beads-sync diverges significantly from main (on source code, not just .beads/), it needs to be reset. After a force-push reset, other clones/contributors will have orphaned local beads-sync branches.

## Symptoms
- Local beads-sync is many commits behind main on source files
- Local beads-sync doesn't share recent history with remote beads-sync (after force-push)
- bd sync may behave unexpectedly

## Proposed bd doctor checks

1. **Check beads-sync alignment with main**
   - If beads-sync exists and is >N commits behind main on non-.beads/ files, warn
   - Suggests: reset beads-sync to main

2. **Check beads-sync alignment with remote**
   - If local beads-sync has diverged from origin/beads-sync (no common recent ancestor)
   - This happens after someone force-pushed a reset
   - Suggests: reset local beads-sync to origin/beads-sync

## Proposed fixes (--fix)

- Reset local beads-sync branch to origin/beads-sync or main
- Handle worktree if present (git worktree remove, then recreate on next sync)

## Context
Discovered when beads-sync drifted 126 commits behind main. Required manual reset and force-push. Contributors will need to reset their local branches too.


Auto-import runs during --no-auto-import operations via stats/ready commands

Even when using --no-auto-import flag, certain commands like 'bd stats' and 'bd ready' still trigger auto-import internally, which can cause the git history backfill bug to corrupt data.

Example:
  bd stats --no-auto-import
  # Still prints 'Purged bd-xxx (recovered from git history...)'

The flag should completely disable auto-import for the command, but it appears some code paths still trigger it.

Workaround: Use --allow-stale instead, or --sandbox mode.


Modify EnsureIDs to support parent resurrection

Update internal/storage/sqlite/ids.go:189-202 to call TryResurrectParent before failing on missing parent. Add resurrection mode flag, log resurrected parents for transparency. Maintain backwards compatibility with strict validation mode.


Update GetStatistics to report tombstone count separately

Per bd-2m7 design: 'Should tombstones appear in bd stats? Recommendation: Yes, as separate counter: 5 deleted (tombstones)'

Currently GetStatistics counts tombstones in TotalIssues without distinguishing them.

Location: internal/storage/sqlite/events.go:114-121

Add to Statistics struct and query:
- DeletedIssues (tombstone count)
- Exclude tombstones from TotalIssues or document that it includes them


Complete remaining sync branch daemon tests

4 remaining test scenarios in daemon_sync_branch_test.go need completion:

⚠ MINOR FIXES (apply same pattern as TestSyncBranchCommitAndPush_Success):
1. TestSyncBranchCommitAndPush_NoChanges
   - Reorder: call initMainBranch() BEFORE creating JSONL
   - Pattern: init branch → create issue → export JSONL → test

2. TestSyncBranchCommitAndPush_WorktreeHealthCheck
   - Same reordering needed
   - Verify worktree corruption detection and auto-repair

🔧 MORE WORK NEEDED (remote branch setup):
3. TestSyncBranchPull_Success
   - Issue: remote doesn't have sync branch after push
   - Need to verify branch is pushed to remote correctly
   - Then test pull from clone2

4. TestSyncBranchIntegration_EndToEnd
   - Full workflow: Agent A commits → Agent B pulls → Agent B commits → Agent A pulls
   - Same remote branch issue

Pattern to apply (from TestSyncBranchCommitAndPush_Success):
- Call initMainBranch(t, dir) BEFORE creating issues/JSONL
- This ensures sync branch worktree has changes to commit

Acceptance:
- All 7 tests pass
- go test -v -run TestSyncBranch ./cmd/bd/ succeeds


Backend task


Add simple cleanup command to delete closed issues

Users want a simple command to delete all closed issues without requiring Anthropic API key (unlike compact). Requested in GH #243.


Add mermaid output format for bd dep tree

Add visual dependency graph output using Mermaid format for better visualization of issue relationships.

Example usage:
  bd dep tree --format mermaid <issue-id>
  bd dep tree --format mermaid bd-42 > graph.md

This would output Mermaid syntax that can be rendered in GitHub, documentation sites, or Mermaid live editor.

Implementation notes:
- Add --format flag to dep tree command
- Support 'text' (default) and 'mermaid' formats
- Mermaid graph should show issue IDs, titles, and dependency types
- Consider using flowchart LR or graph TD syntax


Audit and fix JSONL filename mismatches across all repo clones

## Problem

Multiple clones of repos are configured with different JSONL filenames (issues.jsonl vs beads.jsonl), causing:
1. JSONL files to be resurrected after deletion (one clone pushes issues.jsonl, another pushes beads.jsonl)
2. Agents unable to see issues filed by other agents after sync
3. Merge conflicts and data inconsistencies

## Root Cause

When repos were "bd doctored" or initialized at different times, some got issues.jsonl (old default) and others got beads.jsonl (Beads repo specific). These clones push their respective files, creating duplicates.

## Task

Scan all repo clones under ~/src/ (1-2 levels deep) and standardize their JSONL configuration.

### Step 1: Find all beads-enabled repos

```bash
# Find all directories named 'beads' at levels 1-2 under ~/src/
find ~/src -maxdepth 2 -type d -name beads
```

### Step 2: For each repo found, check configuration

For each directory from Step 1, check:
- Does `.beads/metadata.json` exist?
- What is the `jsonl_export` value?
- What JSONL files actually exist in `.beads/`?
- Are there multiple JSONL files (problem!)?

### Step 3: Create audit report

Generate a report showing:
```
Repo Path                           | Config        | Actual Files           | Status
----------------------------------- | ------------- | ---------------------- | --------
~/src/beads                         | beads.jsonl   | beads.jsonl            | OK
~/src/dave/beads                    | issues.jsonl  | issues.jsonl           | MISMATCH
~/src/emma/beads                    | issues.jsonl  | issues.jsonl, beads.jsonl | DUPLICATE!
```

### Step 4: Determine canonical name for each repo

For repos that are the SAME git repository (check `git remote -v`):
- Group them together
- Determine which JSONL filename should be canonical (majority wins, or beads.jsonl for the beads repo itself)
- List which clones need to be updated

### Step 5: Generate fix script

Create a script that for each mismatched clone:
1. Updates `.beads/metadata.json` to use the canonical name
2. If JSONL file needs renaming: `git mv .beads/old.jsonl .beads/new.jsonl`
3. Removes any duplicate JSONL files: `git rm .beads/duplicate.jsonl`
4. Commits the change
5. Syncs: `bd sync`

### Expected Output

1. Audit report showing all repos and their config status
2. List of repos grouped by git remote (same repository)
3. Fix script or manual instructions for standardizing each repo
4. Verification that after fixes, all clones of the same repo use the same JSONL filename

### Edge Cases

- Handle repos without metadata.json (use default discovery)
- Handle repos with no git remote (standalone/local)
- Handle repos that are not git repositories
- Don't modify repos with uncommitted changes (warn instead)

### Success Criteria

- All clones of the same git repository use the same JSONL filename
- No duplicate JSONL files in any repo
- All configurations documented in metadata.json
- bd doctor passes on all repos


Fix daemon exiting after 5s on macOS due to PID 1 parent monitoring

GitHub issue #278 reports that the daemon exits after <=5 seconds on macOS because it incorrectly treats PID 1 (launchd) as a dead parent.

When the daemon detaches on macOS, it gets reparented to PID 1 (launchd), which is the init process. The checkParentProcessAlive function was incorrectly treating PID 1 as a sign that the parent died.

Fixed by changing the logic to treat PID 1 as a valid parent for detached daemons.


Investigate TestRoutingIntegration failure

TestRoutingIntegration/maintainer_with_SSH_remote failed during pre-commit check with "expected role maintainer, got contributor".
This occurred while running `go test -short ./...` on darwin/arm64.
The failure appears unrelated to storage/sqlite changes.
Need to investigate if this is a flaky test or environmental issue.


Add tests for daemon vs non-daemon parity in list filters

After bd-o43 RPC integration, we need tests to verify daemon mode behaves identically to direct mode for all new filter flags.

Test coverage needed:
- Pattern matching: --title-contains, --desc-contains, --notes-contains
- Date ranges: all 6 date filter flags (created/updated/closed after/before)
- Empty/null checks: --empty-description, --no-assignee, --no-labels
- Priority ranges: --priority-min, --priority-max
- Status normalization: --status all vs no status flag
- Date parsing: YYYY-MM-DD, RFC3339, and error cases
- Backward compat: deprecated --label flag still works

Oracle review findings (bd-o43):
- Date parsing should support multiple formats
- Status 'all' should be treated as unset
- NoLabels field was missing from RPC protocol
- Error messages should be clear and actionable

Test approach:
- Create RPC integration tests in internal/rpc/server_issues_epics_test.go
- Compare daemon client.List() vs direct store.SearchIssues() for same filters
- Verify error messages match between modes
- Test with real daemon instance, not just unit tests


bd validate - Comprehensive health check

Run all validation checks in one command.

Checks:
- Duplicates
- Orphaned dependencies
- Test pollution
- Git conflicts

Supports --fix-all for auto-repair.

Depends on bd-cbed9619.1, bd-0dcea000, bd-2752a7a2, bd-9826b69a.

Files: cmd/bd/validate.go (new)


Add close_reason to JSONL export format documentation

PR #551 now persists close_reason to the database, but there's a question about whether this field should be exported to JSONL format.

## Current State
- close_reason is stored in issues.close_reason column
- close_reason is also stored in events table (audit trail)
- The JSONL export format may or may not include close_reason

## Questions
1. Should close_reason be exported to JSONL format?
2. If yes, where should it go (root level or nested in events)?
3. Should there be any special handling to avoid duplication?
4. How should close_reason be handled during JSONL import?

## Why This Matters
- JSONL is the git-friendly sync format
- Other beads instances import from JSONL
- close_reason is meaningful data that should be preserved across clones

## Suggested Action
- Check if close_reason is currently exported in JSONL
- If not, add it to the export schema
- Document the field in JSONL format spec
- Add tests for round-trip (export -> import -> verify close_reason)