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bd sync: 2025-12-21 11:18:33

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Steve Yegge
2025-12-21 11:18:33 -08:00
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@@ -47,7 +47,7 @@
{"id":"bd-5b6e","title":"Add tests for helper functions (GetDirtyIssueHash, GetAllDependencyRecords, export hashes)","description":"Several utility functions have 0% coverage:\n- GetDirtyIssueHash (dirty.go)\n- GetAllDependencyRecords (dependencies.go)\n- GetExportHash, SetExportHash, ClearAllExportHashes (hash.go)\n\nThese are lower priority but should have basic coverage.","status":"open","priority":4,"issue_type":"task","created_at":"2025-11-01T22:40:58.989976-07:00","updated_at":"2025-11-01T22:40:58.989976-07:00"}
{"id":"bd-5qim","title":"Optimize GetReadyWork performance - 752ms on 10K database (target: \u003c50ms)","notes":"# Performance Analysis (10K Issue Database)\n\nAnalyzed using CPU profiles from benchmark suite on Apple M2 Pro.\n\n## Operation Performance\n\n| Operation | Time | Allocations | Memory |\n|----------------------------------|---------|-------------|--------|\n| bd ready (GetReadyWork) | ~752ms | 167,466 | 16MB |\n| bd list (SearchIssues no filter) | ~11.6ms | 89,214 | 5.8MB |\n| bd list (SearchIssues filtered) | ~9.2ms | 62,365 | 3.5MB |\n| bd create (CreateIssue) | ~2.6ms | 146 | 8.6KB |\n| bd update (UpdateIssue) | ~0.32ms | 364 | 15KB |\n| bd close (UpdateIssue) | ~0.32ms | 364 | 15KB |\n\n**Target: \u003c50ms for all operations on 10K database**\n\n**Current issue: GetReadyWork is 15x over target (752ms vs 50ms)**\n\n## Root Cause\n\nGetReadyWork (internal/storage/sqlite/ready.go:90-128) uses recursive CTE to propagate blocking:\n- 65x slower than SearchIssues\n- Recalculates entire blocked issue tree on every call\n- Algorithm:\n 1. Find directly blocked issues via 'blocks' dependencies\n 2. Recursively propagate blockage to descendants (max depth: 50)\n 3. Exclude all blocked issues from results\n\n## CPU Profile Analysis\n\n- Database syscalls (pthread_cond_signal, syscall6): ~75%\n- SQLite engine overhead: inherent to recursive CTE\n- Application code (query construction): \u003c1%\n\n**Bottleneck is the recursive CTE query execution, not application code.**\n\n## Optimization Recommendations\n\n### High Impact (Likely to achieve \u003c50ms target)\n\n1. **Cache blocked issue calculation**\n - Add `blocked_issues` table updated on dependency changes\n - Trade write complexity for read speed (ready called \u003e\u003e dependency changes)\n - Eliminates recursive CTE on every read\n\n2. **Add/verify database indexes**\n ```sql\n CREATE INDEX IF NOT EXISTS idx_dependencies_blocked \n ON dependencies(issue_id, type, depends_on_id);\n CREATE INDEX IF NOT EXISTS idx_issues_status \n ON issues(status);\n ```\n\n### Medium Impact\n\n3. **Reduce allocations** (167K allocations for GetReadyWork)\n - Profile `scanIssues()` for object pooling opportunities\n - Reuse slice capacity for repeated calls\n\n### Low Impact (Not recommended)\n- Query optimization for CRUD operations (already \u003c3ms)\n- Connection pooling tuning (not showing in profiles)\n\n## Verification\n\nRun benchmarks to validate optimization:\n```bash\nmake bench-quick\ngo tool pprof -http=:8080 internal/storage/sqlite/bench-cpu-*.prof\n```\n\nProfile files automatically generated in `internal/storage/sqlite/`.","status":"closed","issue_type":"bug","created_at":"2025-11-14T09:02:46.507526-08:00","updated_at":"2025-12-17T23:13:40.534258-08:00","closed_at":"2025-12-17T16:21:37.918868-08:00"}
{"id":"bd-66l4","title":"Runtime bonding: bd mol attach","description":"Attach a molecule to an already-running workflow.\n\nCOMMAND: bd mol attach \u003cepic-id\u003e \u003cproto\u003e [--after \u003cissue-id\u003e]\n\nBEHAVIOR:\n- Resolve running epic and proto\n- Spawn proto as new subtree\n- Wire to specified attachment point (or epic root)\n- Handle in-progress issues: new work doesn't block completed work\n\nUSE CASES:\n- Discovered need for docs while implementing feature\n- Hotfix needs attaching to release workflow\n- Additional testing scope identified mid-flight\n\nFLAGS:\n- --after ISSUE: Specific attachment point within epic\n- --type: sequential (default) or parallel\n- --var: Variables for the attached proto\n\nCONSIDERATIONS:\n- What if epic is already closed? Error or reopen?\n- What if attachment point issue is closed? Attach as ready-to-work?","status":"closed","priority":2,"issue_type":"task","created_at":"2025-12-21T00:59:16.920483-08:00","updated_at":"2025-12-21T01:08:43.530597-08:00","closed_at":"2025-12-21T01:08:43.530597-08:00","close_reason":"Merged into bd-o91r: bond command handles all bonding cases polymorphically","dependencies":[{"issue_id":"bd-66l4","depends_on_id":"bd-o5xe","type":"parent-child","created_at":"2025-12-21T00:59:51.435542-08:00","created_by":"daemon"},{"issue_id":"bd-66l4","depends_on_id":"bd-o91r","type":"blocks","created_at":"2025-12-21T00:59:51.813782-08:00","created_by":"daemon"}]}
{"id":"bd-68bf","title":"Code review: bd mol bond implementation","description":"Review the mol bond command implementation before shipping.\n\nFocus areas:\n1. runMolBond() - polymorphic dispatch logic correctness\n2. bondProtoProto() - compound proto creation, dependency wiring\n3. bondProtoMol() / bondMolProto() - spawn and attach logic\n4. bondMolMol() - joining molecules, lineage tracking\n5. BondRef usage - is lineage tracked correctly?\n6. Error handling - are all failure modes covered?\n7. Edge cases - what could go wrong?\n\nFile: cmd/bd/mol.go (lines 485-859)\nCommit: 386b513e","status":"open","priority":2,"issue_type":"task","created_at":"2025-12-21T10:13:09.425229-08:00","updated_at":"2025-12-21T10:13:09.425229-08:00","dependencies":[{"issue_id":"bd-68bf","depends_on_id":"bd-o91r","type":"discovered-from","created_at":"2025-12-21T10:13:09.426471-08:00","created_by":"daemon"}]}
{"id":"bd-68bf","title":"Code review: bd mol bond implementation","description":"Review the mol bond command implementation before shipping.\n\nFocus areas:\n1. runMolBond() - polymorphic dispatch logic correctness\n2. bondProtoProto() - compound proto creation, dependency wiring\n3. bondProtoMol() / bondMolProto() - spawn and attach logic\n4. bondMolMol() - joining molecules, lineage tracking\n5. BondRef usage - is lineage tracked correctly?\n6. Error handling - are all failure modes covered?\n7. Edge cases - what could go wrong?\n\nFile: cmd/bd/mol.go (lines 485-859)\nCommit: 386b513e","status":"closed","priority":2,"issue_type":"task","created_at":"2025-12-21T10:13:09.425229-08:00","updated_at":"2025-12-21T11:18:14.206869-08:00","closed_at":"2025-12-21T11:18:14.206869-08:00","close_reason":"Reviewed and fixed label persistence bug","dependencies":[{"issue_id":"bd-68bf","depends_on_id":"bd-o91r","type":"discovered-from","created_at":"2025-12-21T10:13:09.426471-08:00","created_by":"daemon"}]}
{"id":"bd-6fe4622f","title":"Remove unreachable utility functions","description":"Several small utility functions are unreachable:\n\nFiles to clean:\n1. `internal/storage/sqlite/hash.go` - `computeIssueContentHash` (line 17)\n - Check if entire file can be deleted if only contains this function\n\n2. `internal/config/config.go` - `FileUsed` (line 151)\n - Delete unused config helper\n\n3. `cmd/bd/git_sync_test.go` - `verifyIssueOpen` (line 300)\n - Delete dead test helper\n\n4. `internal/compact/haiku.go` - `HaikuClient.SummarizeTier2` (line 81)\n - Tier 2 summarization not implemented\n - Options: implement feature OR delete method\n\nImpact: Removes 50-100 LOC depending on decisions","status":"closed","priority":2,"issue_type":"task","created_at":"2025-10-28T16:20:02.434573-07:00","updated_at":"2025-12-17T22:58:34.563993-08:00","closed_at":"2025-12-17T22:58:34.563993-08:00","close_reason":"Closed"}
{"id":"bd-6gd","title":"Remove legacy MCP Agent Mail integration","description":"## Summary\n\nRemove 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.\n\n## Background\n\nTwo mail systems exist in the codebase:\n1. **Legacy Agent Mail** (`bd message`) - External server dependency, complex setup\n2. **Native bd mail** (`bd mail`) - Built-in, git-synced, no dependencies\n\nThe legacy system causes confusion and is no longer needed. Gas Town's Town Mail will use the native `bd mail` system.\n\n## Files to Delete\n\n### CLI Command\n- [ ] `cmd/bd/message.go` - The `bd message` command implementation\n\n### MCP Integration\n- [ ] `integrations/beads-mcp/src/beads_mcp/mail.py` - HTTP wrapper for Agent Mail server\n- [ ] `integrations/beads-mcp/src/beads_mcp/mail_tools.py` - MCP tool definitions\n- [ ] `integrations/beads-mcp/tests/test_mail.py` - Tests for legacy mail\n\n### Documentation\n- [ ] `docs/AGENT_MAIL.md`\n- [ ] `docs/AGENT_MAIL_QUICKSTART.md`\n- [ ] `docs/AGENT_MAIL_DEPLOYMENT.md`\n- [ ] `docs/AGENT_MAIL_MULTI_WORKSPACE_SETUP.md`\n- [ ] `docs/adr/002-agent-mail-integration.md`\n\n## Code to Update\n\n- [ ] Remove `message` command registration from `cmd/bd/main.go`\n- [ ] Remove mail tool imports/registration from MCP server `__init__.py` or `server.py`\n- [ ] Check for any other references to Agent Mail in the codebase\n\n## Verification\n\n- [ ] `bd message` command no longer exists\n- [ ] `bd mail` command still works\n- [ ] MCP server starts without errors\n- [ ] Tests pass\n","status":"closed","priority":1,"issue_type":"task","created_at":"2025-12-17T23:04:04.099935-08:00","updated_at":"2025-12-17T23:13:24.128752-08:00","closed_at":"2025-12-17T23:13:24.128752-08:00","close_reason":"Removed legacy MCP Agent Mail integration. Kept native bd mail system."}
{"id":"bd-6pc","title":"Implement bd pin/unpin commands","description":"Add 'bd pin \u003cid\u003e' and 'bd unpin \u003cid\u003e' commands to toggle the pinned status of issues. Should support multiple IDs like other bd commands.","status":"closed","priority":1,"issue_type":"task","created_at":"2025-12-18T23:33:28.292937-08:00","updated_at":"2025-12-19T17:43:35.713398-08:00","closed_at":"2025-12-19T00:35:31.612589-08:00","dependencies":[{"issue_id":"bd-6pc","depends_on_id":"bd-0vg","type":"blocks","created_at":"2025-12-18T23:33:56.119852-08:00","created_by":"daemon"},{"issue_id":"bd-6pc","depends_on_id":"bd-7h5","type":"blocks","created_at":"2025-12-18T23:34:07.352848-08:00","created_by":"daemon"}]}
@@ -183,7 +183,7 @@
{"id":"bd-io8c","title":"Improve test coverage for internal/syncbranch (33.0% → 70%)","description":"The syncbranch package has only 33.0% test coverage. This package handles git sync operations and is critical for data integrity.\n\nCurrent coverage: 33.0%\nTarget coverage: 70%","status":"open","priority":1,"issue_type":"task","created_at":"2025-12-13T20:43:02.079145-08:00","updated_at":"2025-12-13T21:01:14.972533-08:00"}
{"id":"bd-iq19","title":"Distill: promote ad-hoc epic to proto","description":"Extract a reusable proto from an existing ad-hoc epic.\n\nCOMMAND: bd mol distill \u003cepic-id\u003e [--as \u003cproto-name\u003e]\n\nBEHAVIOR:\n- Clone the epic and all children as a new proto\n- Set is_template=true on all cloned issues\n- Replace concrete values with {{variable}} placeholders (interactive or --var flags)\n- Add to proto catalog\n\nFLAGS:\n- --as NAME: Custom proto ID (default: proto-\u003cepic-id\u003e)\n- --var field=placeholder: Replace value with variable placeholder\n- --interactive: Prompt for each field that looks parameterizable\n- --dry-run: Preview the proto structure\n\nEXAMPLE:\n bd mol distill bd-o5xe --as proto-feature-workflow \\\n --var title=feature_name \\\n --var assignee=worker\n\nUSE CASES:\n- Team develops good workflow organically, wants to reuse it\n- Capture tribal knowledge as executable templates\n- Create starting point for similar future work\n\nThe reverse of spawn: instead of proto → molecule, it's molecule → proto.","status":"closed","priority":2,"issue_type":"task","created_at":"2025-12-21T01:05:07.953538-08:00","updated_at":"2025-12-21T10:31:56.814246-08:00","closed_at":"2025-12-21T10:31:56.814246-08:00","close_reason":"Implemented distill command in mol.go","dependencies":[{"issue_id":"bd-iq19","depends_on_id":"bd-o5xe","type":"parent-child","created_at":"2025-12-21T01:05:16.495774-08:00","created_by":"daemon"},{"issue_id":"bd-iq19","depends_on_id":"bd-rnnr","type":"blocks","created_at":"2025-12-21T01:05:16.560404-08:00","created_by":"daemon"}]}
{"id":"bd-iq7n","title":"Audit and fix JSONL filename mismatches across all repo clones","description":"## Problem\n\nMultiple clones of repos are configured with different JSONL filenames (issues.jsonl vs beads.jsonl), causing:\n1. JSONL files to be resurrected after deletion (one clone pushes issues.jsonl, another pushes beads.jsonl)\n2. Agents unable to see issues filed by other agents after sync\n3. Merge conflicts and data inconsistencies\n\n## Root Cause\n\nWhen 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.\n\n## Task\n\nScan all repo clones under ~/src/ (1-2 levels deep) and standardize their JSONL configuration.\n\n### Step 1: Find all beads-enabled repos\n\n```bash\n# Find all directories named 'beads' at levels 1-2 under ~/src/\nfind ~/src -maxdepth 2 -type d -name beads\n```\n\n### Step 2: For each repo found, check configuration\n\nFor each directory from Step 1, check:\n- Does `.beads/metadata.json` exist?\n- What is the `jsonl_export` value?\n- What JSONL files actually exist in `.beads/`?\n- Are there multiple JSONL files (problem!)?\n\n### Step 3: Create audit report\n\nGenerate a report showing:\n```\nRepo Path | Config | Actual Files | Status\n----------------------------------- | ------------- | ---------------------- | --------\n~/src/beads | beads.jsonl | beads.jsonl | OK\n~/src/dave/beads | issues.jsonl | issues.jsonl | MISMATCH\n~/src/emma/beads | issues.jsonl | issues.jsonl, beads.jsonl | DUPLICATE!\n```\n\n### Step 4: Determine canonical name for each repo\n\nFor repos that are the SAME git repository (check `git remote -v`):\n- Group them together\n- Determine which JSONL filename should be canonical (majority wins, or beads.jsonl for the beads repo itself)\n- List which clones need to be updated\n\n### Step 5: Generate fix script\n\nCreate a script that for each mismatched clone:\n1. Updates `.beads/metadata.json` to use the canonical name\n2. If JSONL file needs renaming: `git mv .beads/old.jsonl .beads/new.jsonl`\n3. Removes any duplicate JSONL files: `git rm .beads/duplicate.jsonl`\n4. Commits the change\n5. Syncs: `bd sync`\n\n### Expected Output\n\n1. Audit report showing all repos and their config status\n2. List of repos grouped by git remote (same repository)\n3. Fix script or manual instructions for standardizing each repo\n4. Verification that after fixes, all clones of the same repo use the same JSONL filename\n\n### Edge Cases\n\n- Handle repos without metadata.json (use default discovery)\n- Handle repos with no git remote (standalone/local)\n- Handle repos that are not git repositories\n- Don't modify repos with uncommitted changes (warn instead)\n\n### Success Criteria\n\n- All clones of the same git repository use the same JSONL filename\n- No duplicate JSONL files in any repo\n- All configurations documented in metadata.json\n- bd doctor passes on all repos","status":"closed","issue_type":"task","created_at":"2025-11-21T23:58:35.044762-08:00","updated_at":"2025-12-17T23:13:40.531403-08:00","closed_at":"2025-12-17T16:50:59.510972-08:00"}
{"id":"bd-iw4z","title":"Compound visualization in bd mol show","description":"Enhance bd mol show to display compound structure.\n\nENHANCEMENTS:\n- Show constituent protos and how they're bonded\n- Display bond type (sequential/parallel) between components\n- Indicate attachment points\n- Show combined variable requirements across all protos\n\nEXAMPLE OUTPUT:\n\n Compound: proto-feature-with-tests\n Bonded from:\n └─ proto-feature (root)\n └─ proto-testing (sequential, after completion)\n \n Variables: {{name}}, {{version}}, {{test_suite}}\n \n Structure:\n proto-feature-with-tests\n ├─ Design feature {{name}}\n ├─ Implement core\n ├─ Write unit tests ← from proto-testing\n └─ Run test suite {{test_suite}} ← from proto-testing","status":"open","priority":2,"issue_type":"task","created_at":"2025-12-21T00:59:26.71318-08:00","updated_at":"2025-12-21T00:59:26.71318-08:00","dependencies":[{"issue_id":"bd-iw4z","depends_on_id":"bd-o5xe","type":"parent-child","created_at":"2025-12-21T00:59:51.500865-08:00","created_by":"daemon"},{"issue_id":"bd-iw4z","depends_on_id":"bd-rnnr","type":"blocks","created_at":"2025-12-21T00:59:51.891643-08:00","created_by":"daemon"}]}
{"id":"bd-iw4z","title":"Compound visualization in bd mol show","description":"Enhance bd mol show to display compound structure.\n\nENHANCEMENTS:\n- Show constituent protos and how they're bonded\n- Display bond type (sequential/parallel) between components\n- Indicate attachment points\n- Show combined variable requirements across all protos\n\nEXAMPLE OUTPUT:\n\n Compound: proto-feature-with-tests\n Bonded from:\n └─ proto-feature (root)\n └─ proto-testing (sequential, after completion)\n \n Variables: {{name}}, {{version}}, {{test_suite}}\n \n Structure:\n proto-feature-with-tests\n ├─ Design feature {{name}}\n ├─ Implement core\n ├─ Write unit tests ← from proto-testing\n └─ Run test suite {{test_suite}} ← from proto-testing","status":"deferred","priority":2,"issue_type":"task","created_at":"2025-12-21T00:59:26.71318-08:00","updated_at":"2025-12-21T11:12:44.012871-08:00","dependencies":[{"issue_id":"bd-iw4z","depends_on_id":"bd-o5xe","type":"parent-child","created_at":"2025-12-21T00:59:51.500865-08:00","created_by":"daemon"},{"issue_id":"bd-iw4z","depends_on_id":"bd-rnnr","type":"blocks","created_at":"2025-12-21T00:59:51.891643-08:00","created_by":"daemon"}]}
{"id":"bd-j3il","title":"Add bd reset command for clean slate restart","description":"Implement a command to reset beads to a clean starting state.\n\n**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.\n\n**Current workaround** (from maphew):\n```bash\nbd daemons killall\ngit rm .beads/*.jsonl\ngit commit -m 'remove old issues'\nrm .beads/*\nbd init\nbd onboard\n```\n\n**Desired:** A proper `bd reset` command that handles this cleanly and safely.","status":"closed","priority":2,"issue_type":"feature","created_at":"2025-12-13T08:41:34.956552+11:00","updated_at":"2025-12-13T08:43:49.970591+11:00","closed_at":"2025-12-13T08:43:49.970591+11:00"}
{"id":"bd-j6lr","title":"GH#402: Add --parent flag documentation to bd onboard","description":"bd onboard output is missing --parent flag for epic subtasks. Agents guess wrong syntax (--deps parent:). See GitHub issue #402.","status":"tombstone","priority":2,"issue_type":"task","created_at":"2025-12-16T01:03:56.594829-08:00","updated_at":"2025-12-17T16:11:17.070763-08:00","deleted_at":"2025-12-17T16:11:17.070763-08:00","deleted_by":"batch delete","delete_reason":"batch delete","original_type":"task"}
{"id":"bd-jgxi","title":"Auto-migrate database on CLI version bump","description":"When CLI is upgraded (e.g., 0.24.0 → 0.24.1), database version becomes stale. Add auto-migration in PersistentPreRun or daemon startup. Check dbVersion != CLIVersion and run bd migrate automatically. Fixes recurring UX issue where bd doctor shows version mismatch after every CLI upgrade.","status":"closed","issue_type":"feature","created_at":"2025-11-21T23:16:09.004619-08:00","updated_at":"2025-12-17T23:13:40.535453-08:00","closed_at":"2025-12-17T17:15:43.605762-08:00","dependencies":[{"issue_id":"bd-jgxi","depends_on_id":"bd-tbz3","type":"parent-child","created_at":"2025-11-21T23:16:09.005513-08:00","created_by":"daemon","metadata":"{}"}]}