diff --git a/.beads/issues.jsonl b/.beads/issues.jsonl index 42e86c70..e7471f37 100644 --- a/.beads/issues.jsonl +++ b/.beads/issues.jsonl @@ -139,6 +139,7 @@ {"id":"bd-2b34.6","title":"Add tests for daemon lifecycle module","status":"closed","priority":1,"issue_type":"task","created_at":"2025-10-31T22:28:42.359587-07:00","updated_at":"2025-11-01T21:22:39.009259-07:00","closed_at":"2025-11-01T21:22:39.009259-07:00"} {"id":"bd-2b34.7","title":"Add tests for daemon config module","status":"closed","priority":1,"issue_type":"task","created_at":"2025-10-31T22:28:42.373684-07:00","updated_at":"2025-11-01T21:21:42.431252-07:00","closed_at":"2025-11-01T21:21:42.431252-07:00"} {"id":"bd-2b34.8","title":"Extract daemon lifecycle functions to daemon_lifecycle.go","status":"closed","priority":1,"issue_type":"task","created_at":"2025-10-31T22:28:42.382892-07:00","updated_at":"2025-11-01T21:02:58.350055-07:00","closed_at":"2025-11-01T21:02:58.350055-07:00"} +{"id":"bd-2be4l","title":"Session ended: gt-beads-crew-giles","status":"closed","priority":2,"issue_type":"event","created_at":"2026-01-07T19:20:03.002344-08:00","created_by":"beads/crew/giles","updated_at":"2026-01-07T19:20:03.041926-08:00","closed_at":"2026-01-07T19:20:03.041926-08:00","close_reason":"auto-closed session event"} {"id":"bd-2c5a","title":"Investigate why test issues persist in database","description":"Test issues (bd-0do3, bd-cjxp, bd-phr2, etc.) keep appearing in ready/list output, cluttering real work. These appear to be leftover test data from test runs.\n\nNeed to investigate:\n1. Why are test issues not being cleaned up after tests?\n2. Are tests creating issues in the main database instead of test databases?\n3. Should we add better test isolation or cleanup hooks?\n4. Can we add a label/prefix to distinguish test issues from real issues?\n\nThese test issues have characteristics:\n- Empty descriptions\n- Generic titles like \"Test issue 0\", \"Bug P0\", \"Issue to reopen with reason\"\n- Created around 2025-11-07 19:00-19:07\n- Some assigned to test users like \"alice\", \"bob\", \"testuser\"","notes":"## Root Cause Analysis\n\n**Problem**: Python MCP integration tests created test issues in production `.beads/beads.db` instead of isolated test databases.\n\n**Evidence**:\n- 29 test issues created on Nov 7, 2025 at 19:00-19:07\n- Patterns: \"Bug P0\", \"Test issue X\", assignees \"alice\"/\"bob\"/\"testuser\"\n- Git commit 0e8936b shows test issues committed to .beads/beads.jsonl\n- Tests were being fixed for workspace isolation around the same time\n\n**Why It Happened**:\n1. Before commit 0e8936b, `test_client_lazy_initialization()` didn't set `BEADS_WORKING_DIR`\n2. Tests fell back to discovering `.beads/` in the project root directory\n3. Auto-sync committed test issues to production database\n\n**Resolution**:\n1. ✅ Closed 29 test pollution issues (bd-0do3, bd-cjxp, etc.)\n2. ✅ Added `failIfProductionDatabase()` guard in Go test helpers\n3. ✅ Added production pollution checks in RPC test setup\n4. ✅ Created `conftest.py` with pytest safety checks for Python tests\n5. ✅ Added `BEADS_TEST_MODE` env var to mark test execution\n6. ✅ Tests now fail fast if they detect production database usage\n\n**Prevention**:\n- All test helper functions now verify database paths are in temp directories\n- Python tests fail immediately if BEADS_DB points to production\n- BEADS_TEST_MODE flag helps identify test vs production execution\n- Clear error messages guide developers to use proper test isolation\n\n**Files Modified**:\n- cmd/bd/test_helpers_test.go - Added failIfProductionDatabase()\n- internal/rpc/rpc_test.go - Added temp directory verification\n- integrations/beads-mcp/tests/conftest.py - New file with pytest safeguards","status":"closed","priority":1,"issue_type":"bug","created_at":"2025-11-07T21:31:34.845887-08:00","updated_at":"2025-11-07T21:57:30.892086-08:00","closed_at":"2025-11-07T21:57:30.892086-08:00"} {"id":"bd-2c64","title":"Merge: ruby-1767142029451","description":"branch: polecat/ruby-1767142029451\ntarget: main\nsource_issue: ruby-1767142029451\nrig: beads","status":"closed","priority":2,"issue_type":"merge-request","created_at":"2025-12-30T17:00:14.136568-08:00","created_by":"beads/polecats/ruby","updated_at":"2025-12-30T18:12:30.96303-08:00","closed_at":"2025-12-30T18:11:07.842778-08:00"} {"id":"bd-2cvu","title":"Update AGENTS.md with Agent Mail workflow","description":"Update agent workflow section to include Agent Mail coordination as optional step.\n\nAcceptance Criteria:\n- Add Agent Mail to recommended workflow\n- Show both with/without examples\n- Update \"Multi-Agent Patterns\" section\n- Cross-reference to AGENT_MAIL.md\n\nFile: AGENTS.md (lines 468-475)","status":"closed","priority":1,"issue_type":"task","created_at":"2025-11-07T22:42:51.295729-08:00","updated_at":"2025-11-08T00:52:34.288915-08:00","closed_at":"2025-11-08T00:52:34.288915-08:00","dependencies":[{"issue_id":"bd-2cvu","depends_on_id":"bd-xzrv","type":"blocks","created_at":"2025-11-07T23:04:09.773656-08:00","created_by":"daemon"}]} @@ -403,6 +404,7 @@ {"id":"bd-70419816","title":"Export deduplication breaks when JSONL and export_hashes table diverge","description":"## Problem\n\nThe export deduplication feature (timestamp-only skipping) breaks when the JSONL file and export_hashes table get out of sync, causing exports to skip issues that aren't actually in the file.\n\n## Symptoms\n\n- `bd export` reports \"Skipped 128 issue(s) with timestamp-only changes\"\n- JSONL file only has 38 lines but DB has 149 issues\n- export_hashes table has 149 entries\n- Auto-import doesn't trigger (hash matches despite missing data)\n- Two repos on same commit show different issue counts\n\n## Root Cause\n\nshouldSkipExport() in autoflush.go compares current issue hash with stored export_hashes entry. If they match, it skips export assuming the issue is already in the JSONL.\n\nThis assumption fails when:\n1. Git operations (pull, reset, checkout) change JSONL without clearing export_hashes\n2. Manual JSONL edits or corruption\n3. Import operations that modify DB but don't update export_hashes\n4. Partial exports that update export_hashes but don't complete\n\n## Impact\n\n- **Critical data loss risk**: Issues appear to be tracked but aren't persisted to git\n- Breaks multi-repo sync (root cause of today's debugging session)\n- Auto-import fails to detect staleness (hash matches despite missing data)\n- Silent data corruption (no error messages, just missing issues)\n\n## Reproduction\n\n1. Have DB with 149 issues, all in export_hashes table\n2. Truncate JSONL to 38 lines (simulate git reset or corruption)\n3. Run `bd export` - it skips 128 issues\n4. JSONL still has only 38 lines but export thinks it succeeded\n\n## Current Workaround\n\n```bash\nsqlite3 .beads/beads.db \"DELETE FROM export_hashes\"\nbd export -o .beads/beads.jsonl\n```\n\n## Proposed Solutions\n\n**Option 1: Verify JSONL integrity before skipping**\n- Count lines in JSONL, compare with export_hashes count\n- If mismatch, clear export_hashes and force full export\n- Safe but adds I/O overhead\n\n**Option 2: Hash-based JSONL validation**\n- Store hash of entire JSONL file in metadata\n- Before export, check if JSONL hash matches\n- If mismatch, clear export_hashes\n- More efficient, detects any JSONL corruption\n\n**Option 3: Disable timestamp-only deduplication**\n- Remove the feature entirely\n- Always export all issues\n- Simplest and safest, but creates larger git commits\n\n**Option 4: Clear export_hashes on git operations**\n- Add post-merge hook to clear export_hashes\n- Clear on any import operation\n- Defensive approach but may over-clear\n\n## Recommended Fix\n\nCombination of Options 2 + 4:\n1. Store JSONL file hash in metadata after export\n2. Check hash before export, clear export_hashes if mismatch \n3. Clear export_hashes on import operations\n4. Add `bd validate` check for JSONL/export_hashes sync\n\n## Files Involved\n\n- cmd/bd/autoflush.go (shouldSkipExport)\n- cmd/bd/export.go (export with deduplication)\n- internal/storage/sqlite/metadata.go (export_hashes table)","status":"closed","priority":0,"issue_type":"bug","created_at":"2025-10-29T23:05:13.960352-07:00","updated_at":"2025-10-30T17:12:58.19679-07:00","closed_at":"2025-10-29T22:22:20.406934-07:00"} {"id":"bd-70an","title":"test pin","status":"closed","priority":2,"issue_type":"task","created_at":"2025-12-21T11:19:16.760214-08:00","updated_at":"2025-12-21T11:19:46.500688-08:00","closed_at":"2025-12-21T11:19:46.500688-08:00"} {"id":"bd-70c4","title":"Gate await fields cleared by --no-daemon CLI access (not multi-repo)","status":"closed","priority":1,"issue_type":"bug","created_at":"2025-12-25T23:30:38.648182-08:00","updated_at":"2025-12-26T23:38:47.972075-08:00","closed_at":"2025-12-26T23:38:47.972075-08:00","comments":[{"id":3,"issue_id":"bd-70c4","author":"mayor","text":"## Summary\nGate await fields (await_type, await_id, timeout_ns, waiters) are cleared when a CLI command accesses the database directly (--no-daemon) while the daemon is running. This is separate from the multi-repo issue fixed in bd-gr4q.\n\n## Reproduction\n1. Start daemon: bd daemon --start\n2. Create gate: bd gate create --await timer:5s (fields stored correctly)\n3. Verify: sqlite3 .beads/beads.db shows timer|5s\n4. Run CLI with --no-daemon: bd show \u003cid\u003e --no-daemon --no-auto-import --no-auto-flush\n5. Check again: fields are now empty\n\n## Investigation Notes\n- NOT caused by autoImportIfNewer (verified with --no-auto-import flag)\n- NOT caused by HydrateFromMultiRepo (no multi-repo config, returns early)\n- NOT caused by molecule loader (only creates new issues)\n- NOT caused by migrations (gate_columns only adds columns)\n- No database triggers found\n\nThe clearing happens somewhere in sqlite.NewWithTimeout() initialization or command execution path.\n\n## Related\n- bd-gr4q fixed the multi-repo path but this is a different code path\n- The fix pattern (COALESCE/NULLIF) may need to be applied elsewhere","created_at":"2025-12-26T07:30:49Z"}]} +{"id":"bd-70txm","title":"Session ended: gt-beads-crew-emma","status":"closed","priority":2,"issue_type":"event","created_at":"2026-01-07T19:20:03.303066-08:00","created_by":"beads/crew/emma","updated_at":"2026-01-07T19:20:03.351526-08:00","closed_at":"2026-01-07T19:20:03.351526-08:00","close_reason":"auto-closed session event"} {"id":"bd-710a4916","title":"CRDT-based architecture for guaranteed convergence (v2.0)","description":"## Vision\nRedesign beads around Conflict-Free Replicated Data Types (CRDTs) to provide mathematical guarantees for N-way collision resolution at arbitrary scale.\n\n## Current Limitations\n- Content-hash based collision resolution fails at 5+ clones\n- Non-deterministic convergence in multi-round scenarios\n- UNIQUE constraint violations during rename operations\n- No formal proof of convergence properties\n\n## CRDT Benefits\n- Provably convergent (Strong Eventual Consistency)\n- Commutative/Associative/Idempotent operations\n- No coordination required between clones\n- Scales to 100+ concurrent workers\n- Well-understood mathematical foundations\n\n## Proposed Architecture\n\n### 1. UUID-Based IDs\nReplace sequential IDs with UUIDs:\n- Current: bd-1c63eb84, bd-9063acda, bd-4d80b7b1\n- CRDT: bd-a1b2c3d4-e5f6-7890-abcd-ef1234567890\n- Human aliases maintained separately: #42 maps to UUID\n\n### 2. Last-Write-Wins (LWW) Elements\nEach field becomes an LWW register:\n- title: (timestamp, clone_id, value)\n- status: (timestamp, clone_id, value)\n- Deterministic conflict resolution via Lamport timestamp + clone_id tiebreaker\n\n### 3. Operation Log\nTrack all operations as CRDT ops:\n- CREATE(uuid, timestamp, clone_id, fields)\n- UPDATE(uuid, field, timestamp, clone_id, value)\n- DELETE(uuid, timestamp, clone_id) - tombstone, not hard delete\n\n### 4. Sync as Merge\nSyncing becomes merging two CRDT states:\n- No merge conflicts possible\n- Deterministic merge function\n- Guaranteed convergence\n\n## Implementation Phases\n\n### Phase 1: Research \u0026 Design (4 weeks)\n- Study existing CRDT implementations (Automerge, Yjs, Loro)\n- Design schema for CRDT-based issue tracking\n- Prototype LWW-based Issue CRDT\n- Benchmark performance vs current system\n\n### Phase 2: Parallel Implementation (6 weeks)\n- Implement CRDT storage layer alongside SQLite\n- Build conversion tools: SQLite ↔ CRDT\n- Maintain backward compatibility with v1.x format\n- Migration path for existing databases\n\n### Phase 3: Testing \u0026 Validation (4 weeks)\n- Formal verification of convergence properties\n- Stress testing with 100+ clone scenario\n- Performance profiling and optimization\n- Documentation and examples\n\n### Phase 4: Migration \u0026 Rollout (4 weeks)\n- Release v2.0-beta with CRDT backend\n- Gradual migration from v1.x\n- Monitoring and bug fixes\n- Final v2.0 release\n\n## Risks \u0026 Mitigations\n\n**Risk 1: Performance overhead**\n- Mitigation: Benchmark early, optimize hot paths\n- CRDTs can be slower than append-only logs\n- May need compaction strategy\n\n**Risk 2: Storage bloat**\n- Mitigation: Implement operation log compaction\n- Tombstone garbage collection for deleted issues\n- Periodic snapshots to reduce log size\n\n**Risk 3: Breaking changes**\n- Mitigation: Maintain v1.x compatibility layer\n- Gradual migration tools\n- Dual-mode operation during transition\n\n**Risk 4: Complexity**\n- Mitigation: Use battle-tested CRDT libraries\n- Comprehensive documentation\n- Clear migration guide\n\n## Success Criteria\n- 100-clone collision test passes without failures\n- Formal proof of convergence properties\n- Performance within 2x of current system\n- Zero manual conflict resolution required\n- Backward compatible with v1.x databases\n\n## Timeline\n18-20 weeks total (4-5 months)\n\n## References\n- Automerge: https://automerge.org\n- Yjs: https://docs.yjs.dev\n- Loro: https://loro.dev\n- CRDT theory: Shapiro et al, A comprehensive study of CRDTs\n- Related issues: bd-e6d71828, bd-7a2b58fc,-1","status":"closed","priority":3,"issue_type":"feature","created_at":"2025-10-29T10:23:57.978339-07:00","updated_at":"2025-12-14T12:12:46.52828-08:00","closed_at":"2025-11-08T00:54:51.171319-08:00"} {"id":"bd-71107098","title":"Make two-clone workflow actually work (no hacks)","description":"TestTwoCloneCollision proves beads CANNOT handle two independent clones filing issues simultaneously. This is the basic collaborative workflow and it must work cleanly.\n\nTest location: beads_twoclone_test.go\n\nThe test creates two git clones, both file issues with same ID (test-1), --resolve-collisions remaps clone B's to test-2, but after sync:\n- Clone A has test-1=\"Issue from clone A\", test-2=\"Issue from clone B\" \n- Clone B has test-1=\"Issue from clone B\", test-2=\"Issue from clone A\"\n\nThe TITLES are swapped! Both clones have 2 issues but with opposite title assignments.\n\nWe've tried many fixes (per-project daemons, auto-sync, lamport hashing, precommit hooks) but nothing has made the test pass.\n\nGoal: Make the test pass WITHOUT hacks. The two clones should converge to identical state after sync.","notes":"**Major progress achieved!** The two-clone workflow now converges correctly.\n\n**What was fixed:**\n--3d844c58: Implemented content-hash based rename detection\n- bd-64c05d00.1: Fixed test to compare content not timestamps\n- Both clones now converge to identical issue databases\n- test-1 and test-2 have correct titles in both clones\n- No more title swapping!\n\n**Current status (VERIFIED):**\n✅ Acceptance criteria 1: TestTwoCloneCollision passes (confirmed Oct 28)\n✅ Acceptance criteria 2: Both clones converge to identical issue database (content matches)\n✅ Acceptance criteria 3: No manual conflict resolution required (automatic)\n✅ Acceptance criteria 4: Git status clean\n✅ Acceptance criteria 5: bd ready output identical (timestamps are expected difference)\n\n**ALL ACCEPTANCE CRITERIA MET!** This issue is complete and can be closed.","status":"closed","priority":0,"issue_type":"epic","created_at":"2025-10-28T16:34:53.278793-07:00","updated_at":"2025-10-31T19:38:09.206303-07:00","closed_at":"2025-10-28T19:20:04.143242-07:00"} {"id":"bd-71ky","title":"Fix bd --version and bd completion to work without database","status":"closed","priority":1,"issue_type":"bug","created_at":"2025-11-08T02:06:00.78393-08:00","updated_at":"2025-11-08T02:06:11.452474-08:00","closed_at":"2025-11-08T02:06:11.452474-08:00"}