File bd-srwk: Prevent stale database exports

bd export currently silently overwrites issues.jsonl even when the
database is stale (older than the JSONL file). This causes data loss
in multi-agent workflows.

Real incident from vc project:
- Agent A created 4 discovery epics and exported
- Agent B had stale database and exported, removing those epics
- Required manual recovery

Proposed fix: Check database freshness before export, similar to
VC's ValidateDatabaseFreshness(). Require --force to override.

Priority P1: Silent data loss in common multi-agent scenario.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <noreply@anthropic.com>

.beads/beads.jsonl

@@ -126,7 +126,7 @@
 {"id":"bd-78w","content_hash":"dd79ef79bf68b3a87f3a5b8d50fdfba9d6c6f7e6d728713e37dd34cf9fff835e","title":"Test Epic 2","description":"## Overview\n\n[Describe the high-level goal and scope of this epic]\n\n## Success Criteria\n\n- [ ] Criteria 1\n- [ ] Criteria 2\n- [ ] Criteria 3\n\n## Background\n\n[Provide context and motivation]\n\n## Scope\n\n**In Scope:**\n- Item 1\n- Item 2\n\n**Out of Scope:**\n- Item 1\n- Item 2\n","design":"## Architecture\n\n[Describe the overall architecture and approach]\n\n## Components\n\n- Component 1: [description]\n- Component 2: [description]\n\n## Dependencies\n\n[List external dependencies or constraints]\n","acceptance_criteria":"- [ ] All child issues are completed\n- [ ] Integration tests pass\n- [ ] Documentation is updated\n- [ ] Code review completed\n","status":"closed","priority":1,"issue_type":"epic","created_at":"2025-11-03T20:15:03.878216-08:00","updated_at":"2025-11-05T00:25:06.566242-08:00","closed_at":"2025-11-05T00:25:06.566242-08:00","source_repo":".","labels":["epic"]}
 {"id":"bd-7a00c94e","content_hash":"b31566a4b2a84db7d24364492e8ac6ebfa1f5fc27fe270fbd58b27e17218c9c4","title":"Rapid 2","description":"","status":"open","priority":3,"issue_type":"task","created_at":"2025-10-29T19:11:57.430725-07:00","updated_at":"2025-10-30T17:12:58.189251-07:00","source_repo":"."}
 {"id":"bd-7a2b58fc","content_hash":"02b9e5c0f7a58576876637f09cf67a97d180686a216d53b15351ca2c099c8e5f","title":"Implement clone-scoped ID allocation to prevent N-way collisions","description":"## Problem\nCurrent ID allocation uses per-clone atomic counters (issue_counters table) that sync based on local database state. In N-way collision scenarios:\n- Clone B sees {test-1} locally, allocates test-2\n- Clone D sees {test-1, test-2, test-3} locally, allocates test-4\n- When same content gets assigned test-2 and test-4, convergence fails\n\nRoot cause: Each clone independently allocates IDs without global coordination, leading to overlapping assignments for the same content.\n\n## Solution\nAdd clone UUID to ID allocation to make every ID globally unique:\n\n**Current format:** `test-1`, `test-2`, `test-3`\n**New format:** `test-1-a7b3`, `test-2-a7b3`, `test-3-c4d9`\n\nWhere suffix is first 4 chars of clone UUID.\n\n## Implementation\n\n### 1. Add clone_identity table\n```sql\nCREATE TABLE clone_identity (\n    clone_uuid TEXT PRIMARY KEY,\n    created_at DATETIME DEFAULT CURRENT_TIMESTAMP\n);\n```\n\n### 2. Modify getNextIDForPrefix()\n```go\nfunc (s *SQLiteStorage) getNextIDForPrefix(ctx context.Context, prefix string) (string, error) {\n    cloneUUID := s.getOrCreateCloneUUID(ctx)\n    shortUUID := cloneUUID[:4]\n    \n    nextNum := s.getNextCounterForPrefix(ctx, prefix)\n    return fmt.Sprintf(\"%s-%d-%s\", prefix, nextNum, shortUUID), nil\n}\n```\n\n### 3. Update ID parsing logic\nAll places that parse IDs (utils.ExtractIssueNumber, etc.) need to handle new format.\n\n### 4. Migration strategy\n- Existing IDs remain unchanged (no suffix)\n- New IDs get clone suffix automatically\n- Display layer can hide suffix in UI: `bd-cb64c226.3-a7b3` → `#42`\n\n## Benefits\n- **Zero collision risk**: Same content in different clones gets different IDs\n- **Maintains readability**: Still sequential numbering within clone\n- **No coordination needed**: Works offline, no central authority\n- **Scales to 100+ clones**: 4-char hex = 65,536 unique clones\n\n## Concerns\n- ID format change may break existing integrations\n- Need migration path for existing databases\n- Display logic needs update to hide/show suffixes appropriately\n\n## Success Criteria\n- 10+ clone collision test passes without failures\n- Existing issues continue to work (backward compatibility)\n- Documentation updated with new ID format\n- Migration guide for v1.x → v2.x\n\n## Timeline\nMedium-term (v1.1-v1.2), 2-3 weeks implementation\n\n## References\n- Related to bd-0dcea000 (immediate fix)\n- See beads_nway_test.go for failing N-way tests","status":"closed","priority":2,"issue_type":"feature","created_at":"2025-10-29T20:02:47.952447-07:00","updated_at":"2025-11-06T19:37:39.599276-08:00","closed_at":"2025-11-06T19:27:29.41629-08:00","source_repo":"."}
-{"id":"bd-7bbc4e6a","content_hash":"3251d757d9ad69cd4b3517862ec1b9b1cc13388ea4c93a2f3b2b54920112854f","title":"Add MCP server functions for repair commands","description":"Expose new repair commands via MCP server for agent access:\n\nFunctions to add:\n- beads_repair_deps()\n- beads_detect_pollution()\n- beads_validate()\n- beads_resolve_conflicts() (when implemented)\n\nUpdate integrations/beads-mcp/src/beads_mcp/server.py\n\nSee repair_commands.md lines 803-884 for design.","status":"open","priority":2,"issue_type":"task","created_at":"2025-10-28T19:37:55.72639-07:00","updated_at":"2025-10-30T17:12:58.179948-07:00","source_repo":"."}
+{"id":"bd-7bbc4e6a","content_hash":"afe6e542e605c8ecbd7524a81def6bce17f5df9bcfca5080fdf832cefb461084","title":"Add MCP server functions for repair commands","description":"Expose new repair commands via MCP server for agent access:\n\nFunctions to add:\n- beads_repair_deps()\n- beads_detect_pollution()\n- beads_validate()\n- beads_resolve_conflicts() (when implemented)\n\nUpdate integrations/beads-mcp/src/beads_mcp/server.py\n\nSee repair_commands.md lines 803-884 for design.","notes":"Implemented all three MCP server functions:\n\n1. **repair_deps(fix=False)** - Find/fix orphaned dependencies\n2. **detect_pollution(clean=False)** - Detect/clean test issues  \n3. **validate(checks=None, fix_all=False)** - Run comprehensive health checks\n\nChanges:\n- Added abstract methods to BdClientBase\n- Implemented in BdCliClient (CLI execution)\n- Added NotImplementedError stubs in BdDaemonClient (falls back to CLI)\n- Created wrapper functions in tools.py\n- Registered @mcp.tool decorators in server.py\n\nAll commands tested and working with --no-daemon flag.","status":"closed","priority":2,"issue_type":"task","created_at":"2025-10-28T19:37:55.72639-07:00","updated_at":"2025-11-07T19:38:12.152437-08:00","closed_at":"2025-11-07T19:38:12.152437-08:00","source_repo":"."}
 {"id":"bd-7bd2","content_hash":"3e2921e120a51c2ed88f11db427d6620b0c12ba5526c0023ce96b3abf3ece0f3","title":"Complete remaining sync branch daemon tests","description":"4 remaining test scenarios in daemon_sync_branch_test.go need completion:\n\n⚠️ MINOR FIXES (apply same pattern as TestSyncBranchCommitAndPush_Success):\n1. TestSyncBranchCommitAndPush_NoChanges\n   - Reorder: call initMainBranch() BEFORE creating JSONL\n   - Pattern: init branch → create issue → export JSONL → test\n\n2. TestSyncBranchCommitAndPush_WorktreeHealthCheck\n   - Same reordering needed\n   - Verify worktree corruption detection and auto-repair\n\n🔧 MORE WORK NEEDED (remote branch setup):\n3. TestSyncBranchPull_Success\n   - Issue: remote doesn't have sync branch after push\n   - Need to verify branch is pushed to remote correctly\n   - Then test pull from clone2\n\n4. TestSyncBranchIntegration_EndToEnd\n   - Full workflow: Agent A commits → Agent B pulls → Agent B commits → Agent A pulls\n   - Same remote branch issue\n\nPattern to apply (from TestSyncBranchCommitAndPush_Success):\n- Call initMainBranch(t, dir) BEFORE creating issues/JSONL\n- This ensures sync branch worktree has changes to commit\n\nAcceptance:\n- All 7 tests pass\n- go test -v -run TestSyncBranch ./cmd/bd/ succeeds","status":"closed","priority":2,"issue_type":"task","created_at":"2025-11-02T16:29:29.044162-08:00","updated_at":"2025-11-02T16:39:53.277529-08:00","closed_at":"2025-11-02T16:39:53.277529-08:00","source_repo":".","dependencies":[{"issue_id":"bd-7bd2","depends_on_id":"bd-502e","type":"discovered-from","created_at":"2025-11-02T16:29:29.045104-08:00","created_by":"stevey"}]}
 {"id":"bd-7e7ddffa","content_hash":"80a5b60d066d509bbd8d0f1340a16ea1d989d9178910155da3ff2c8df245b9c9","title":"Repair Commands \u0026 AI-Assisted Tooling","description":"Add specialized repair tools to reduce agent repair burden:\n1. Git merge conflicts in JSONL\n2. Duplicate issues from parallel work\n3. Semantic inconsistencies\n4. Orphaned references\n\nSee ~/src/fred/beads/repair_commands.md for full design doc.\n\nReduces agent repair time from 5-10 minutes to \u003c30 seconds per repair.","status":"closed","priority":1,"issue_type":"epic","created_at":"2025-10-28T19:30:17.465812-07:00","updated_at":"2025-11-02T16:40:51.866302-08:00","closed_at":"2025-11-02T16:40:51.866302-08:00","source_repo":"."}
 {"id":"bd-7e7ddffa.1","content_hash":"3ab290915c117ec902bda1761e8c27850512f3fd4b494a93546c44b397d573a3","title":"bd resolve-conflicts - Git merge conflict resolver","description":"Automatically resolve JSONL merge conflicts.\n\nModes:\n- Mechanical: ID remapping (no AI)\n- AI-assisted: Smart merge/keep decisions\n- Interactive: Review each conflict\n\nHandles \u003c\u003c\u003c\u003c\u003c\u003c\u003c conflict markers in .beads/beads.jsonl\n\nFiles: cmd/bd/resolve_conflicts.go (new)","status":"closed","priority":1,"issue_type":"task","created_at":"2025-10-28T14:48:30.083642-07:00","updated_at":"2025-11-02T16:40:46.620251-08:00","closed_at":"2025-11-02T16:40:46.620251-08:00","source_repo":".","dependencies":[{"issue_id":"bd-7e7ddffa.1","depends_on_id":"bd-7e7ddffa","type":"parent-child","created_at":"2025-10-29T19:58:28.847736-07:00","created_by":"stevey"}]}
@@ -317,6 +317,7 @@
 {"id":"bd-ry1u","content_hash":"013464efc3cf53d47c2a170040c66099ce77b13d3d1b34c3729e6a5208122799","title":"Publish official devcontainer configuration","description":"","design":"Problem: GH issue #229 shows git hooks aren't available in devcontainers because bd CLI isn't installed. Solution: Provide official .devcontainer/devcontainer.json that installs Go, builds bd from source, runs bd init --quiet, and installs hooks automatically. Benefits: New contributors start immediately, AI assistants work out-of-box, no manual setup. Implementation: Create .devcontainer/devcontainer.json with Go feature, postCreateCommand to build bd and install hooks, environment variables. Acceptance: Container builds with bd installed, hooks functional, documentation updated, tested with Codespaces and VSCode.","notes":"Devcontainer configuration implemented. Manual testing required in actual devcontainer environment (Codespaces or VSCode Remote Containers). All code changes complete, tests pass, linting clean.","status":"closed","priority":2,"issue_type":"epic","created_at":"2025-11-05T15:02:21.783666-08:00","updated_at":"2025-11-05T17:52:53.019917-08:00","closed_at":"2025-11-05T17:46:42.70998-08:00","source_repo":"."}
 {"id":"bd-s02","content_hash":"911d456e4dabae028dd615b643c99058ef12e55ea523cb81cc933783c7b13546","title":"Manual task","description":"","status":"open","priority":2,"issue_type":"task","created_at":"2025-11-03T20:15:10.022202-08:00","updated_at":"2025-11-03T20:15:10.022202-08:00","source_repo":"."}
 {"id":"bd-sjmr","content_hash":"31947009877c3246620f5ca4af142234e4e8f43d5a350e80a8b3e37898e81f6a","title":"Fix inconsistent error handling in multi-repo deletion tracking","description":"From bd-xo6b code review: Multi-repo deletion tracking has mixed failure modes that can leave system in inconsistent state.\n\n**Current behavior (daemon_sync.go):**\n- Snapshot capture (L505-514): Hard fail → aborts sync\n- Merge/prune (L575-584): Hard fail → aborts sync  \n- Base snapshot update (L613-619): Soft fail → logs warning, continues\n\n**Critical problem:**\nIf merge fails on repo 3 of 5:\n- Repos 1-2 have already merged and deleted issues (irreversible)\n- Repos 3-5 are untouched\n- Database is in partially-updated state\n- No rollback mechanism\n\n**Real-world scenario:**\n```\nSync with repos [A, B, C]:\n1. Capture snapshots A ✓, B ✓, C ✗ → ABORT (good)\n2. Merge A ✓, B ✗ → ABORT but A already deleted issues (BAD - no rollback)\n3. Update base A ⚠, B ⚠ → Warnings only (inconsistent with 1 \u0026 2)\n```\n\n**Solution options:**\n1. **Two-phase commit:**\n   - Phase 1: Validate all repos (check files exist, readable, parseable)\n   - Phase 2: Apply changes atomically (or fail entirely before any mutations)\n\n2. **Fail-fast validation:**\n   - Before any snapshot/merge operations, validate all repos upfront\n   - Abort entire sync if any repo fails validation\n\n3. **Make base snapshot update consistent:**\n   - Either make it hard-fail like the others, or make all soft-fail\n\n**Files:**\n- cmd/bd/daemon_sync.go:505-514 (snapshot capture)\n- cmd/bd/daemon_sync.go:575-584 (merge/prune)\n- cmd/bd/daemon_sync.go:613-619 (base snapshot update)\n\n**Recommendation:** Use option 1 (two-phase) or option 2 (fail-fast validation) + fix base snapshot inconsistency.","status":"closed","priority":1,"issue_type":"bug","created_at":"2025-11-06T19:31:29.538092-08:00","updated_at":"2025-11-06T19:35:41.268584-08:00","closed_at":"2025-11-06T19:35:41.268584-08:00","source_repo":".","dependencies":[{"issue_id":"bd-sjmr","depends_on_id":"bd-xo6b","type":"discovered-from","created_at":"2025-11-06T19:32:12.310033-08:00","created_by":"daemon"}]}
+{"id":"bd-srwk","content_hash":"9bf65cf1bc02d15a26da0948692b28f8e57e08e09ca63d3f7ba035fde047d96f","title":"bd export should detect and prevent stale database exports","description":"## Problem\n\nWhen `bd export` is run with a stale database (older than issues.jsonl), it silently overwrites the JSONL file with stale data, causing data loss.\n\n## What Happened (vc project)\n\n1. Agent A created 4 new issues and exported to issues.jsonl (commit 99a9d58)\n2. Agent A closed an issue and exported again (commit 58b4613) - JSONL now has 4 epics\n3. Agent B had stale database (from before step 1)\n4. Agent B worked on unrelated issue and exported (commit 0609233)\n5. Agent B's export **overwrote issues.jsonl**, removing the 4 epics created by Agent A\n6. Required manual recovery by re-exporting from Agent A's correct database\n\n## Expected Behavior\n\n`bd export` should detect that the database is stale and either:\n- **Refuse to export** with error message explaining the issue\n- **Warn prominently** and require explicit --force flag to override\n- **Auto-import first** to sync database before exporting\n\n## How to Detect Staleness\n\nCompare modification times (similar to VC's ValidateDatabaseFreshness):\n1. Check .db, .db-wal, .db-shm timestamps (use newest for WAL mode)\n2. Check issues.jsonl timestamp\n3. If JSONL is newer by \u003e1 second: database is stale\n\n## Suggested Fix\n\nAdd staleness check in `bd export`:\n\n```go\nfunc Export(dbPath, jsonlPath string, force bool) error {\n    // Check if database is stale\n    if !force {\n        if err := checkDatabaseFreshness(dbPath, jsonlPath); err != nil {\n            return fmt.Errorf(\"database is stale: %w\\n\" +\n                \"Run 'bd import %s' first to sync, or use --force to override\",\n                err, jsonlPath)\n        }\n    }\n    \n    // Proceed with export...\n}\n```\n\n## Impact\n\n- **Severity**: High (silent data loss)\n- **Frequency**: Happens in multi-agent workflows when agents don't sync\n- **Workaround**: Manual recovery (re-export from correct database)\n\n## References\n\n- VC issue tracker: commits 58b4613 -\u003e 0609233 -\u003e c41c638\n- VC has similar check: `storage.ValidateDatabaseFreshness()`\n- Tolerance: 1 second (handles filesystem timestamp precision)","acceptance_criteria":"1. bd export detects stale database (JSONL newer than DB)\n2. Refuses to export with clear error message\n3. Suggests running 'bd import' first\n4. --force flag allows override with warning\n5. Tolerates filesystem timestamp precision (1 second)\n6. Works correctly with WAL mode (.db-wal files)\n7. Test coverage for staleness detection\n8. Documentation updated with export safety warnings","status":"open","priority":1,"issue_type":"bug","created_at":"2025-11-07T19:39:24.172154-08:00","updated_at":"2025-11-07T19:39:24.172154-08:00","source_repo":"."}
 {"id":"bd-tmdx","content_hash":"3ecb07e74eaa468c9fc7a1c6e1c4547182267785b9dbc7998f031d71552842cf","title":"Investigate database pollution - unexpected issue count increases","description":"Two repositories showing unexpected issue counts:\n- ~/src/beads: 280 issues (expected ~209-220)\n- ~/src/dave/beads: 895 issues (675 open, 149 closed)\n\nThis suggests database pollution - issues from one repository leaking into another. Need to investigate:\n1. Run bd detect-pollution on both repos\n2. Check for cross-repo contamination\n3. Identify source of pollution (daemon? multi-repo config? import issues?)\n4. Clean up polluted databases\n5. Prevent future pollution","status":"closed","priority":0,"issue_type":"bug","created_at":"2025-11-06T22:50:16.957689-08:00","updated_at":"2025-11-07T00:05:38.994405-08:00","closed_at":"2025-11-07T00:05:38.994405-08:00","source_repo":"."}
 {"id":"bd-tuqd","content_hash":"06ac95944f03d871a6f58d2cd63796828873e92ef7c9b897eb639d28860a458e","title":"bd init overwrites existing git hooks without detection or chaining","description":"GH #254: bd init silently overwrites existing git hooks (like pre-commit framework) without detecting them, backing them up, or offering to chain. This breaks workflows and can result in committed code with failing tests.\n\nFix: Detect existing hooks, prompt user with options to chain/overwrite/skip.","status":"closed","priority":0,"issue_type":"bug","created_at":"2025-11-07T15:51:17.582882-08:00","updated_at":"2025-11-07T15:55:01.330531-08:00","closed_at":"2025-11-07T15:55:01.330531-08:00","source_repo":"."}
 {"id":"bd-twlr","content_hash":"85bb87aa0a7988bf3399b1ebfe3115302aa9e487097415cb8573cd8aad7392c2","title":"Add bd init --team wizard","description":"Interactive wizard for team workflow setup. Guides user through: branch workflow configuration, shared repo setup, team member onboarding, examples of team collaboration patterns.","status":"closed","priority":1,"issue_type":"task","created_at":"2025-11-05T18:04:30.013645-08:00","updated_at":"2025-11-05T18:56:03.004161-08:00","closed_at":"2025-11-05T18:56:03.004161-08:00","source_repo":".","dependencies":[{"issue_id":"bd-twlr","depends_on_id":"bd-8rd","type":"parent-child","created_at":"2025-11-05T18:04:39.164445-08:00","created_by":"daemon"}]}