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bd sync: 2025-12-23 12:06:48

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Steve Yegge
2025-12-23 12:06:48 -08:00
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{"id":"bd-28db","title":"Add 'bd status' command for issue database overview","description":"Implement a bd status command that provides a quick snapshot of the issue database state, similar to how git status shows working tree state.\n\nExpected output: Show summary including counts by state (open, in-progress, blocked, closed), recent activity (last 7 days), and quick overview without needing multiple queries.\n\nExample output showing issue counts, recent activity stats, and pointer to bd list for details.\n\nProposed options: --all (show all issues), --assigned (show issues assigned to current user), --json (JSON format output)\n\nUse cases: Quick project health check, onboarding for new contributors, integration with shell prompts or CI/CD, daily standup reference","status":"closed","priority":2,"issue_type":"feature","created_at":"2025-11-02T17:25:59.203549-08:00","updated_at":"2025-12-21T17:54:00.205191-08:00","closed_at":"2025-12-21T17:54:00.205191-08:00","close_reason":"Already implemented - bd status shows summary and activity"}
{"id":"bd-29fb","title":"Implement bd close --continue flag","description":"Auto-advance to next step in molecule when closing an issue. Referenced by gt-um6q, gt-lz13. Needed for molecule navigation workflow.","status":"closed","priority":1,"issue_type":"feature","created_at":"2025-12-23T00:17:55.032875-08:00","updated_at":"2025-12-23T01:26:47.255313-08:00","closed_at":"2025-12-23T01:26:47.255313-08:00","close_reason":"Already implemented: --continue flag auto-advances to next step in molecule, --no-auto prevents auto-claiming"}
{"id":"bd-2ep8","title":"Update CHANGELOG.md with release notes","description":"Add meaningful release notes to CHANGELOG.md describing what changed in 0.30.7","status":"closed","priority":1,"issue_type":"task","created_at":"2025-12-19T22:56:48.649053-08:00","updated_at":"2025-12-19T22:57:31.69559-08:00","closed_at":"2025-12-19T22:57:31.69559-08:00","dependencies":[{"issue_id":"bd-2ep8","depends_on_id":"bd-8pyn","type":"parent-child","created_at":"2025-12-19T22:56:48.650816-08:00","created_by":"stevey"},{"issue_id":"bd-2ep8","depends_on_id":"bd-rupw","type":"blocks","created_at":"2025-12-19T22:56:48.651136-08:00","created_by":"stevey"}]}
{"id":"bd-2l03","title":"Implement await type handlers (gh:run, gh:pr, timer, human, mail)","description":"Implement condition checking for each await type.\n\n## Handlers Needed\n- gh:run:\u003cid\u003e - Check GitHub Actions run status via gh CLI\n- gh:pr:\u003cid\u003e - Check PR merged/closed status via gh CLI \n- timer:\u003cduration\u003e - Simple elapsed time check\n- human:\u003cprompt\u003e - Check for human approval (via mail?)\n- mail:\u003cpattern\u003e - Check for mail matching pattern\n\n## Implementation Location\nThis is Deacon logic, so likely in Gas Town (gt) not beads.\n\n## Interface\n```go\ntype AwaitHandler interface {\n Check(awaitID string) (completed bool, result string, err error)\n}\n```","status":"open","priority":2,"issue_type":"task","created_at":"2025-12-23T11:44:38.492837-08:00","updated_at":"2025-12-23T11:44:38.492837-08:00","dependencies":[{"issue_id":"bd-2l03","depends_on_id":"bd-udsi","type":"parent-child","created_at":"2025-12-23T11:44:52.990746-08:00","created_by":"daemon"},{"issue_id":"bd-2l03","depends_on_id":"bd-is6m","type":"blocks","created_at":"2025-12-23T11:44:56.510792-08:00","created_by":"daemon"}]}
{"id":"bd-2oo","title":"Edge Schema Consolidation: Unify all edges in dependencies table","description":"Consolidate all edge types into the dependency table per decision 004.\n\n## Changes\n- Add metadata column to dependencies table\n- Add thread_id column for conversation grouping\n- Remove redundant Issue fields: replies_to, relates_to, duplicate_of, superseded_by\n- Update all code to use dependencies API\n- Migration script for existing data\n- JSONL format change (breaking)\n\nReference: ~/gt/hop/decisions/004-edge-schema-consolidation.md","status":"closed","priority":0,"issue_type":"epic","created_at":"2025-12-18T02:01:48.785558-08:00","updated_at":"2025-12-18T02:49:10.61237-08:00","closed_at":"2025-12-18T02:49:10.61237-08:00","close_reason":"Phase 4 complete: all edge fields removed, dependencies API used exclusively"}
{"id":"bd-2oo.1","title":"Add metadata and thread_id columns to dependencies table","description":"Schema changes:\n- ALTER TABLE dependencies ADD COLUMN metadata TEXT DEFAULT '{}'\n- ALTER TABLE dependencies ADD COLUMN thread_id TEXT DEFAULT ''\n- CREATE INDEX idx_dependencies_thread ON dependencies(thread_id) WHERE thread_id != ''","status":"closed","priority":0,"issue_type":"task","created_at":"2025-12-18T02:02:00.468223-08:00","updated_at":"2025-12-18T02:49:10.575133-08:00","closed_at":"2025-12-18T02:49:10.575133-08:00","close_reason":"Phase 4 complete: all edge fields removed, dependencies API used exclusively","dependencies":[{"issue_id":"bd-2oo.1","depends_on_id":"bd-2oo","type":"parent-child","created_at":"2025-12-18T02:02:00.470012-08:00","created_by":"daemon","metadata":"{}"}]}
{"id":"bd-2oo.2","title":"Remove redundant edge fields from Issue struct","description":"Remove from Issue struct:\n- RepliesTo -\u003e dependency with type replies-to\n- RelatesTo -\u003e dependencies with type relates-to \n- DuplicateOf -\u003e dependency with type duplicates\n- SupersededBy -\u003e dependency with type supersedes\n\nKeep: Sender, Ephemeral (these are attributes, not relationships)","status":"closed","priority":0,"issue_type":"task","created_at":"2025-12-18T02:02:00.891206-08:00","updated_at":"2025-12-18T02:49:10.584381-08:00","closed_at":"2025-12-18T02:49:10.584381-08:00","close_reason":"Phase 4 complete: all edge fields removed, dependencies API used exclusively","dependencies":[{"issue_id":"bd-2oo.2","depends_on_id":"bd-2oo","type":"parent-child","created_at":"2025-12-18T02:02:00.891655-08:00","created_by":"daemon","metadata":"{}"}]}
{"id":"bd-2oo.3","title":"Update all code to use dependencies API for edges","description":"Find and update all code that reads/writes:\n- replies_to field -\u003e use dependency API\n- relates_to field -\u003e use dependency API\n- duplicate_of field -\u003e use dependency API\n- superseded_by field -\u003e use dependency API\n\nCommands affected: bd mail, bd relate, bd duplicate, bd supersede, bd show, etc.","status":"closed","priority":0,"issue_type":"task","created_at":"2025-12-18T02:02:01.317006-08:00","updated_at":"2025-12-18T02:49:10.59233-08:00","closed_at":"2025-12-18T02:49:10.59233-08:00","close_reason":"Phase 4 complete: all edge fields removed, dependencies API used exclusively","dependencies":[{"issue_id":"bd-2oo.3","depends_on_id":"bd-2oo","type":"parent-child","created_at":"2025-12-18T02:02:01.31856-08:00","created_by":"daemon","metadata":"{}"}]}
{"id":"bd-2oo.4","title":"Create migration script for edge field to dependency conversion","description":"Migration must:\n1. Read existing JSONL with old fields\n2. Convert field values to dependency records\n3. Write updated JSONL without old fields\n4. Handle edge cases (missing refs, duplicates)\n\nRun via: bd migrate or automatic on bd prime","status":"closed","priority":0,"issue_type":"task","created_at":"2025-12-18T02:02:01.760277-08:00","updated_at":"2025-12-18T02:49:10.602446-08:00","closed_at":"2025-12-18T02:49:10.602446-08:00","close_reason":"Phase 4 complete: all edge fields removed, dependencies API used exclusively","dependencies":[{"issue_id":"bd-2oo.4","depends_on_id":"bd-2oo","type":"parent-child","created_at":"2025-12-18T02:02:01.760694-08:00","created_by":"daemon","metadata":"{}"}]}
{"id":"bd-2q6d","title":"Beads commands operate on stale database without warning","description":"All beads read operations should validate database is in sync with JSONL before proceeding.\n\n**Current Behavior:**\n- Commands can query/read from stale database\n- Only mutation operations (like 'bd sync') check if JSONL is newer\n- User gets incorrect results without realizing database is out of sync\n\n**Expected Behavior:**\n- All beads commands should have pre-flight check for database freshness\n- If JSONL is newer than database, refuse to operate with error: \"Database out of sync. Run 'bd import' first.\"\n- Same safety check that exists for 'bd sync' should apply to ALL operations\n\n**Impact:**\n- Users make decisions based on incomplete/outdated data\n- Silent failures lead to confusion (e.g., thinking issues don't exist when they do)\n- Similar to running git commands on stale repo without being warned to pull\n\n**Example:**\n- Searched for bd-g9eu issue file: not found\n- Issue exists in .beads/issues.jsonl (in git)\n- Database was stale, but no warning was given\n- Led to incorrect conclusion that issue was already closed/deleted","notes":"## Implementation Complete\n\n**Phase 1: Created staleness check (cmd/bd/staleness.go)**\n- ensureDatabaseFresh() function checks JSONL mtime vs last_import_time\n- Returns error with helpful message when database is stale\n- Auto-skips in daemon mode (daemon has auto-import)\n\n**Phase 2: Added to all read commands**\n- list, show, ready, status, stale, info, duplicates, validate\n- Check runs before database queries in direct mode\n- Daemon mode already protected via checkAndAutoImportIfStale()\n\n**Phase 3: Code Review Findings**\nSee follow-up issues:\n- bd-XXXX: Add warning when staleness check errors\n- bd-YYYY: Improve CheckStaleness error handling\n- bd-ZZZZ: Refactor redundant daemon checks (low priority)\n\n**Testing:**\n- Build successful: go build ./cmd/bd\n- Binary works: ./bd --version\n- Ready for manual testing\n\n**Next Steps:**\n1. Test with stale database scenario\n2. Implement review improvements\n3. Close issue when tests pass","status":"closed","priority":1,"issue_type":"bug","created_at":"2025-11-20T19:33:40.019297-05:00","updated_at":"2025-12-17T23:13:40.535149-08:00","closed_at":"2025-12-17T19:11:12.982639-08:00"}
{"id":"bd-2v0f","title":"Add gate issue type to beads","description":"Add 'gate' as a new issue type for async coordination.\n\n## Changes Needed\n- Add 'gate' to IssueType enum in internal/types/types.go\n- Update validation to accept gate type\n- Update CLI help text and completion\n\n## Gate Type Semantics\n- Gates are ephemeral (live in wisp storage)\n- Managed by Deacon patrol\n- Have special fields: await_type, await_id, timeout, waiters[]","status":"closed","priority":1,"issue_type":"task","created_at":"2025-12-23T11:44:31.331897-08:00","updated_at":"2025-12-23T11:47:06.287781-08:00","closed_at":"2025-12-23T11:47:06.287781-08:00","close_reason":"Added TypeGate constant and IsValid() validation. Updated CLI help text in create.go, list.go, show.go, search.go, count.go, export.go.","dependencies":[{"issue_id":"bd-2v0f","depends_on_id":"bd-udsi","type":"parent-child","created_at":"2025-12-23T11:44:52.659005-08:00","created_by":"daemon"}]}
{"id":"bd-2vh3","title":"Ephemeral issue cleanup and history compaction","description":"## Problem\n\nBeads history grows without bound. Every message, handoff, work assignment\nstays in issues.jsonl forever. Enterprise users will balk at \"git as database.\"\n\n## Solution: Two-Tier Cleanup\n\n### Tier 1: Ephemeral Cleanup (v1)\n\nbd cleanup --ephemeral --closed\n\n- Deletes closed issues where ephemeral=true from issues.jsonl\n- Safe: only removes explicitly marked ephemeral + closed\n- Preserves git history (commits still exist)\n- Run after swarm completion\n\n### Tier 2: History Compaction (v2)\n\nbd compact --squash\n\n- Rewrites issues.jsonl to remove tombstones\n- Optionally squashes git history (interactive rebase equivalent)\n- Preserves Merkle proofs for deleted items\n- Advanced: cold storage tiering\n\n## HOP Context\n\n| Layer | HOP Role | Persistence |\n|-------|----------|-------------|\n| Execution trace | None | Ephemeral |\n| Work scaffolding | None | Summarizable |\n| Work outcome | CV entry | Permanent |\n| Validation record | Stake proof | Permanent |\n\n\"Execution is ephemeral. Outcomes are permanent. You can't squash your CV.\"\n\n## Success Criteria\n\n- After cleanup --ephemeral: issues.jsonl only contains persistent work\n- Work outcomes preserved (CV entries)\n- Validation records preserved (stake proofs)\n- Execution scaffolding removed (transient coordination)","notes":"## Implementation Plan (REVISED after code review)\n\nSee history/EPHEMERAL_MOLECULES_DESIGN.md for comprehensive design + review.\n\n## Key Simplification\n\nAfter code review, Tier 1 is MUCH simpler than originally designed:\n\n- **Original**: Separate ephemeral repo with routing.ephemeral config\n- **Revised**: Just set Wisp: true in cloneSubgraph()\n\nThe wisp field and bd cleanup --wisp already exist\\!\n\n## Child Tasks (in dependency order)\n\n1. **bd-2vh3.2**: Tier 1 - Ephemeral spawning (SIMPLIFIED) [READY]\n - Just add Wisp: true to template.go:474\n - Add --persistent flag to opt out\n2. **bd-2vh3.3**: Tier 2 - Basic bd mol squash command\n3. **bd-2vh3.4**: Tier 3 - AI-powered squash summarization\n4. **bd-2vh3.5**: Tier 4 - Auto-squash on molecule completion\n5. **bd-2vh3.6**: Tier 5 - JSONL archive rotation (DEFERRED: post-1.0)\n\n## What Already Exists\n\n| Component | Location |\n|-----------|----------|\n| Ephemeral field | internal/types/types.go:45 |\n| bd cleanup --wisp | cmd/bd/cleanup.go:72 |\n| cloneSubgraph() | cmd/bd/template.go:456 |\n| loadTemplateSubgraph() | cmd/bd/template.go |\n\n## HOP Alignment\n\n'Execution is ephemeral. Outcomes are permanent. You can't squash your CV.'","status":"closed","priority":1,"issue_type":"feature","created_at":"2025-12-20T21:02:20.101367-08:00","updated_at":"2025-12-21T17:50:02.958155-08:00","closed_at":"2025-12-21T17:50:02.958155-08:00","close_reason":"Core feature complete: bd cleanup --wisp works, molecules marked as wisps. bd-2vh3.6 (archive rotation) deferred post-1.0."}
{"id":"bd-2vh3.1","title":"Tier 1: Ephemeral repo routing","description":"Add routing.ephemeral config option to route ephemeral=true issues to separate location.\n\n## Changes Required\n\n1. Add `routing.ephemeral` config option (default: empty = disabled)\n2. Update routing logic in `determineRepo()` to check ephemeral flag\n3. Update `bd create` to respect ephemeral routing\n4. Update import/export for multi-location support\n5. Ephemeral repo can be:\n - Separate git repo (~/.beads-ephemeral)\n - Non-git directory (just filesystem)\n - Same repo, different branch (future)\n\n## Config\n\n```bash\nbd config set routing.ephemeral \"~/.beads-ephemeral\"\n```\n\n## Acceptance Criteria\n\n- `bd create \"test\" --ephemeral` creates in ephemeral repo when configured\n- `bd list` shows issues from both repos\n- Ephemeral repo never synced to remote","status":"tombstone","priority":1,"issue_type":"task","created_at":"2025-12-21T12:57:26.648052-08:00","updated_at":"2025-12-21T12:59:01.815357-08:00","deleted_at":"2025-12-21T12:59:01.815357-08:00","deleted_by":"stevey","delete_reason":"manual delete","original_type":"task"}
{"id":"bd-2vh3.2","title":"Tier 1: Ephemeral repo routing","description":"Simplified: Make mol spawn set ephemeral=true on spawned issues.\n\n## The Fix\n\nModify cloneSubgraph() in template.go to set Ephemeral: true:\n\n```go\n// template.go:474\nnewIssue := \u0026types.Issue{\n Title: substituteVariables(oldIssue.Title, vars),\n // ... existing fields ...\n Ephemeral: true, // ADD THIS LINE\n}\n```\n\n## Optional: Add --persistent flag\n\nAdd flag to bd mol spawn for when you want spawned issues to persist:\n\n```bash\nbd mol spawn mol-code-review --var pr=123 # ephemeral (default)\nbd mol spawn mol-code-review --var pr=123 --persistent # not ephemeral\n```\n\n## Why This Is Simpler Than Original Design\n\nOriginal design proposed separate ephemeral repo routing. After code review:\n\n- Ephemeral field already exists in schema\n- bd cleanup --ephemeral already works\n- No new config needed\n- No multi-repo complexity\n\n## Acceptance Criteria\n\n- bd mol spawn creates issues with ephemeral=true\n- bd cleanup --ephemeral -f deletes them after closing\n- --persistent flag opts out of ephemeral\n- Existing molecules continue to work","status":"closed","priority":1,"issue_type":"task","created_at":"2025-12-21T12:57:36.661604-08:00","updated_at":"2025-12-21T13:43:22.990244-08:00","closed_at":"2025-12-21T13:43:22.990244-08:00","close_reason":"Implemented: mol spawn now creates ephemeral issues by default. Use --persistent to opt out. Changes in template.go, mol.go, mol_spawn.go, mol_bond.go, mol_run.go.","dependencies":[{"issue_id":"bd-2vh3.2","depends_on_id":"bd-2vh3","type":"parent-child","created_at":"2025-12-21T12:57:36.662118-08:00","created_by":"stevey"}]}
@@ -253,6 +255,7 @@
{"id":"bd-ipva","title":"Update go install bd to 0.33.2","description":"Rebuild and install bd to ~/go/bin:\n\n```bash\ngo install ./cmd/bd\n~/go/bin/bd version # Verify shows 0.33.2\n```\n\nNote: If ~/go/bin is in PATH before /opt/homebrew/bin, this is the version that runs by default.","status":"tombstone","priority":1,"issue_type":"task","created_at":"2025-12-21T16:10:13.760715-08:00","updated_at":"2025-12-21T17:29:31.791368-08:00","close_reason":"Local dev build used instead of go install","deleted_at":"2025-12-21T17:29:31.791368-08:00","deleted_by":"batch delete","delete_reason":"batch delete","original_type":"task","wisp":true}
{"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","priority":0,"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-is6m","title":"Add gate checking to Deacon patrol loop","description":"Integrate gate checking into Deacon's patrol cycle.\n\n## Patrol Integration\n```go\nfunc (d *Deacon) checkGates(ctx context.Context) {\n gates, _ := d.store.ListOpenGates(ctx)\n \n for _, gate := range gates {\n // Check timeout\n if time.Since(gate.CreatedAt) \u003e gate.Timeout {\n d.notifyWaiters(gate, \"timeout\")\n d.closeGate(gate, \"timed out\")\n continue\n }\n \n // Check condition\n if d.checkCondition(gate.AwaitType, gate.AwaitID) {\n d.notifyWaiters(gate, \"cleared\")\n d.closeGate(gate, \"condition met\")\n }\n }\n}\n```\n\n## Note\nThis task is in Gas Town (gt), not beads. May need to be moved there.","status":"open","priority":2,"issue_type":"task","created_at":"2025-12-23T11:44:36.839709-08:00","updated_at":"2025-12-23T11:44:36.839709-08:00","dependencies":[{"issue_id":"bd-is6m","depends_on_id":"bd-udsi","type":"parent-child","created_at":"2025-12-23T11:44:52.909253-08:00","created_by":"daemon"},{"issue_id":"bd-is6m","depends_on_id":"bd-u66e","type":"blocks","created_at":"2025-12-23T11:44:56.428084-08:00","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-j0tr","title":"Phase 1.3: Basic TOON read/write operations","description":"Add basic TOON read/write operations to bdt executable. Implement create, list, and show commands that use the internal/toon package for encoding/decoding to TOON format.\n\n## Subtasks\n1. Implement bdt create command - Create issues and serialize to TOON format\n2. Implement bdt list command - Read issues.toon and display all issues\n3. Implement bdt show command - Display single issue by ID\n4. Add file I/O operations for issues.toon\n5. Integrate internal/toon package (EncodeTOON, DecodeJSON)\n6. Write tests for create, list, show operations\n\n## Files to Create/Modify\n- cmd/bdt/create.go - Create command\n- cmd/bdt/list.go - List command \n- cmd/bdt/show.go - Show command\n- cmd/bdt/storage.go - File I/O helper\n\n## Success Criteria\n- bdt create \"Issue title\" creates and saves to issues.toon\n- bdt list displays all issues in human-readable format\n- bdt list --json shows JSON output\n- bdt show \u003cid\u003e displays single issue\n- Issues round-trip correctly: create → list → show\n- All tests passing with \u003e80% coverage","status":"closed","priority":1,"issue_type":"task","created_at":"2025-12-19T12:59:54.270296918-07:00","updated_at":"2025-12-19T13:09:00.196045685-07:00","closed_at":"2025-12-19T13:09:00.196045685-07:00"}
{"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"}
@@ -297,6 +300,7 @@
{"id":"bd-lsv4","title":"GH#444: Fix inconsistent status naming in_progress vs in-progress","description":"Documentation uses in-progress (hyphen) but code expects in_progress (underscore). Update all docs to use canonical in_progress. See GitHub issue #444.","status":"tombstone","priority":2,"issue_type":"bug","created_at":"2025-12-16T01:03:14.349425-08:00","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":"bug"}
{"id":"bd-lw0x","title":"Fix bd sync race condition with daemon causing dirty working directory","description":"After bd sync completes with sync.branch mode, subsequent bd commands or daemon file watcher would see a hash mismatch and trigger auto-import, which then schedules re-export, dirtying the working directory.\n\n**Root cause:**\n1. bd sync exports JSONL with NEW content (hash H1)\n2. bd sync updates jsonl_content_hash = H1 in DB\n3. bd sync restores JSONL from HEAD (OLD content, hash H0)\n4. Now: file hash = H0, DB hash = H1 (MISMATCH)\n5. Daemon or next CLI command sees mismatch, imports from OLD JSONL\n6. Import triggers re-export → file is dirty\n\n**Fix:**\nAfter restoreBeadsDirFromBranch(), update jsonl_content_hash to match the restored file's hash. This ensures daemon and CLI see file hash = DB hash → no spurious import/export cycle.\n\nRelated: bd-c83r (multiple daemon prevention)","status":"closed","priority":2,"issue_type":"bug","created_at":"2025-12-13T06:42:17.130839-08:00","updated_at":"2025-12-13T06:43:33.329042-08:00","closed_at":"2025-12-13T06:43:33.329042-08:00"}
{"id":"bd-lxzx","title":"Add close_reason to JSONL export format documentation","description":"PR #551 now persists close_reason to the database, but there's a question about whether this field should be exported to JSONL format.\n\n## Current State\n- close_reason is stored in issues.close_reason column\n- close_reason is also stored in events table (audit trail)\n- The JSONL export format may or may not include close_reason\n\n## Questions\n1. Should close_reason be exported to JSONL format?\n2. If yes, where should it go (root level or nested in events)?\n3. Should there be any special handling to avoid duplication?\n4. How should close_reason be handled during JSONL import?\n\n## Why This Matters\n- JSONL is the git-friendly sync format\n- Other beads instances import from JSONL\n- close_reason is meaningful data that should be preserved across clones\n\n## Suggested Action\n- Check if close_reason is currently exported in JSONL\n- If not, add it to the export schema\n- Document the field in JSONL format spec\n- Add tests for round-trip (export -\u003e import -\u003e verify close_reason)","status":"open","priority":2,"issue_type":"task","created_at":"2025-12-14T14:25:17.414916-08:00","updated_at":"2025-12-14T14:25:17.414916-08:00","dependencies":[{"issue_id":"bd-lxzx","depends_on_id":"bd-z86n","type":"discovered-from","created_at":"2025-12-14T14:25:17.416131-08:00","created_by":"stevey","metadata":"{}"}]}
{"id":"bd-lz49","title":"Add gate fields: await_type, await_id, timeout, waiters","description":"Add gate-specific fields to the Issue type.\n\n## New Fields\n- await_type: string - Type of condition (gh:run, gh:pr, timer, human, mail)\n- await_id: string - Identifier for the condition\n- timeout: duration - Max time to wait before escalation\n- waiters: []string - Mail addresses to notify when gate clears\n\n## Implementation\n- Add fields to Issue struct in internal/types/types.go\n- Update SQLite schema for new columns\n- Add JSONL serialization/deserialization\n- Update import/export logic","status":"closed","priority":1,"issue_type":"task","created_at":"2025-12-23T11:44:32.720196-08:00","updated_at":"2025-12-23T12:00:03.837691-08:00","closed_at":"2025-12-23T12:00:03.837691-08:00","close_reason":"Gate fields added to Issue struct, ComputeContentHash, SQLite migration created, all storage queries updated","dependencies":[{"issue_id":"bd-lz49","depends_on_id":"bd-udsi","type":"parent-child","created_at":"2025-12-23T11:44:52.738823-08:00","created_by":"daemon"},{"issue_id":"bd-lz49","depends_on_id":"bd-2v0f","type":"blocks","created_at":"2025-12-23T11:44:56.269351-08:00","created_by":"daemon"}]}
{"id":"bd-m0tl","title":"bd create -f crashes with nil pointer dereference","description":"GitHub issue #674. The markdown import feature crashes at markdown.go:338 because global variables (store, ctx, actor) aren't initialized when createIssuesFromMarkdown is called. The function uses globals set by cobra command framework but is being called before they're ready. Need to either initialize globals at start of function or pass them as parameters.","status":"closed","priority":1,"issue_type":"bug","created_at":"2025-12-21T14:35:14.813012-08:00","updated_at":"2025-12-21T15:41:14.600953-08:00","closed_at":"2025-12-21T15:41:14.600953-08:00","close_reason":"Fixed: added nil check for store in createIssuesFromMarkdown"}
{"id":"bd-m164","title":"Add 0.33.2 to versionChanges in info.go","description":"Add new entry at the TOP of versionChanges array in cmd/bd/info.go:\n\n```go\n{\n Version: \"0.33.2\",\n Date: \"2025-12-21\",\n Changes: []string{\n // Add notable changes here\n },\n},\n```\n\nCopy changes from CHANGELOG.md [Unreleased] section.","status":"tombstone","priority":1,"issue_type":"task","created_at":"2025-12-21T16:10:13.761218-08:00","updated_at":"2025-12-21T17:29:31.791368-08:00","deleted_at":"2025-12-21T17:29:31.791368-08:00","deleted_by":"batch delete","delete_reason":"batch delete","original_type":"task","wisp":true}
{"id":"bd-m7ib","title":"Add creator field to Issue struct","description":"Add Creator *EntityRef field to Issue. Tracks who created the issue. Optional, omitted if nil in JSONL. This enables CV chain tracking - every piece of work is attributed to its creator.","status":"closed","priority":1,"issue_type":"task","created_at":"2025-12-22T17:53:31.599447-08:00","updated_at":"2025-12-22T20:03:24.264672-08:00","closed_at":"2025-12-22T20:03:24.264672-08:00","close_reason":"Added Creator *EntityRef field to Issue struct. Included in content hash. Test coverage added.","dependencies":[{"issue_id":"bd-m7ib","depends_on_id":"bd-7pwh","type":"parent-child","created_at":"2025-12-22T17:53:43.39957-08:00","created_by":"daemon"},{"issue_id":"bd-m7ib","depends_on_id":"bd-nmch","type":"blocks","created_at":"2025-12-22T17:53:47.826309-08:00","created_by":"daemon"}]}
@@ -396,6 +400,7 @@
{"id":"bd-rece","title":"Phase 1.1: TOON Library Integration - Add gotoon dependency","description":"Add gotoon (github.com/alpkeskin/gotoon) to go.mod and create internal/toon wrapper package for TOON encoding/decoding. This enables bdtoon to encode Issue structs to TOON format and decode TOON back to issues.\n\n## Subtasks\n1. Add gotoon dependency: go get github.com/alpkeskin/gotoon\n2. Create internal/toon package with wrapper functions\n3. Write encode tests for Issue struct round-trip conversion\n4. Write decode tests for TOON to Issue conversion\n5. Add gotoon API options to wrapper (indent, delimiter, length markers)\n\n## Success Criteria\n- go.mod includes gotoon dependency\n- internal/toon/encode.go exports EncodeTOON(issues) ([]byte, error)\n- internal/toon/decode.go exports DecodeTOON(data []byte) ([]Issue, error)\n- Round-trip tests verify Issue → TOON → Issue produces identical data\n- Tests pass with: go test ./internal/toon -v","status":"closed","priority":1,"issue_type":"task","created_at":"2025-12-19T11:48:30.018161133-07:00","updated_at":"2025-12-19T12:53:56.808833405-07:00","closed_at":"2025-12-19T12:53:56.808833405-07:00"}
{"id":"bd-rgd7","title":"Update CHANGELOG.md with release notes","description":"Add release notes for 0.32.1: MCP output control params (#667), pin field fix","status":"closed","priority":1,"issue_type":"task","created_at":"2025-12-20T21:53:16.031879-08:00","updated_at":"2025-12-20T21:54:07.982164-08:00","closed_at":"2025-12-20T21:54:07.982164-08:00","close_reason":"Added 0.32.1 release notes","dependencies":[{"issue_id":"bd-rgd7","depends_on_id":"bd-an4s","type":"parent-child","created_at":"2025-12-20T21:53:16.034926-08:00","created_by":"daemon"}]}
{"id":"bd-rgyd","title":"Split internal/storage/sqlite/queries.go (1586 lines)","description":"Code health review found queries.go is too large at 1586 lines with:\n\n- Issue scanning logic duplicated between transaction.go and queries.go\n- Timestamp defensive fixes duplicated in CreateIssue, CreateIssues, batch_ops.go\n- Multiple similar patterns that should be consolidated\n\nAlso: transaction.go at 1284 lines, dependencies.go at 893 lines\n\nRecommendation:\n1. Extract common scanning into shared function\n2. Consolidate timestamp defensive fixes\n3. Split queries.go by domain (CRUD, search, batch, events)","status":"open","priority":2,"issue_type":"task","created_at":"2025-12-16T18:17:23.85869-08:00","updated_at":"2025-12-16T18:17:23.85869-08:00"}
{"id":"bd-rl5t","title":"Integration test: agent waits for CI via gate","description":"End-to-end test of the gate workflow.\n\n## Test Scenario\n1. Agent creates gate: bd gate create --await gh:run:123 --timeout 5m --notify beads/dave\n2. Agent writes handoff and exits\n3. Deacon patrol checks gate condition\n4. (Mock) GitHub run completes\n5. Deacon notifies waiter and closes gate\n6. New agent session reads mail and resumes\n\n## Test Requirements\n- Mock GitHub API responses\n- Test timeout path\n- Test multiple waiters\n- Verify mail notifications sent","status":"open","priority":2,"issue_type":"task","created_at":"2025-12-23T11:44:41.725752-08:00","updated_at":"2025-12-23T11:44:41.725752-08:00","dependencies":[{"issue_id":"bd-rl5t","depends_on_id":"bd-udsi","type":"parent-child","created_at":"2025-12-23T11:44:53.157037-08:00","created_by":"daemon"},{"issue_id":"bd-rl5t","depends_on_id":"bd-2l03","type":"blocks","created_at":"2025-12-23T11:44:56.674866-08:00","created_by":"daemon"},{"issue_id":"bd-rl5t","depends_on_id":"bd-ykqu","type":"blocks","created_at":"2025-12-23T11:44:56.753264-08:00","created_by":"daemon"}]}
{"id":"bd-rnnr","title":"BondRef data model for compound lineage","description":"Add data model support for tracking compound molecule lineage.\n\nNEW FIELDS on Issue:\n bonded_from: []BondRef // For compounds: constituent protos\n\nNEW TYPE:\n type BondRef struct {\n ProtoID string // Source proto ID\n BondType string // sequential, parallel, conditional\n BondPoint string // Attachment site (issue ID or empty for root)\n }\n\nJSONL SERIALIZATION:\n {\n \"id\": \"proto-feature-tested\",\n \"title\": \"Feature with tests\",\n \"bonded_from\": [\n {\"proto_id\": \"proto-feature\", \"bond_type\": \"root\"},\n {\"proto_id\": \"proto-testing\", \"bond_type\": \"sequential\"}\n ],\n ...\n }\n\nQUERIES:\n- GetCompoundConstituents(id) → []BondRef\n- IsCompound(id) → bool\n- GetCompoundsUsing(protoID) → []Issue // Reverse lookup","status":"closed","priority":1,"issue_type":"task","created_at":"2025-12-21T00:59:38.582509-08:00","updated_at":"2025-12-21T01:19:43.922416-08:00","closed_at":"2025-12-21T01:19:43.922416-08:00","close_reason":"Added BondRef type to types.go with ProtoID, BondType, BondPoint fields; added BondedFrom field to Issue; added IsCompound() and GetConstituents() helpers; added BondType constants","dependencies":[{"issue_id":"bd-rnnr","depends_on_id":"bd-o5xe","type":"parent-child","created_at":"2025-12-21T00:59:51.234246-08:00","created_by":"daemon"}]}
{"id":"bd-rp4o","title":"Deleted issues resurrect during bd sync (tombstones not propagating)","description":"## Problem\n\nWhen issues are deleted with bd delete --force, they get deleted from the local DB but resurrect during the next bd sync.\n\n## Reproduction\n\n1. Observe orphan warnings (bd-cb64c226.*, bd-cbed9619.*)\n2. Delete them: bd delete bd-cb64c226.1 ... --force\n3. Run bd sync\n4. Orphan warnings reappear - issues were resurrected!\n\n## Root Cause Hypothesis\n\nThe sync branch workflow (beads-sync) has the old state before deletions. When bd sync pulls from beads-sync and copies JSONL to main, the deleted issues are re-imported.\n\nTombstones may not be properly:\n1. Written to beads-sync during export\n2. Propagated during pull/merge\n3. Honored during import\n\n## Related\n\n- bd-7b7h: chicken-and-egg sync.branch bug (same workflow)\n- bd-ncwo: ID-based fallback matching to prevent ghost resurrection\n\n## Files to Investigate\n\n- cmd/bd/sync.go (export/import flow)\n- internal/syncbranch/worktree.go (PullFromSyncBranch, copyJSONLToMainRepo)\n- internal/importer/ (tombstone handling)","status":"tombstone","priority":1,"issue_type":"bug","created_at":"2025-12-16T23:09:43.072696-08:00","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":"bug"}
{"id":"bd-rupw","title":"Run bump-version.sh 0.30.7","description":"Run ./scripts/bump-version.sh 0.30.7 to update version in all files","status":"closed","priority":1,"issue_type":"task","created_at":"2025-12-19T22:56:48.649647-08:00","updated_at":"2025-12-19T22:57:31.512956-08:00","closed_at":"2025-12-19T22:57:31.512956-08:00","dependencies":[{"issue_id":"bd-rupw","depends_on_id":"bd-8pyn","type":"parent-child","created_at":"2025-12-19T22:56:48.653475-08:00","created_by":"stevey"}]}
@@ -428,6 +433,8 @@
{"id":"bd-u2sc.2","title":"Migrate sort.Slice to slices.SortFunc","description":"Go 1.21+ provides slices.SortFunc which is cleaner and slightly faster than sort.Slice.\n\nFound 15+ instances of sort.Slice in:\n- cmd/bd/autoflush.go\n- cmd/bd/count.go\n- cmd/bd/daemon_sync.go\n- cmd/bd/doctor.go\n- cmd/bd/export.go\n- cmd/bd/import.go\n- cmd/bd/integrity.go\n- cmd/bd/jira.go\n- cmd/bd/list.go\n- cmd/bd/migrate_hash_ids.go\n- cmd/bd/rename_prefix.go\n- cmd/bd/show.go\n\nExample migration:\n```go\n// Before\nsort.Slice(issues, func(i, j int) bool {\n return issues[i].Priority \u003c issues[j].Priority\n})\n\n// After\nslices.SortFunc(issues, func(a, b *types.Issue) int {\n return cmp.Compare(a.Priority, b.Priority)\n})\n```\n\nBenefits:\n- Cleaner 3-way comparison\n- Slightly better performance\n- Modern idiomatic Go","status":"closed","priority":3,"issue_type":"task","created_at":"2025-12-22T14:26:55.573524-08:00","updated_at":"2025-12-22T15:10:12.639807-08:00","closed_at":"2025-12-22T15:10:12.639807-08:00","close_reason":"Migrated all 19 instances of sort.Slice to slices.SortFunc across 17 files in cmd/bd/. Used cmp.Compare for orderable types, time.Compare for time comparisons, and cmp.Or for multi-field sorts.","dependencies":[{"issue_id":"bd-u2sc.2","depends_on_id":"bd-u2sc","type":"parent-child","created_at":"2025-12-22T14:26:55.573978-08:00","created_by":"daemon"}]}
{"id":"bd-u2sc.3","title":"Split large cmd/bd files into logical modules","description":"Several cmd/bd files exceed 1000 lines and should be split for maintainability:\n\n| File | Lines | Recommendation |\n|------|-------|----------------|\n| sync.go | 2201 | Split: sync_core.go, sync_branch.go, sync_remote.go |\n| init.go | 1742 | Split: init.go, init_wizard.go, init_hooks.go |\n| show.go | 1380 | Split: show.go, show_formatters.go, show_threads.go |\n| compact.go | 1112 | Split: compact.go, compact_tiers.go |\n\nGuidelines:\n- Each file should focus on one aspect\n- Keep public API in main file\n- Move helpers/formatters to separate files\n- Consider internal/ packages for complex logic\n\nNote: This is a lower priority task - large files are inconvenient but not blocking.","status":"open","priority":3,"issue_type":"task","created_at":"2025-12-22T14:27:06.146343-08:00","updated_at":"2025-12-22T14:27:06.146343-08:00","dependencies":[{"issue_id":"bd-u2sc.3","depends_on_id":"bd-u2sc","type":"parent-child","created_at":"2025-12-22T14:27:06.146704-08:00","created_by":"daemon"}]}
{"id":"bd-u2sc.4","title":"Introduce slog for structured daemon logging","description":"The daemon currently uses fmt.Fprintf for logging which produces unstructured output. Migrating to slog would provide:\n\n- Structured, parseable logs (JSON format option)\n- Log levels (debug, info, warn, error)\n- Context propagation\n- Better log aggregation\n\nFiles to update:\n- cmd/bd/daemon_logger.go\n- Debug output throughout daemon code\n\nExample:\n```go\n// Before\nfmt.Fprintf(os.Stderr, \"Warning: failed to detect user role: %v\\n\", err)\n\n// After\nslog.Warn(\"failed to detect user role\", \"error\", err)\n```\n\nThis is particularly valuable for daemon troubleshooting since daemon logs are often reviewed after the fact.","status":"open","priority":3,"issue_type":"task","created_at":"2025-12-22T14:27:16.47144-08:00","updated_at":"2025-12-22T14:27:16.47144-08:00","dependencies":[{"issue_id":"bd-u2sc.4","depends_on_id":"bd-u2sc","type":"parent-child","created_at":"2025-12-22T14:27:16.471878-08:00","created_by":"daemon"}]}
{"id":"bd-u66e","title":"Implement bd gate create/show/list/close/wait commands","description":"Implement the gate CLI commands.\n\n## Commands\n```bash\n# Create gate (returns gate ID)\nbd gate create --await \u003ctype\u003e:\u003cid\u003e --timeout \u003cduration\u003e --notify \u003caddr\u003e\n\n# Check gate status\nbd gate show \u003cid\u003e\n\n# List open gates\nbd gate list\n\n# Close gate (usually done by Deacon)\nbd gate close \u003cid\u003e --reason \"completed\"\n\n# Add waiter to existing gate\nbd gate wait \u003cid\u003e --notify \u003caddr\u003e\n```\n\n## Implementation\n- Add cmd/bd/gate.go with subcommands\n- Gate create creates wisp issue of type gate\n- Gate list filters for open gates\n- Gate wait adds to waiters[] array\n- All support --json output","status":"closed","priority":1,"issue_type":"task","created_at":"2025-12-23T11:44:34.022464-08:00","updated_at":"2025-12-23T12:06:18.550673-08:00","closed_at":"2025-12-23T12:06:18.550673-08:00","close_reason":"Implemented bd gate commands: create, show, list, close, wait. All support --json output and work with wisp/gate fields.","dependencies":[{"issue_id":"bd-u66e","depends_on_id":"bd-udsi","type":"parent-child","created_at":"2025-12-23T11:44:52.823353-08:00","created_by":"daemon"},{"issue_id":"bd-u66e","depends_on_id":"bd-lz49","type":"blocks","created_at":"2025-12-23T11:44:56.349662-08:00","created_by":"daemon"}]}
{"id":"bd-udsi","title":"Async Gates for Agent Coordination","description":"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.\n\n## Core Concepts\n\n**Gate** = wisp issue that blocks until external condition is met\n- Type: gate\n- Phase: wisp (never synced, ephemeral)\n- Assignee: deacon/ (Deacon monitors it)\n- Fields: await_type, await_id, timeout, waiters[]\n\n**Await Types:**\n- gh:run:\u003cid\u003e - GitHub Actions run completion\n- gh:pr:\u003cid\u003e - PR merged/closed\n- timer:\u003cduration\u003e - Simple delay\n- human:\u003cprompt\u003e - Human approval required\n- mail:\u003cpattern\u003e - Wait for mail matching pattern\n\n## Open Questions\n- Should gates live in wisp storage or main storage with wisp flag?\n- Do we need a gate catalog (like molecule catalog)?\n- Should waits-for dep type work with gates?","status":"open","priority":1,"issue_type":"epic","created_at":"2025-12-23T11:44:02.711062-08:00","updated_at":"2025-12-23T11:44:02.711062-08:00"}
{"id":"bd-umbf","title":"Design contributor namespace isolation for beads pollution prevention","description":"## Problem\n\nWhen contributors work on beads-the-project using beads-the-tool, their personal work-tracking issues leak into PRs. The .beads/issues.jsonl is intentionally tracked (it's the project's issue database), but contributors' local issues pollute the diff.\n\nThis is a recursion problem unique to self-hosting projects.\n\n## Possible Solutions to Explore\n\n1. **Contributor namespaces** - Each contributor gets a private prefix (e.g., `bd-steve-xxxx`) that's gitignored or filtered\n2. **Separate database** - Contributors use BEADS_DIR pointing elsewhere for personal tracking\n3. **Issue ownership/visibility flags** - Mark issues as \"local-only\" vs \"project\"\n4. **Prefix-based filtering** - Configure which prefixes are committed vs ignored\n\n## Design Considerations\n\n- Should be zero-friction for contributors (no manual setup)\n- Must not break existing workflows\n- Needs to work with sync/collaboration features\n- Consider: what if a \"personal\" issue graduates to \"project\" issue?\n\n## Expansion Needed\n\nThis is a placeholder. Needs detailed design exploration before implementation.","status":"open","priority":2,"issue_type":"feature","created_at":"2025-12-13T18:00:29.638743-08:00","updated_at":"2025-12-13T18:00:41.345673-08:00"}
{"id":"bd-uqfn","title":"Work on beads-wkt: Output control parameters for MCP tool...","description":"Work on beads-wkt: Output control parameters for MCP tools (GH#622). Add brief, fields, max_description_length params to ready/list/show. When done, submit MR (not PR) to integration branch for Refinery.","status":"closed","priority":2,"issue_type":"task","created_at":"2025-12-19T22:57:10.675535-08:00","updated_at":"2025-12-20T00:49:51.929271-08:00","closed_at":"2025-12-19T23:28:25.362931-08:00","close_reason":"Implemented output control parameters for MCP tools (GH#622)"}
{"id":"bd-usro","title":"Rename 'template instantiate' to 'mol bond'","description":"Rename the template instantiation command to match molecule metaphor.\n\nCurrent: bd template instantiate \u003cid\u003e --var key=value\nTarget: bd mol bond \u003cid\u003e --var key=value\n\nChanges needed:\n- Add 'mol' command group (or extend existing)\n- Add 'bond' subcommand that wraps template instantiate logic\n- Keep 'template instantiate' as deprecated alias for backward compat\n- Update help text and docs to use molecule terminology\n\nThe 'bond' verb captures:\n1. Chemistry metaphor (molecules bond to form structures)\n2. Dependency linking (child issues bonded in a DAG)\n3. Short and active\n\nSee also: molecule execution model in Gas Town","status":"closed","priority":1,"issue_type":"feature","created_at":"2025-12-20T16:56:37.582795-08:00","updated_at":"2025-12-20T23:22:43.567337-08:00","closed_at":"2025-12-20T23:22:43.567337-08:00","close_reason":"Implemented mol command: catalog, show, bond"}
@@ -465,6 +472,7 @@
{"id":"bd-y8tn","title":"Test Molecule","description":"A test molecule","status":"closed","priority":2,"issue_type":"molecule","created_at":"2025-12-19T18:30:24.491279-08:00","updated_at":"2025-12-19T18:31:12.49898-08:00","closed_at":"2025-12-19T18:31:12.49898-08:00","close_reason":"test molecule - deleting"}
{"id":"bd-yck","title":"Fix checkExistingBeadsData to be worktree-aware","description":"The checkExistingBeadsData function in cmd/bd/init.go checks for .beads in the current working directory, but for worktrees it should check the main repository root instead. This prevents proper worktree compatibility.","status":"open","priority":2,"issue_type":"bug","created_at":"2025-12-07T16:48:32.082776345-07:00","updated_at":"2025-12-07T16:48:32.082776345-07:00"}
{"id":"bd-ykd9","title":"Add bd doctor --fix flag to automatically repair issues","description":"Implement a --fix flag for bd doctor that can automatically repair detected issues.\n\nRequirements:\n- Add --fix flag to bd doctor command\n- Show all fixable issues and prompt for confirmation before applying fixes\n- Organize fix implementations under doctor/fix/\u003ctype_of_fix\u003e.go\n- Each fix type should have its own file (e.g., doctor/fix/hooks.go, doctor/fix/sync.go)\n- Display what will be fixed and ask user to confirm (Y/n) before proceeding\n- Support fixing issues like:\n - Missing or broken git hooks\n - Sync problems with remote\n - File permission issues\n - Any other auto-repairable issues doctor detects\n\nImplementation notes:\n- Maintain separation between detection (existing doctor code) and repair (new fix code)\n- Each fix should be idempotent and safe to run multiple times\n- Provide clear output about what was fixed\n- Log any fixes that fail with actionable error messages","status":"open","priority":2,"issue_type":"feature","created_at":"2025-11-14T18:17:48.411264-08:00","updated_at":"2025-11-14T18:17:58.88609-08:00"}
{"id":"bd-ykqu","title":"Add gate timeout tracking and notification","description":"Implement timeout and notification logic for gates.\n\n## Timeout Behavior\n1. Gate created with timeout (e.g., 30m)\n2. Deacon tracks elapsed time during patrol\n3. If timeout reached:\n - Notify all waiters: \"Gate timed out\"\n - Close gate with timeout reason\n - Waiter can retry, escalate, or fail gracefully\n\n## Notification\n- Use gt mail send to notify waiters\n- Include gate ID, await type, and reason in message\n- Support multiple waiters notification\n\n## Escalation Path\n- Witness sees stuck worker, nudges them\n- Worker can escalate to human if needed","status":"open","priority":2,"issue_type":"task","created_at":"2025-12-23T11:44:40.1825-08:00","updated_at":"2025-12-23T11:44:40.1825-08:00","dependencies":[{"issue_id":"bd-ykqu","depends_on_id":"bd-udsi","type":"parent-child","created_at":"2025-12-23T11:44:53.072862-08:00","created_by":"daemon"},{"issue_id":"bd-ykqu","depends_on_id":"bd-is6m","type":"blocks","created_at":"2025-12-23T11:44:56.595085-08:00","created_by":"daemon"}]}
{"id":"bd-ymqn","title":"Code review: bd mol bond --ref and bd activity (bd-xo1o work)","description":"Review dave's recent commits for bd-xo1o (Dynamic Molecule Bonding):\n\n## Commits to Review\n- ee04b1ea: feat: add dynamic molecule bonding with --ref flag (bd-xo1o.1)\n- be520d90: feat: add bd activity command for real-time state feed (bd-xo1o.3)\n\n## Review Focus\n1. Code quality and correctness\n2. Error handling\n3. Edge cases\n4. Test coverage\n5. Documentation\n\n## Deliverables\n- File beads for any issues found\n- Note any concerns or suggestions\n- Verify the implementation matches the bd-xo1o epic requirements","status":"closed","priority":1,"issue_type":"task","assignee":"beads/ace","created_at":"2025-12-23T03:47:55.217363-08:00","updated_at":"2025-12-23T04:11:00.226326-08:00","closed_at":"2025-12-23T04:11:00.226326-08:00","close_reason":"Code review completed by ace"}
{"id":"bd-yqhh","title":"bd list --parent: filter by parent issue","description":"Add --parent flag to bd list to filter issues by parent.\n\nExample:\n```bash\nbd list --parent=gt-h5n --status=open\n```\n\nWould show all open children of gt-h5n.\n\nUseful for:\n- Checking epic progress\n- Finding swarmable work within an epic\n- Molecule step listing","status":"closed","priority":2,"issue_type":"feature","created_at":"2025-12-23T01:51:26.830952-08:00","updated_at":"2025-12-23T02:10:12.909803-08:00","closed_at":"2025-12-23T02:10:12.909803-08:00","close_reason":"Implemented --parent flag for bd list. Filters children by parent issue using parent-child dependencies."}
{"id":"bd-z3rf","title":"dave Handoff","description":"attached_molecule: bd-ifuw\nattached_at: 2025-12-23T12:49:44Z","status":"pinned","priority":2,"issue_type":"task","created_at":"2025-12-23T04:33:42.874554-08:00","updated_at":"2025-12-23T04:49:44.1246-08:00"}