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{"id":"bd-nqyp","title":"mol-beads-release","description":"Release checklist for beads version {{version}}.\n\nThis molecule ensures all release steps are completed properly.\nVariable: {{version}} - target version (e.g., 0.35.0)\n\n## Step: update-release-notes\nUpdate cmd/bd/info.go with release notes for {{version}}.\n\nAdd a new VersionChange entry at the top of versionChanges slice:\n```go\n{\n Version: \"{{version}}\",\n Date: \"YYYY-MM-DD\",\n Changes: []string{\n \"NEW: Feature description\",\n \"FIX: Bug fix description\",\n \"IMPROVED: Enhancement description\",\n },\n},\n```\n\nRun `git log --oneline v\u003cprevious\u003e..HEAD` to see what changed.\n\n## Step: update-changelog\nUpdate CHANGELOG.md with detailed release notes.\n\nAdd a new section after [Unreleased]:\n```markdown\n## [{{version}}] - YYYY-MM-DD\n\n### Added\n- **Feature name** (issue-id) - Description\n\n### Changed\n- **Change description** (issue-id)\n\n### Fixed\n- **Bug fix** (issue-id) - Description\n```\n\nSort by importance, not chronologically.\nNeeds: update-release-notes\n\n## Step: bump-version\nRun the version bump script.\n\n```bash\n./scripts/bump-version.sh {{version}}\n```\n\nThis updates version in all files:\n- cmd/bd/version.go\n- .claude-plugin/*.json\n- integrations/beads-mcp/pyproject.toml\n- npm-package/package.json\n- Hook templates\n\nNeeds: update-changelog\n\n## Step: run-tests\nRun tests and verify lint passes.\n\n```bash\ngo test -short ./...\n```\n\nCI will run full lint, but fix any obvious issues first.\nNeeds: bump-version\n\n## Step: commit-release\nCommit the release changes.\n\n```bash\ngit add -A\ngit commit -m \"chore: bump version to v{{version}}\"\n```\n\nNeeds: run-tests\n\n## Step: push-and-tag\nPush commit and create release tag.\n\n```bash\ngit push origin main\ngit tag v{{version}}\ngit push origin v{{version}}\n```\n\nThis triggers GitHub Actions release workflow.\nNeeds: commit-release\n\n## Step: wait-for-ci\nWait for GitHub Actions to complete.\n\nMonitor: https://github.com/steveyegge/beads/actions\n\nCI will:\n- Build binaries via GoReleaser\n- Create GitHub Release with assets\n- Publish to npm (@beads/bd)\n- Publish to PyPI (beads-mcp)\n- Update Homebrew tap\n\nWait until all jobs succeed (~5-10 min).\nNeeds: push-and-tag\n\n## Step: verify-release\nVerify the release is complete.\n\n```bash\n# Check GitHub release\ngh release view v{{version}}\n\n# Check Homebrew\nbrew update \u0026\u0026 brew info steveyegge/beads/bd\n\n# Check npm\nnpm view @beads/bd version\n\n# Check PyPI\npip index versions beads-mcp\n```\n\nNeeds: wait-for-ci\n\n## Step: update-local\nUpdate local installations.\n\n```bash\n# Upgrade Homebrew\nbrew upgrade steveyegge/beads/bd\n\n# Or install from source\n./scripts/bump-version.sh {{version}} --install\n\n# Install MCP locally\npip install -e integrations/beads-mcp\n\n# Restart daemons\npkill -f \"bd daemon\" || true\n```\n\nVerify: `bd --version` shows {{version}}\nNeeds: verify-release\n\n## Step: manual-publish\n(Optional) Manual publish if CI failed.\n\n```bash\n# npm (requires npm login)\n./scripts/bump-version.sh {{version}} --publish-npm\n\n# PyPI (requires TWINE credentials)\n./scripts/bump-version.sh {{version}} --publish-pypi\n\n# Or both\n./scripts/bump-version.sh {{version}} --publish-all\n```\n\nOnly needed if CI publishing failed.\nNeeds: wait-for-ci","status":"open","priority":2,"issue_type":"molecule","created_at":"2025-12-23T11:29:39.087936-08:00","updated_at":"2025-12-23T11:29:39.087936-08:00"}
{"id":"bd-nuh1","title":"GH#403: bd doctor --fix circular error message","description":"bd doctor --fix suggests running bd doctor --fix for deletions manifest issue. Fix to provide actual resolution. See GitHub issue #403.","status":"tombstone","priority":2,"issue_type":"bug","created_at":"2025-12-16T01:03:16.290018-08:00","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-nurq","title":"Implement bd mol current command","description":"Show what molecule the agent should currently be working on. Referenced by gt-um6q, gt-lz13. Needed for molecule navigation workflow in templates.","status":"closed","priority":1,"issue_type":"feature","created_at":"2025-12-23T00:17:54.069983-08:00","updated_at":"2025-12-23T01:23:59.523404-08:00","closed_at":"2025-12-23T01:23:59.523404-08:00","close_reason":"Implementation already existed, added tests (TestGetMoleculeProgress, TestFindParentMolecule, TestAdvanceToNextStep*), rebuilt and installed binary"}
{"id":"bd-o34a","title":"Design auto-squash behavior for wisps","description":"Explore the design space for automatic wisp squashing.\n\n**Context:**\nWisps are ephemeral molecules that should be squashed (digest) or burned (no trace)\nwhen complete. Currently this is manual. Should it be automatic?\n\n**Questions to answer:**\n1. When should auto-squash trigger?\n - On molecule completion?\n - On session end/handoff?\n - On patrol detection?\n \n2. What's the default summary for auto-squash?\n - Generic: 'Auto-squashed on completion'\n - Step-based: List closed steps\n - AI-generated: Require agent to provide\n\n3. Should this be configurable?\n - Per-molecule setting in formula?\n - Global config: auto_squash: true/false\n - Per-wisp flag at creation time?\n\n4. Who decides - Beads or Gas Town?\n - Beads: Provides operators (squash, burn)\n - Gas Town: Makes policy decisions\n - Proposal: GT patrol molecules call bd mol squash\n\n**Constraints:**\n- Don't lose important context (summary matters)\n- Don't create noise in digest history\n- Respect agent's intent (some wisps should burn, not squash)\n\n**Recommendation:**\nGas Town patrol molecules should have explicit squash/burn steps.\nBeads provides primitives, GT makes policy decisions.\nAuto-squash at Beads level is probably wrong layer.","status":"open","priority":4,"issue_type":"task","created_at":"2025-12-24T18:23:24.833877-08:00","updated_at":"2025-12-24T18:23:24.833877-08:00"}
{"id":"bd-o34a","title":"Design auto-squash behavior for wisps","description":"Explore the design space for automatic wisp squashing.\n\n**Context:**\nWisps are ephemeral molecules that should be squashed (digest) or burned (no trace)\nwhen complete. Currently this is manual. Should it be automatic?\n\n**Questions to answer:**\n1. When should auto-squash trigger?\n - On molecule completion?\n - On session end/handoff?\n - On patrol detection?\n \n2. What's the default summary for auto-squash?\n - Generic: 'Auto-squashed on completion'\n - Step-based: List closed steps\n - AI-generated: Require agent to provide\n\n3. Should this be configurable?\n - Per-molecule setting in formula?\n - Global config: auto_squash: true/false\n - Per-wisp flag at creation time?\n\n4. Who decides - Beads or Gas Town?\n - Beads: Provides operators (squash, burn)\n - Gas Town: Makes policy decisions\n - Proposal: GT patrol molecules call bd mol squash\n\n**Constraints:**\n- Don't lose important context (summary matters)\n- Don't create noise in digest history\n- Respect agent's intent (some wisps should burn, not squash)\n\n**Recommendation:**\nGas Town patrol molecules should have explicit squash/burn steps.\nBeads provides primitives, GT makes policy decisions.\nAuto-squash at Beads level is probably wrong layer.","status":"closed","priority":4,"issue_type":"task","created_at":"2025-12-24T18:23:24.833877-08:00","updated_at":"2025-12-25T22:56:59.210809-08:00","closed_at":"2025-12-25T22:56:59.210809-08:00","close_reason":"Already resolved: Gas Town handles squash/burn policy via templates, Beads provides primitives. Design matches recommendation in issue."}
{"id":"bd-o4qy","title":"Improve CheckStaleness error handling","description":"## Problem\n\nCheckStaleness returns 'false' (not stale) for multiple error conditions instead of returning errors. This masks problems.\n\n**Location:** internal/autoimport/autoimport.go:253-285\n\n## Edge Cases That Return False\n\n1. **Invalid last_import_time format** (line 259-262)\n2. **No JSONL file found** (line 267-277) \n3. **JSONL stat fails** (line 279-282)\n\n## Fix\n\nReturn errors for abnormal conditions:\n\n```go\nlastImportTime, err := time.Parse(time.RFC3339, lastImportStr)\nif err != nil {\n return false, fmt.Errorf(\"corrupted last_import_time: %w\", err)\n}\n\nif jsonlPath == \"\" {\n return false, fmt.Errorf(\"no JSONL file found\")\n}\n\nstat, err := os.Stat(jsonlPath)\nif err != nil {\n return false, fmt.Errorf(\"cannot stat JSONL: %w\", err)\n}\n```\n\n## Impact\nMedium - edge cases are rare but should be handled\n\n## Effort \n30 minutes - requires updating callers in RPC server","status":"tombstone","priority":2,"issue_type":"bug","created_at":"2025-11-20T20:17:27.606219-05:00","updated_at":"2025-12-25T01:21:01.952723-08:00","dependencies":[{"issue_id":"bd-o4qy","depends_on_id":"bd-2q6d","type":"blocks","created_at":"2025-11-20T20:18:26.81065-05:00","created_by":"stevey","metadata":"{}"}],"deleted_at":"2025-12-25T01:21:01.952723-08:00","deleted_by":"batch delete","delete_reason":"batch delete","original_type":"bug"}
{"id":"bd-o55a","title":"GH#509: bd doesn't find .beads when running from nested worktrees","description":"When worktrees are nested under main repo (.worktrees/feature/), bd stops at worktree git root instead of continuing to find .beads in parent. See GitHub issue #509 for detailed fix suggestion.","status":"tombstone","priority":2,"issue_type":"bug","created_at":"2025-12-16T01:03:20.281591-08:00","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-o5xe","title":"Molecule bonding: composable workflow templates","description":"Vision: Molecules should be composable like LEGO bricks or Mad Max war rig sections. Bonding lets you attach molecules together to create compound workflows.\n\nTHREE BONDING CONTEXTS:\n1. Template-time: bd mol bond A B → Create reusable compound proto\n2. Spawn-time: bd mol spawn A --attach B → Attach modules when instantiating \n3. Runtime: bd mol attach epic B → Add to running workflow\n\nBOND TYPES:\n- Sequential: B after A completes (feature → deploy)\n- Parallel: B runs alongside A (feature + docs)\n- Conditional: B only if A fails (feature → hotfix)\n\nBOND POINTS (Attachment Sites):\n- Default: B depends on A root epic completion\n- Explicit: --after issue-id for specific attachment\n- Future: Named bond points in proto definitions\n\nVARIABLE FLOW:\n- Shared namespace between bonded molecules\n- Warn on variable name conflicts\n- Future: explicit mapping with --map\n\nDATA MODEL: Issues track bonded_from to preserve compound lineage.\n\nSUCCESS CRITERIA:\n- Can bond two protos into a compound proto\n- Can spawn with --attach for on-the-fly composition\n- Can attach molecules to running workflows\n- Compound structure visible in bd mol show\n- Variables flow correctly between bonded molecules","design":"SIMPLIFIED API (per design review):\n\nCORE COMMANDS:\n- bd mol spawn \u003cproto\u003e - Instantiate proto → molecule\n- bd mol bond \u003cA\u003e \u003cB\u003e - Polymorphic bonding (any combination)\n- bd mol distill \u003cmol\u003e - Extract molecule → proto\n- bd mol show/catalog - Inspect\n\nBOND IS POLYMORPHIC:\n| bond A B | Result |\n|---------------|-------------------------------------|\n| proto + proto | compound proto |\n| proto + mol | spawn proto, attach to mol |\n| mol + proto | spawn proto, attach to mol |\n| mol + mol | join into compound molecule |\n\nBOND TYPES: sequential (default), parallel, conditional\n\nTERMINOLOGY:\n- Proto: Uninstantiated template (easter egg: 'protomolecule')\n- Molecule: Spawned instance of a proto\n- Compound: Result of bonding (proto or molecule)\n- Distill: Extract proto from ad-hoc epic","status":"closed","priority":1,"issue_type":"epic","created_at":"2025-12-21T00:58:35.479009-08:00","updated_at":"2025-12-21T17:19:45.871164-08:00","closed_at":"2025-12-21T17:19:45.871164-08:00","close_reason":"All core bonding features implemented (6/7 children closed, 1 deferred for future polish)"}
@@ -509,7 +509,7 @@
{"id":"bd-u8g4","title":"Merge: bd-dxtc","description":"branch: polecat/cheedo\ntarget: main\nsource_issue: bd-dxtc\nrig: beads","status":"closed","priority":1,"issue_type":"merge-request","created_at":"2025-12-23T20:42:17.222567-08:00","updated_at":"2025-12-23T21:21:57.696047-08:00","closed_at":"2025-12-23T21:21:57.696047-08:00","close_reason":"stale - no code pushed"}
{"id":"bd-ucgz","title":"Migration invariants should exclude external dependencies from orphan check","description":"## Summary\n\nThe `checkForeignKeys` function in `migration_invariants.go` flags external dependencies as orphaned because they dont exist in the local issues table.\n\n## Location\n\n`internal/storage/sqlite/migration_invariants.go` around line 150-162\n\n## Current Code (buggy)\n\n```go\n// Check for orphaned dependencies\nvar orphanCount int\nerr = db.QueryRowContext(ctx, \\`\n SELECT COUNT(*)\n FROM dependencies d\n WHERE NOT EXISTS (SELECT 1 FROM issues WHERE id = d.depends_on_id)\n\\`).Scan(\u0026orphanCount)\n```\n\n## Fix\n\nExclude external references (format: `external:\u003cproject\u003e:\u003ccapability\u003e`):\n\n```go\n// Check for orphaned dependencies (excluding external refs)\nvar orphanCount int\nerr = db.QueryRowContext(ctx, \\`\n SELECT COUNT(*)\n FROM dependencies d\n WHERE NOT EXISTS (SELECT 1 FROM issues WHERE id = d.depends_on_id)\n AND d.depends_on_id NOT LIKE 'external:%'\n\\`).Scan(\u0026orphanCount)\n```\n\n## Reproduction\n\n```bash\n# Add external dependency\nbd dep add bd-xxx external:other-project:some-capability\n\n# Try to sync - fails\nbd sync\n# Error: found 1 orphaned dependencies\n```\n\n## Files to Modify\n\n1. **internal/storage/sqlite/migration_invariants.go** - Add WHERE clause\n\n## Testing\n\n```bash\n# Create issue with external dep\nbd create \"Test external deps\" -t task\nbd dep add bd-xxx external:beads:release-workflow\n\n# Sync should succeed\nbd sync\n\n# Verify dep exists\nbd show bd-xxx --json | jq .dependencies\n```\n\n## Success Criteria\n- External dependencies dont trigger orphan check\n- `bd sync` succeeds with external deps\n- Regular orphan detection still works for internal deps","status":"closed","priority":2,"issue_type":"bug","created_at":"2025-12-23T12:37:08.99387-08:00","updated_at":"2025-12-23T12:42:03.722691-08:00","closed_at":"2025-12-23T12:42:03.722691-08:00","close_reason":"Fixed in commit 90196eca - added NOT LIKE 'external:%' exclusion"}
{"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":"closed","priority":1,"issue_type":"epic","created_at":"2025-12-23T11:44:02.711062-08:00","updated_at":"2025-12-23T12:24:43.537615-08:00","closed_at":"2025-12-23T12:24:43.537615-08:00","close_reason":"Core beads implementation complete (types, migration, CLI). Remaining Deacon integration work moved to gastown (gt-dh65, gt-ng6g, gt-fqcz, gt-gswn)."}
{"id":"bd-ujz5","title":"Explore wiki-style documentation structure","description":"Our docs are growing into a book. Evaluate options for wiki-like structure:\n\n**Options to evaluate:**\n- GitHub Wiki (built-in, limited features)\n- mdBook (Rust, CLI-friendly, produces HTML/PDF/ePub)\n- MkDocs / Material for MkDocs (Python, beautiful themes)\n- Docusaurus (React, powerful but complex)\n- Plain markdown with good structure (current approach)\n\n**Requirements:**\n- Git-backed (version control)\n- Markdown-native (agents can edit)\n- Table of contents / navigation\n- Cross-linking between pages\n- Searchable\n- Can be hosted on GitHub Pages\n\n**Deliverables:**\n- Recommendation with pros/cons\n- If switching: migration plan\n- If staying with markdown: structure guidelines for wiki-like organization\n\nReferences:\n- https://squidfunk.github.io/mkdocs-material/alternatives/\n- https://www.archbee.com/blog/gitbook-alternatives","status":"open","priority":3,"issue_type":"task","created_at":"2025-12-24T18:23:23.665509-08:00","updated_at":"2025-12-24T18:23:23.665509-08:00"}
{"id":"bd-ujz5","title":"Explore wiki-style documentation structure","description":"Our docs are growing into a book. Evaluate options for wiki-like structure:\n\n**Options to evaluate:**\n- GitHub Wiki (built-in, limited features)\n- mdBook (Rust, CLI-friendly, produces HTML/PDF/ePub)\n- MkDocs / Material for MkDocs (Python, beautiful themes)\n- Docusaurus (React, powerful but complex)\n- Plain markdown with good structure (current approach)\n\n**Requirements:**\n- Git-backed (version control)\n- Markdown-native (agents can edit)\n- Table of contents / navigation\n- Cross-linking between pages\n- Searchable\n- Can be hosted on GitHub Pages\n\n**Deliverables:**\n- Recommendation with pros/cons\n- If switching: migration plan\n- If staying with markdown: structure guidelines for wiki-like organization\n\nReferences:\n- https://squidfunk.github.io/mkdocs-material/alternatives/\n- https://www.archbee.com/blog/gitbook-alternatives","status":"closed","priority":3,"issue_type":"task","created_at":"2025-12-24T18:23:23.665509-08:00","updated_at":"2025-12-25T22:55:41.578876-08:00","closed_at":"2025-12-25T22:55:41.578876-08:00","close_reason":"Rejected: will address with formula-based patrols instead"}
{"id":"bd-ul59","title":"Update molecular chemistry docs with discoveries","description":"Document recent discoveries about molecule/epic relationship and lifecycle:\n\n**Layer Cake (corrected order):**\n```\nFormulas (YAML compile-time macros)\n ↓\nProtos (template label, read-only)\n ↓\nMolecules (pour, bond, squash, burn)\n ↓\nEpics (parent-child, dependencies) ← DATA PLANE\n ↓\nIssues (JSONL, git-backed) ← STORAGE\n```\n\n**Key insight:** Molecules work without protos - you can create ad-hoc molecules.\nProtos are templates FOR molecules, not the other way around.\n\n**New concepts to document:**\n1. Orphan vs Stale matrix (blocking × assigned dimensions)\n2. Graph pressure as staleness indicator (not time)\n3. Parallelism via absence of depends_on (default parallel, opt-in sequential)\n4. progress.Completed/Total are computed, not stored\n5. WaitsFor: all-children for dynamic fanout gates\n\n**Common pitfalls for agents:**\n- Thinking phases/steps imply sequence (NO - deps do)\n- Confusing protos with molecules\n- Temporal language inverting dependencies\n- Forgetting to squash/burn wisps\n\n**Consider splitting docs:**\n- molecules.md → conceptual overview\n- formulas.md → YAML syntax reference\n- lifecycle.md → pour/squash/burn/bond operations\n- patterns.md → Christmas Ornament, factory assembly, etc.","status":"closed","priority":2,"issue_type":"task","assignee":"beads/crew/dave","created_at":"2025-12-24T18:23:23.968937-08:00","updated_at":"2025-12-24T19:30:49.011831-08:00","closed_at":"2025-12-24T19:30:49.011831-08:00","close_reason":"Created docs/MOLECULES.md with comprehensive molecular chemistry documentation: layer cake architecture, phase metaphor, agent pitfalls, CLI commands. Updated CLI_REFERENCE.md and ARCHITECTURE.md with cross-references."}
{"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)"}