From 5eacec482daed53ac7a8b02728282903734035fb Mon Sep 17 00:00:00 2001 From: Steve Yegge Date: Wed, 24 Dec 2025 18:24:08 -0800 Subject: [PATCH] bd sync: 2025-12-24 18:24:08 --- .beads/issues.jsonl | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/.beads/issues.jsonl b/.beads/issues.jsonl index 2cc3df54..4dad12c8 100644 --- a/.beads/issues.jsonl +++ b/.beads/issues.jsonl @@ -82,6 +82,7 @@ {"id":"bd-687v","title":"Consider caching external dep resolution results","description":"Each call to GetReadyWork re-checks all external dependencies by:\n1. Querying for external deps in the local database\n2. Opening each external project's database\n3. Querying for closed issues with provides: labels\n\nFor workloads with many external deps or slow external databases, this adds latency on every bd ready call.\n\nPotential optimizations:\n- In-memory TTL cache for external dep status (e.g., 60 second TTL)\n- Store resolved status in a local cache table with timestamp\n- Batch resolution of common project/capability pairs\n\nThis is not urgent - current implementation is correct and performant for typical workloads. Only becomes an issue with many external deps across many projects.","status":"deferred","priority":3,"issue_type":"task","created_at":"2025-12-21T23:45:16.360877-08:00","updated_at":"2025-12-23T12:27:02.223409-08:00","dependencies":[{"issue_id":"bd-687v","depends_on_id":"bd-zmmy","type":"discovered-from","created_at":"2025-12-21T23:45:16.361493-08:00","created_by":"daemon"}]} {"id":"bd-68bf","title":"Code review: bd mol bond implementation","description":"Review the mol bond command implementation before shipping.\n\nFocus areas:\n1. runMolBond() - polymorphic dispatch logic correctness\n2. bondProtoProto() - compound proto creation, dependency wiring\n3. bondProtoMol() / bondMolProto() - spawn and attach logic\n4. bondMolMol() - joining molecules, lineage tracking\n5. BondRef usage - is lineage tracked correctly?\n6. Error handling - are all failure modes covered?\n7. Edge cases - what could go wrong?\n\nFile: cmd/bd/mol.go (lines 485-859)\nCommit: 386b513e","status":"closed","priority":2,"issue_type":"task","created_at":"2025-12-21T10:13:09.425229-08:00","updated_at":"2025-12-21T11:18:14.206869-08:00","closed_at":"2025-12-21T11:18:14.206869-08:00","close_reason":"Reviewed and fixed label persistence bug","dependencies":[{"issue_id":"bd-68bf","depends_on_id":"bd-o91r","type":"discovered-from","created_at":"2025-12-21T10:13:09.426471-08:00","created_by":"daemon"}]} {"id":"bd-68e4","title":"doctor --fix should export when DB has more issues than JSONL","description":"When 'bd doctor' detects a count mismatch (DB has more issues than JSONL), it currently recommends 'bd sync --import-only', which imports JSONL into DB. But JSONL is the source of truth, not the DB.\n\n**Current behavior:**\n- Doctor detects: DB has 355 issues, JSONL has 292\n- Recommends: 'bd sync --import-only' \n- User runs it: Returns '0 created, 0 updated' (no-op, because JSONL hasn't changed)\n- User is stuck\n\n**Root cause:**\nThe doctor fix is one-directional (JSONL→DB) when it should be bidirectional. If DB has MORE issues, they haven't been exported yet - the fix should be 'bd export' (DB→JSONL), not import.\n\n**Desired fix:**\nIn fix.DBJSONLSync(), detect which has more data:\n- If DB \u003e JSONL: Run 'bd export' to sync JSONL (since DB is the working copy)\n- If JSONL \u003e DB: Run 'bd sync --import-only' to import (JSONL is source of truth)\n- If equal but timestamps differ: Detect based on file mtime\n\nThis makes 'bd doctor --fix' actually fix the problem instead of being a no-op.","status":"closed","priority":2,"issue_type":"bug","created_at":"2025-12-21T11:17:20.994319182-07:00","updated_at":"2025-12-21T11:23:24.38523731-07:00","closed_at":"2025-12-21T11:23:24.38523731-07:00"} +{"id":"bd-6a5z","title":"Add stale molecule check to bd doctor","description":"Extend bd doctor to detect stale molecules.\n\n**New check:**\n- Name: 'Stale Molecules'\n- Category: Workflow\n- Severity: Warning (don't fail overall check)\n\n**Detection:**\nReuse logic from bd mol stale command:\n- Find mols where Completed \u003e= Total but root is open\n- Filter to orphaned (not assigned, not pinned)\n- Extra weight if blocking other work\n\n**Output:**\n```\n⚠ Stale Molecules\n Found 2 complete-but-unclosed molecules:\n - bd-xyz: Version bump v0.36.0 (blocking 1 issue)\n - bd-uvw: Old patrol (not blocking)\n Fix: bd close \u003cid\u003e or bd mol squash \u003cid\u003e\n```\n\n**--fix behavior:**\n- Auto-close stale mols (with reason 'Auto-closed by bd doctor')\n- Or prompt interactively with -i flag\n\nDepends on: bd mol stale command","status":"open","priority":3,"issue_type":"task","created_at":"2025-12-24T18:23:24.549941-08:00","updated_at":"2025-12-24T18:23:24.549941-08:00","dependencies":[{"issue_id":"bd-6a5z","depends_on_id":"bd-anv2","type":"blocks","created_at":"2025-12-24T18:23:48.682552-08:00","created_by":"daemon"}]} {"id":"bd-6fe4622f","title":"Remove unreachable utility functions","description":"Several small utility functions are unreachable:\n\nFiles to clean:\n1. `internal/storage/sqlite/hash.go` - `computeIssueContentHash` (line 17)\n - Check if entire file can be deleted if only contains this function\n\n2. `internal/config/config.go` - `FileUsed` (line 151)\n - Delete unused config helper\n\n3. `cmd/bd/git_sync_test.go` - `verifyIssueOpen` (line 300)\n - Delete dead test helper\n\n4. `internal/compact/haiku.go` - `HaikuClient.SummarizeTier2` (line 81)\n - Tier 2 summarization not implemented\n - Options: implement feature OR delete method\n\nImpact: Removes 50-100 LOC depending on decisions","status":"closed","priority":2,"issue_type":"task","created_at":"2025-10-28T16:20:02.434573-07:00","updated_at":"2025-12-17T22:58:34.563993-08:00","closed_at":"2025-12-17T22:58:34.563993-08:00","close_reason":"Closed"} {"id":"bd-6gd","title":"Remove legacy MCP Agent Mail integration","description":"## Summary\n\nRemove the legacy MCP Agent Mail system that requires an external HTTP server. Keep the native `bd mail` system which stores messages as git-synced issues.\n\n## Background\n\nTwo mail systems exist in the codebase:\n1. **Legacy Agent Mail** (`bd message`) - External server dependency, complex setup\n2. **Native bd mail** (`bd mail`) - Built-in, git-synced, no dependencies\n\nThe legacy system causes confusion and is no longer needed. Gas Town's Town Mail will use the native `bd mail` system.\n\n## Files to Delete\n\n### CLI Command\n- [ ] `cmd/bd/message.go` - The `bd message` command implementation\n\n### MCP Integration\n- [ ] `integrations/beads-mcp/src/beads_mcp/mail.py` - HTTP wrapper for Agent Mail server\n- [ ] `integrations/beads-mcp/src/beads_mcp/mail_tools.py` - MCP tool definitions\n- [ ] `integrations/beads-mcp/tests/test_mail.py` - Tests for legacy mail\n\n### Documentation\n- [ ] `docs/AGENT_MAIL.md`\n- [ ] `docs/AGENT_MAIL_QUICKSTART.md`\n- [ ] `docs/AGENT_MAIL_DEPLOYMENT.md`\n- [ ] `docs/AGENT_MAIL_MULTI_WORKSPACE_SETUP.md`\n- [ ] `docs/adr/002-agent-mail-integration.md`\n\n## Code to Update\n\n- [ ] Remove `message` command registration from `cmd/bd/main.go`\n- [ ] Remove mail tool imports/registration from MCP server `__init__.py` or `server.py`\n- [ ] Check for any other references to Agent Mail in the codebase\n\n## Verification\n\n- [ ] `bd message` command no longer exists\n- [ ] `bd mail` command still works\n- [ ] MCP server starts without errors\n- [ ] Tests pass\n","status":"closed","priority":1,"issue_type":"task","created_at":"2025-12-17T23:04:04.099935-08:00","updated_at":"2025-12-17T23:13:24.128752-08:00","closed_at":"2025-12-17T23:13:24.128752-08:00","close_reason":"Removed legacy MCP Agent Mail integration. Kept native bd mail system."} {"id":"bd-6ns7","title":"test hook pin","status":"tombstone","priority":2,"issue_type":"task","assignee":"stevey","created_at":"2025-12-23T04:39:16.619755-08:00","updated_at":"2025-12-23T04:51:29.436788-08:00","deleted_at":"2025-12-23T04:51:29.436788-08:00","deleted_by":"daemon","delete_reason":"delete","original_type":"task"} @@ -157,6 +158,7 @@ {"id":"bd-akcq","title":"Design molecule step hooks","description":"Hooks that fire between molecule steps. When a bead in a molecule closes, trigger hook that can spawn agent attention to prompts/requests. This enables reactive orchestration - the molecule drives, hooks respond. Gas Town feature built on Beads data plane.","status":"closed","priority":2,"issue_type":"feature","created_at":"2025-12-20T23:52:18.63487-08:00","updated_at":"2025-12-21T17:53:19.284064-08:00","closed_at":"2025-12-21T17:53:19.284064-08:00","close_reason":"Moved to gastown: gt-ne1t","dependencies":[{"issue_id":"bd-akcq","depends_on_id":"bd-icnf","type":"blocks","created_at":"2025-12-20T23:52:25.935274-08:00","created_by":"daemon"}]} {"id":"bd-aks","title":"Add tests for import/export functionality","description":"Import/export functions like ImportIssues, exportToJSONLWithStore, and AutoImportIfNewer have low coverage. These are critical for data integrity and multi-repo synchronization.","status":"closed","priority":1,"issue_type":"task","created_at":"2025-12-18T07:00:53.067006711-07:00","updated_at":"2025-12-19T09:54:57.011374404-07:00","closed_at":"2025-12-18T10:13:11.821944156-07:00","dependencies":[{"issue_id":"bd-aks","depends_on_id":"bd-6ss","type":"discovered-from","created_at":"2025-12-18T07:00:53.07185201-07:00","created_by":"matt"}]} {"id":"bd-an4s","title":"Version Bump: 0.32.1","description":"Release checklist for version 0.32.1. Patch release with MCP output control params and pin field fix.","status":"closed","priority":1,"issue_type":"epic","created_at":"2025-12-20T21:53:01.315592-08:00","updated_at":"2025-12-20T21:57:13.909864-08:00","closed_at":"2025-12-20T21:57:13.909864-08:00","close_reason":"Version 0.32.1 released"} +{"id":"bd-anv2","title":"Implement bd mol stale command","description":"Add command to detect complete-but-unclosed molecules.\n\n**Definition of stale:**\nA molecule is stale if:\n1. All children are closed (Completed \u003e= Total)\n2. Root issue is still open\n3. Not assigned to anyone\n4. Not pinned to any hook\n5. AND it's blocking other assigned work (graph pressure)\n\n**Command design:**\n```bash\nbd mol stale # List stale mols\nbd mol stale --json # Machine-readable\nbd mol stale --blocking # Only show those blocking other work\nbd mol stale --all # Include orphaned-but-not-blocking\n```\n\n**Output:**\n```\nStale molecules (complete but unclosed, blocking work):\n\n bd-xyz \"Version bump v0.36.0\" (blocking: bd-abc, bd-def)\n → Close with: bd close bd-xyz\n → Or squash: bd mol squash bd-xyz\n\nOrphaned molecules (complete but unclosed, not blocking):\n bd-uvw \"Old patrol cycle\"\n → Consider: bd mol burn bd-uvw\n```\n\n**Implementation:**\n1. Query all open issues with children (potential mols)\n2. Compute progress for each (Completed vs Total)\n3. Filter to complete ones\n4. Check assigned_to field\n5. Check pinned status (may need gt integration)\n6. Check if blocking other assigned work\n\nDoes NOT use time-based staleness. Graph pressure only.","status":"open","priority":2,"issue_type":"feature","created_at":"2025-12-24T18:23:24.27032-08:00","updated_at":"2025-12-24T18:23:24.27032-08:00"} {"id":"bd-ao0s","title":"bd graph crashes with --no-daemon on closed issues","description":"The `bd graph` command panics with nil pointer dereference when using `--no-daemon` flag on an issue with closed children.\n\n**Reproduction:**\n```bash\nbd graph bd-qqc --no-daemon\n# panic: runtime error: invalid memory address or nil pointer dereference\n# in main.computeDependencyCounts\n```\n\n**Stack trace:**\n```\npanic: runtime error: invalid memory address or nil pointer dereference\n[signal SIGSEGV: segmentation violation code=0x2 addr=0x20 pc=0x1010bdfb0]\n\ngoroutine 1 [running]:\nmain.computeDependencyCounts(...)\n /Users/stevey/gt/beads/crew/emma/cmd/bd/graph.go:428\nmain.renderGraph(0x1400033bb80, 0x0)\n /Users/stevey/gt/beads/crew/emma/cmd/bd/graph.go:307 +0x300\n```\n\n**Location:** cmd/bd/graph.go:428 - computeDependencyCounts() not handling nil case","status":"closed","priority":2,"issue_type":"bug","created_at":"2025-12-18T22:57:36.972585-08:00","updated_at":"2025-12-20T01:13:29.206821-08:00","closed_at":"2025-12-20T01:13:29.206821-08:00","close_reason":"Fixed: pass subgraph instead of nil to renderGraph"} {"id":"bd-aq3s","title":"Merge: bd-u2sc.3","description":"branch: polecat/Modular\ntarget: main\nsource_issue: bd-u2sc.3\nrig: beads","status":"closed","priority":3,"issue_type":"merge-request","created_at":"2025-12-23T13:47:14.281479-08:00","updated_at":"2025-12-23T19:12:08.354548-08:00","closed_at":"2025-12-23T19:12:08.354548-08:00","close_reason":"Stale merge-requests from orphaned polecat branches - refinery not processing"} {"id":"bd-au0","title":"Command Set Standardization \u0026 Flag Consistency","description":"Comprehensive improvements to bd command set based on 2025 audit findings.\n\n## Background\nSee docs/command-audit-2025.md for detailed analysis.\n\n## Goals\n1. Standardize flag naming and behavior across all commands\n2. Add missing flags for feature parity\n3. Fix naming confusion\n4. Improve consistency in JSON output\n\n## Success Criteria\n- All mutating commands support --dry-run (no --preview variants)\n- bd update supports label operations\n- bd search has filter parity with bd list\n- Priority flags accept both int and P0-P4 format everywhere\n- JSON output is consistent across all commands","status":"open","priority":2,"issue_type":"epic","created_at":"2025-11-21T21:05:55.672749-05:00","updated_at":"2025-11-21T21:05:55.672749-05:00"} @@ -378,6 +380,7 @@ {"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-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":"closed","priority":2,"issue_type":"bug","created_at":"2025-11-20T20:17:27.606219-05:00","updated_at":"2025-12-17T23:13:40.536905-08:00","closed_at":"2025-12-17T19:11:12.965289-08:00","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":"{}"}]} {"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)"} @@ -498,6 +501,8 @@ {"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-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":"open","priority":2,"issue_type":"task","created_at":"2025-12-24T18:23:23.968937-08:00","updated_at":"2025-12-24T18:23:23.968937-08:00"} {"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"}