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refactor(mol): remove molecule.go (superseded by mol.go)

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The simple single-issue instantiation in molecule.go is superseded by
the full DAG-based mol commands. Use 'bd mol bond' for all molecule
instantiation - it handles both single-issue and multi-issue molecules.

Closes: bd-8b0x

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
This commit is contained in:
Steve Yegge
2025-12-21 00:04:25 -08:00
parent ca678ca5ba
commit b950604e0a
3 changed files with 42 additions and 355 deletions
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4
.beads/issues.jsonl
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@@ -64,7 +64,7 @@
{"id":"bd-7tuu","title":"Commit and push release","description":"git add -A \u0026\u0026 git commit \u0026\u0026 git push to trigger CI","status":"closed","priority":1,"issue_type":"task","created_at":"2025-12-19T22:56:02.053382-08:00","updated_at":"2025-12-20T01:23:52.484043-08:00","closed_at":"2025-12-20T01:23:52.484043-08:00","close_reason":"Superseded by 0.30.7 release - already committed and pushed","dependencies":[{"issue_id":"bd-7tuu","depends_on_id":"bd-6s61","type":"parent-child","created_at":"2025-12-19T22:56:15.021087-08:00","created_by":"daemon"},{"issue_id":"bd-7tuu","depends_on_id":"bd-hw3w","type":"blocks","created_at":"2025-12-19T22:56:23.291591-08:00","created_by":"daemon"}]}
{"id":"bd-7yg","title":"Git merge driver uses invalid placeholders (%L, %R instead of %A, %B)","description":"## Problem\n\nThe beads git merge driver is configured with invalid Git placeholders:\n\n```\ngit config merge.beads.driver \"bd merge %A %O %L %R\"\n```\n\nGit doesn't recognize `%L` or `%R` as valid merge driver placeholders. The valid placeholders are:\n- `%O` = base (common ancestor)\n- `%A` = current version (ours)\n- `%B` = other version (theirs)\n\n## Impact\n\n- Affects ALL users when they have `.beads/beads.jsonl` merge conflicts\n- Automatic JSONL merge fails with error: \"error reading left file: failed to open file: open 7: no such file or directory\"\n- Users must manually resolve conflicts instead of getting automatic merge\n\n## Root Cause\n\nThe `bd init` command (or wherever the merge driver is configured) is using non-standard placeholders. When Git encounters `%L` and `%R`, it either passes them literally or interprets them incorrectly.\n\n## Fix\n\nUpdate the merge driver configuration to:\n```\ngit config merge.beads.driver \"bd merge %A %O %A %B\"\n```\n\nWhere:\n- 1st `%A` = output file (current file, will be overwritten)\n- `%O` = base (common ancestor)\n- 2nd `%A` = left/current version\n- `%B` = right/other version\n\n## Action Items\n\n1. Fix `bd init` (or equivalent setup command) to use correct placeholders\n2. Add migration/warning for existing users with misconfigured merge driver\n3. Update documentation with correct merge driver setup\n4. Consider adding validation when `bd init` is run","status":"closed","priority":1,"issue_type":"bug","created_at":"2025-11-21T19:51:55.747608-05:00","updated_at":"2025-12-17T23:13:40.532368-08:00","closed_at":"2025-12-17T17:24:52.678668-08:00"}
{"id":"bd-89f89fc0","title":"Remove unreachable RPC methods","description":"Several RPC server and client methods are unreachable and should be removed:\n\nServer methods (internal/rpc/server.go):\n- `Server.GetLastImportTime` (line 2116)\n- `Server.SetLastImportTime` (line 2123)\n- `Server.findJSONLPath` (line 2255)\n\nClient methods (internal/rpc/client.go):\n- `Client.Import` (line 311) - RPC import not used (daemon uses autoimport)\n\nEvidence:\n```bash\ngo run golang.org/x/tools/cmd/deadcode@latest -test ./...\n```\n\nImpact: Removes ~80 LOC of unused RPC code","status":"closed","priority":2,"issue_type":"task","created_at":"2025-10-28T16:20:02.432202-07:00","updated_at":"2025-12-17T22:58:34.564401-08:00","closed_at":"2025-12-17T22:58:34.564401-08:00","close_reason":"Closed"}
{"id":"bd-8b0x","title":"Remove molecule.go (simple instantiation)","description":"molecule.go uses is_template field for simple single-issue cloning. This is too simple for what molecules should be - full DAG orchestration. The use case is covered by bd mol bond with a single-issue molecule. Delete molecule.go and its commands.","status":"open","priority":2,"issue_type":"task","created_at":"2025-12-20T23:52:15.041776-08:00","updated_at":"2025-12-20T23:52:15.041776-08:00","dependencies":[{"issue_id":"bd-8b0x","depends_on_id":"bd-ffjt","type":"blocks","created_at":"2025-12-20T23:52:25.807967-08:00","created_by":"daemon"}]}
{"id":"bd-8b0x","title":"Remove molecule.go (simple instantiation)","description":"molecule.go uses is_template field for simple single-issue cloning. This is too simple for what molecules should be - full DAG orchestration. The use case is covered by bd mol bond with a single-issue molecule. Delete molecule.go and its commands.","status":"in_progress","priority":2,"issue_type":"task","created_at":"2025-12-20T23:52:15.041776-08:00","updated_at":"2025-12-21T00:03:59.388461-08:00","dependencies":[{"issue_id":"bd-8b0x","depends_on_id":"bd-ffjt","type":"blocks","created_at":"2025-12-20T23:52:25.807967-08:00","created_by":"daemon"}]}
{"id":"bd-8e0q","title":"Merge: beads-ocs","description":"branch: polecat/valkyrie\ntarget: main\nsource_issue: beads-ocs\nrig: beads","status":"closed","priority":2,"issue_type":"merge-request","created_at":"2025-12-19T23:24:45.281478-08:00","updated_at":"2025-12-20T23:17:26.995706-08:00","closed_at":"2025-12-20T23:17:26.995706-08:00","close_reason":"Branches nuked, MRs obsolete"}
{"id":"bd-8fgn","title":"test hash length","status":"tombstone","priority":2,"issue_type":"task","created_at":"2025-12-16T13:49:32.113843-08:00","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":"task"}
{"id":"bd-8g8","title":"Fix G304 potential file inclusion in cmd/bd/tips.go:259","description":"Linting issue: G304: Potential file inclusion via variable (gosec) at cmd/bd/tips.go:259:18. Error: if data, err := os.ReadFile(settingsPath); err == nil {","status":"closed","issue_type":"bug","created_at":"2025-12-07T15:34:57.189730843-07:00","updated_at":"2025-12-17T23:13:40.534569-08:00","closed_at":"2025-12-17T16:46:11.029837-08:00"}
@@ -148,7 +148,7 @@
{"id":"bd-f3ll","title":"Merge: bd-ot0w","description":"branch: polecat/dementus\ntarget: main\nsource_issue: bd-ot0w\nrig: beads","status":"closed","priority":2,"issue_type":"merge-request","created_at":"2025-12-19T23:20:33.495772-08:00","updated_at":"2025-12-20T23:17:27.000252-08:00","closed_at":"2025-12-20T23:17:27.000252-08:00","close_reason":"Branches nuked, MRs obsolete"}
{"id":"bd-f5cc","title":"Thread Test","description":"Testing the thread feature","status":"tombstone","priority":2,"issue_type":"message","created_at":"2025-12-16T18:21:01.244501-08:00","updated_at":"2025-12-17T16:11:17.070763-08:00","dependencies":[{"issue_id":"bd-f5cc","depends_on_id":"bd-x36g","type":"supersedes","created_at":"2025-12-18T13:45:31.137191-08:00","created_by":"migration"}],"deleted_at":"2025-12-17T16:11:17.070763-08:00","deleted_by":"batch delete","delete_reason":"batch delete","original_type":"message"}
{"id":"bd-fa2h","title":"🤝 HANDOFF: v0.31.0 released, molecules discussion","description":"Session completed 0.31.0 release and had important molecules discussion.\n\n## Completed\n- v0.31.0 released (deferred status, audit trail, directory labels, etc.)\n- Fixed lint issues, hook version markers, codesigning\n- All CI green, artifacts verified\n\n## Filed Issues\n- bd-usro: Rename template instantiate → bd mol bond\n- bd-y8bj: Auto-detect identity for bd mail (P1 bug)\n- gt-975: Molecule execution support for polecats/crew\n- gt-976: Crew lifecycle support in Deacon\n\n## Key Insight\nMolecules are the future - TodoWrite is ephemeral, molecules are persistent institutional memory on the world chain. I tried to use TodoWrite for version bump and missed steps (codesigning, MCP verification). Molecules would have caught this.\n\n## Next Steps\n- bd mol bond implementation is priority\n- Max has gt-976 for crew lifecycle (enables automated refresh mid-molecule)\n\nCheck bd ready and gt-975/976 status.","status":"open","priority":2,"issue_type":"message","assignee":"beads/crew/dave","created_at":"2025-12-20T17:23:09.889562-08:00","updated_at":"2025-12-20T17:23:09.889562-08:00","sender":"Steve Yegge","ephemeral":true}
{"id":"bd-ffjt","title":"Unify template.go and mol.go under bd mol","description":"Consolidate the two DAG-template systems into one under the mol command. mol.go (on rictus branch) has the right UX (catalog/show/bond), template.go has the mechanics. Merge them, deprecate bd template commands.","status":"in_progress","priority":1,"issue_type":"task","created_at":"2025-12-20T23:52:13.208972-08:00","updated_at":"2025-12-20T23:55:11.522661-08:00"}
{"id":"bd-ffjt","title":"Unify template.go and mol.go under bd mol","description":"Consolidate the two DAG-template systems into one under the mol command. mol.go (on rictus branch) has the right UX (catalog/show/bond), template.go has the mechanics. Merge them, deprecate bd template commands.","status":"closed","priority":1,"issue_type":"task","created_at":"2025-12-20T23:52:13.208972-08:00","updated_at":"2025-12-21T00:01:59.283765-08:00","closed_at":"2025-12-21T00:01:59.283765-08:00","close_reason":"Implemented mol commands with deprecation for template commands"}
{"id":"bd-fgw3","title":"Update local installation","description":"Run install script or brew upgrade to get new version locally: curl -fsSL .../install.sh | bash","status":"closed","priority":1,"issue_type":"task","created_at":"2025-12-19T22:56:05.052016-08:00","updated_at":"2025-12-20T00:49:51.928221-08:00","closed_at":"2025-12-20T00:25:52.805029-08:00","dependencies":[{"issue_id":"bd-fgw3","depends_on_id":"bd-6s61","type":"parent-child","created_at":"2025-12-19T22:56:15.248427-08:00","created_by":"daemon"},{"issue_id":"bd-fgw3","depends_on_id":"bd-si4g","type":"blocks","created_at":"2025-12-19T22:56:23.497325-08:00","created_by":"daemon"}]}
{"id":"bd-fi05","title":"bd sync fails with orphaned issues and duplicate ID conflict","description":"After fixing the deleted_at TEXT column scanning bug (commit 18b1eb2), bd sync still fails with two issues:\n\n1. Orphan Detection Warning: 12 orphaned child issues whose parents no longer exist (bd-cb64c226.* and bd-cbed9619.*)\n\n2. Import Failure: UNIQUE constraint failed for bd-360 - this tombstone exists in both DB and JSONL\n\nError: \"Import failed: error creating depth-0 issues: bulk insert issues: failed to insert issue bd-360: sqlite3: constraint failed: UNIQUE constraint failed: issues.id\"\n\nFix options:\n- Delete orphaned child issues with bd delete\n- Resolve bd-360 duplicate (in deletions.jsonl vs tombstone in DB)\n- Reset sync branch: git branch -f beads-sync main \u0026\u0026 git push --force-with-lease origin beads-sync","notes":"Fixed tombstone constraint violation bug. When deleting closed issues, the CHECK constraint (status = 'closed') = (closed_at IS NOT NULL) was violated because CreateTombstone didn't clear closed_at. Fix: set closed_at = NULL in tombstone creation SQL.\n\nThe sync data corruption (orphaned issues in beads-sync branch) requires manual cleanup: reset sync branch with 'git branch -f beads-sync main \u0026\u0026 git push --force-with-lease origin beads-sync'","status":"closed","priority":2,"issue_type":"bug","created_at":"2025-12-13T07:14:33.831346-08:00","updated_at":"2025-12-13T10:50:48.545465-08:00","closed_at":"2025-12-13T07:30:33.843986-08:00"}
{"id":"bd-fom","title":"Remove all deletions.jsonl code except migration","description":"There's deletions manifest code spread across the entire codebase that should have been removed after tombstone migration:\n\nFiles with deletions code (non-migration):\n- internal/deletions/ - entire package\n- cmd/bd/sync.go - 25+ references, auto-compact, sanitize\n- cmd/bd/delete.go - dual-writes to deletions.jsonl\n- internal/importer/importer.go - checks deletions manifest\n- internal/syncbranch/worktree.go - merges deletions.jsonl\n- cmd/bd/doctor/fix/sync.go - cleanupDeletionsManifest\n- cmd/bd/doctor/fix/deletions.go - HydrateDeletionsManifest\n- cmd/bd/integrity.go - checks deletions for data loss\n- cmd/bd/deleted.go - entire command\n- cmd/bd/compact.go - pruneDeletionsManifest\n- cmd/bd/doctor.go - checkDeletionsManifest\n- Plus many more\n\nAction: Aggressively remove all non-migration deletions code. Tombstones are the only deletion mechanism now.","status":"tombstone","priority":1,"issue_type":"task","created_at":"2025-12-16T13:29:04.960863-08:00","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":"task"}