diff --git a/.beads/issues.jsonl b/.beads/issues.jsonl index be505c05..f6ebd362 100644 --- a/.beads/issues.jsonl +++ b/.beads/issues.jsonl @@ -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Superseded by 0.30.7 release - already committed and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":"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-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":"closed","priority":2,"issue_type":"task","created_at":"2025-12-20T23:52:15.041776-08:00","updated_at":"2025-12-21T00:04:32.335849-08:00","closed_at":"2025-12-21T00:04:32.335849-08:00","close_reason":"Removed molecule.go - use bd mol bond instead","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"} @@ -169,7 +169,7 @@ {"id":"bd-hy9p","title":"Add --body-file flag to bd create for reading descriptions from files","description":"## Problem\n\nCreating issues with long/complex descriptions via CLI requires shell escaping gymnastics:\n\n```bash\n# Current workaround - awkward heredoc quoting\nbd create --title=\"...\" --description=\"$(cat \u003c\u003c'EOF'\n...markdown...\nEOF\n)\"\n\n# Often fails with quote escaping errors in eval context\n# Agents resort to writing temp files then reading them\n```\n\n## Proposed Solution\n\nAdd `--body-file` and `--description-file` flags to read description from a file, matching `gh` CLI pattern.\n\n```bash\n# Natural pattern that aligns with training data\ncat \u003e /tmp/desc.md \u003c\u003c 'EOF'\n...markdown content...\nEOF\n\nbd create --title=\"...\" --body-file=/tmp/desc.md\n```\n\n## Implementation\n\n### 1. Add new flags to `bd create`\n\n```go\ncreateCmd.Flags().String(\"body-file\", \"\", \"Read description from file (use - for stdin)\")\ncreateCmd.Flags().String(\"description-file\", \"\", \"Alias for --body-file\")\n```\n\n### 2. Flag precedence\n\n- If `--body-file` or `--description-file` is provided, read from file\n- If value is `-`, read from stdin\n- Otherwise fall back to `--body` or `--description` flag\n- If neither provided, description is empty (current behavior)\n\n### 3. Error handling\n\n- File doesn't exist → clear error message\n- File not readable → clear error message\n- stdin specified but not available → clear error message\n\n## Benefits\n\n✅ **Matches training data**: `gh issue create --body-file file.txt` is a common pattern\n✅ **No shell escaping issues**: File content is read directly\n✅ **Works with any content**: Markdown, special characters, quotes, etc.\n✅ **Agent-friendly**: Agents already write complex content to temp files\n✅ **User-friendly**: Easier for humans too when pasting long descriptions\n\n## Related Commands\n\nConsider adding similar support to:\n- `bd update --body-file` (for updating descriptions)\n- `bd comment --body-file` (if/when we add comments)\n\n## Examples\n\n```bash\n# From file\nbd create --title=\"Add new feature\" --body-file=feature.md\n\n# From stdin\necho \"Quick description\" | bd create --title=\"Bug fix\" --body-file=-\n\n# With other flags\nbd create \\\n --title=\"Security issue\" \\\n --type=bug \\\n --priority=0 \\\n --body-file=security-report.md \\\n --label=security\n```\n\n## Testing\n\n- Test with normal files\n- Test with stdin (`-`)\n- Test with non-existent files (error handling)\n- Test with binary files (should handle gracefully)\n- Test with empty files (valid - empty description)\n- Test that `--description-file` and `--body-file` are equivalent aliases","status":"closed","priority":1,"issue_type":"feature","created_at":"2025-11-22T00:02:08.762684-08:00","updated_at":"2025-12-17T23:13:40.536024-08:00","closed_at":"2025-12-17T17:28:52.505239-08:00"} {"id":"bd-hzvz","title":"Update info.go versionChanges","description":"Add entry to versionChanges in cmd/bd/info.go with agent-actionable changes for 0.30.7","status":"closed","priority":1,"issue_type":"task","created_at":"2025-12-19T22:56:48.649359-08:00","updated_at":"2025-12-19T22:57:31.604229-08:00","closed_at":"2025-12-19T22:57:31.604229-08:00","dependencies":[{"issue_id":"bd-hzvz","depends_on_id":"bd-8pyn","type":"parent-child","created_at":"2025-12-19T22:56:48.652068-08:00","created_by":"stevey"},{"issue_id":"bd-hzvz","depends_on_id":"bd-2ep8","type":"blocks","created_at":"2025-12-19T22:56:48.652376-08:00","created_by":"stevey"}]} {"id":"bd-i0rx","title":"Merge: bd-ao0s","description":"branch: polecat/rictus\ntarget: main\nsource_issue: bd-ao0s\nrig: beads","status":"closed","priority":2,"issue_type":"merge-request","created_at":"2025-12-20T01:13:42.716658-08:00","updated_at":"2025-12-20T23:17:26.993744-08:00","closed_at":"2025-12-20T23:17:26.993744-08:00","close_reason":"Branches nuked, MRs obsolete"} -{"id":"bd-icnf","title":"Add bd mol run command (bond + assign + pin)","description":"bd mol run = bond + assign root to caller + pin to startup mail. This is the Gas Town integration point. When agent restarts, check startup mail, find pinned molecule root, query bd ready for next step. Makes molecules immortal.","status":"open","priority":1,"issue_type":"feature","created_at":"2025-12-20T23:52:17.462882-08:00","updated_at":"2025-12-20T23:52:17.462882-08:00","dependencies":[{"issue_id":"bd-icnf","depends_on_id":"bd-ffjt","type":"blocks","created_at":"2025-12-20T23:52:25.871742-08:00","created_by":"daemon"}]} +{"id":"bd-icnf","title":"Add bd mol run command (bond + assign + pin)","description":"bd mol run = bond + assign root to caller + pin to startup mail. This is the Gas Town integration point. When agent restarts, check startup mail, find pinned molecule root, query bd ready for next step. Makes molecules immortal.","status":"in_progress","priority":1,"issue_type":"feature","created_at":"2025-12-20T23:52:17.462882-08:00","updated_at":"2025-12-21T00:04:59.466069-08:00","dependencies":[{"issue_id":"bd-icnf","depends_on_id":"bd-ffjt","type":"blocks","created_at":"2025-12-20T23:52:25.871742-08:00","created_by":"daemon"}]} {"id":"bd-in7","title":"Test message","description":"Hello world","status":"closed","priority":2,"issue_type":"message","created_at":"2025-12-17T23:16:13.184946-08:00","updated_at":"2025-12-18T17:42:26.000073-08:00","closed_at":"2025-12-17T23:37:38.563369-08:00"} {"id":"bd-indn","title":"bd template commands fail with daemon mode","description":"The `bd template show` and `bd template instantiate` commands fail with 'Error loading template: no database connection' when daemon is running.\n\n**Reproduction:**\n```bash\nbd daemon --start\nbd template show bd-qqc # Error: no database connection\nbd template show bd-qqc --no-daemon # Works\n```\n\n**Expected:** Template commands should work with daemon like other commands.\n\n**Workaround:** Use `--no-daemon` flag.\n\n**Location:** Likely in cmd/bd/template.go - daemon RPC path not implemented for template operations.","status":"open","priority":2,"issue_type":"bug","created_at":"2025-12-18T22:57:35.16596-08:00","updated_at":"2025-12-18T22:57:35.16596-08:00"} {"id":"bd-io8c","title":"Improve test coverage for internal/syncbranch (33.0% → 70%)","description":"The syncbranch package has only 33.0% test coverage. This package handles git sync operations and is critical for data integrity.\n\nCurrent coverage: 33.0%\nTarget coverage: 70%","status":"open","priority":1,"issue_type":"task","created_at":"2025-12-13T20:43:02.079145-08:00","updated_at":"2025-12-13T21:01:14.972533-08:00"} diff --git a/cmd/bd/mol.go b/cmd/bd/mol.go index e2945963..a8c485b4 100644 --- a/cmd/bd/mol.go +++ b/cmd/bd/mol.go @@ -292,14 +292,134 @@ Example: }, } +var molRunCmd = &cobra.Command{ + Use: "run ", + Short: "Bond molecule and start execution (bond + assign + pin)", + Long: `Run a molecule by bonding it and setting up for durable execution. + +This command: + 1. Bonds the molecule (creates issues from template) + 2. Assigns the root issue to the caller + 3. Sets root status to in_progress + 4. Pins the root issue for session recovery + +After a crash or session reset, the pinned root issue ensures the agent +can resume from where it left off by checking 'bd ready'. + +Example: + bd mol run mol-version-bump --var version=1.2.0 + bd mol run bd-qqc --var version=0.32.0 --var date=2025-01-01`, + Args: cobra.ExactArgs(1), + Run: func(cmd *cobra.Command, args []string) { + CheckReadonly("mol run") + + ctx := rootCtx + + // mol run requires direct store access + if store == nil { + if daemonClient != nil { + fmt.Fprintf(os.Stderr, "Error: mol run requires direct database access\n") + fmt.Fprintf(os.Stderr, "Hint: use --no-daemon flag: bd --no-daemon mol run %s ...\n", args[0]) + } else { + fmt.Fprintf(os.Stderr, "Error: no database connection\n") + } + os.Exit(1) + } + + varFlags, _ := cmd.Flags().GetStringSlice("var") + + // Parse variables + vars := make(map[string]string) + for _, v := range varFlags { + parts := strings.SplitN(v, "=", 2) + if len(parts) != 2 { + fmt.Fprintf(os.Stderr, "Error: invalid variable format '%s', expected 'key=value'\n", v) + os.Exit(1) + } + vars[parts[0]] = parts[1] + } + + // Resolve molecule ID + moleculeID, err := utils.ResolvePartialID(ctx, store, args[0]) + if err != nil { + fmt.Fprintf(os.Stderr, "Error resolving molecule ID %s: %v\n", args[0], err) + os.Exit(1) + } + + // Load the molecule subgraph + subgraph, err := loadTemplateSubgraph(ctx, store, moleculeID) + if err != nil { + fmt.Fprintf(os.Stderr, "Error loading molecule: %v\n", err) + os.Exit(1) + } + + // Check for missing variables + requiredVars := extractAllVariables(subgraph) + var missingVars []string + for _, v := range requiredVars { + if _, ok := vars[v]; !ok { + missingVars = append(missingVars, v) + } + } + if len(missingVars) > 0 { + fmt.Fprintf(os.Stderr, "Error: missing required variables: %s\n", strings.Join(missingVars, ", ")) + fmt.Fprintf(os.Stderr, "Provide them with: --var %s=\n", missingVars[0]) + os.Exit(1) + } + + // Bond the molecule with actor as assignee + result, err := bondMolecule(ctx, store, subgraph, vars, actor, actor) + if err != nil { + fmt.Fprintf(os.Stderr, "Error bonding molecule: %v\n", err) + os.Exit(1) + } + + // Update root issue: set status=in_progress and pinned=true + rootID := result.NewEpicID + updates := map[string]interface{}{ + "status": string(types.StatusInProgress), + "pinned": true, + } + if err := store.UpdateIssue(ctx, rootID, updates, actor); err != nil { + fmt.Fprintf(os.Stderr, "Error updating root issue: %v\n", err) + os.Exit(1) + } + + // Schedule auto-flush + markDirtyAndScheduleFlush() + + if jsonOutput { + outputJSON(map[string]interface{}{ + "root_id": rootID, + "created": result.Created, + "id_mapping": result.IDMapping, + "pinned": true, + "status": "in_progress", + "assignee": actor, + }) + return + } + + fmt.Printf("%s Molecule running: created %d issues\n", ui.RenderPass("✓"), result.Created) + fmt.Printf(" Root issue: %s (pinned, in_progress)\n", rootID) + fmt.Printf(" Assignee: %s\n", actor) + fmt.Println("\nNext steps:") + fmt.Printf(" bd ready # Find unblocked work in this molecule\n") + fmt.Printf(" bd show %s # View molecule status\n", rootID[:8]) + }, +} + func init() { molBondCmd.Flags().StringSlice("var", []string{}, "Variable substitution (key=value)") molBondCmd.Flags().Bool("dry-run", false, "Preview what would be created") molBondCmd.Flags().String("assignee", "", "Assign the root issue to this agent/user") + molRunCmd.Flags().StringSlice("var", []string{}, "Variable substitution (key=value)") + molCmd.AddCommand(molCatalogCmd) molCmd.AddCommand(molShowCmd) molCmd.AddCommand(molBondCmd) + molCmd.AddCommand(molRunCmd) rootCmd.AddCommand(molCmd) }