Created 7 new beads to track TODOs that were previously inline comments:
- bd-7l27: Integrate migration detection into bd doctor (5 files)
- bd-6x6g: Add multi-repo target repo switching in bd create
- bd-ag35: Add daemon RPC endpoints for config and stale check
- bd-2dwo: Remove deprecated daemon logger function
- bd-0qx5: Implement Jira issue timestamp comparison for sync
- bd-7zka: Implement formula features (repeat, for_each, branch, gate, split)
- bd-h048: Refactor sync_test to use direct import logic
Updated 16 TODO comments to include bead ID references for tracking.
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Extracted 8 helper functions from the monolithic flushToJSONLWithState:
- recordFlushFailure/recordFlushSuccess: Failure tracking and counter management
- readExistingJSONL: Parse existing JSONL file for incremental merging
- fetchAndMergeIssues: Fetch dirty issues from DB and merge into map
- filterWisps: Remove ephemeral (wisp) issues from export
- filterByMultiRepoPrefix: Multi-repo prefix filtering for non-primary repos
- updateFlushExportMetadata: Store hashes and timestamps after export
- getIssuesToExport: Determine full vs incremental export issue list
Main function now reads as a clear pipeline:
1. Validate integrity -> 2. Get issues -> 3. Read existing JSONL
4. Merge from DB -> 5. Filter wisps -> 6. Filter by prefix
7. Write atomically -> 8. Update metadata
Benefits:
- Each helper is single-responsibility and testable
- Main function reduced from ~280 to ~94 lines
- Logic is clearly separated and documented
- Easier to understand and maintain
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Replaced three near-identical functions with a single unified collectSteps()
that uses a callback strategy for label handling:
- Removed collectStepsRecursive() (DB version)
- Removed collectStepsToSubgraph() (in-memory version)
- Removed collectStepIDMappings() (now handled by unified function)
The new collectSteps() function:
- Takes optional labelHandler callback for DB path (extracts labels separately)
- Takes optional issueMap for in-memory path
- Always builds idMapping for dependency resolution
- Eliminates ~60 lines of duplicated code
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Extracted duplicated switch statement for mapping step type strings to
types.IssueType into a single helper function. This removes code
duplication between collectStepsToSubgraph() and collectStepsRecursive().
The new stepTypeToIssueType() function:
- Converts 'task', 'bug', 'feature', 'epic', 'chore' to types
- Returns types.TypeTask for empty or unrecognized types
- Used by both functions with children-override-to-epic logic preserved
- migrate-* commands → subcommands of `bd migrate`
- relate/unrelate → subcommands of `bd dep`
- daemons subcommands → available under `bd daemon`
- comment alias → hidden with deprecation warning
All old commands still work with deprecation warnings for backwards
compatibility. Reduces visible top-level commands from ~73 to 66.
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
New commands and features:
- bd worktree for parallel development
- bd slot commands for agent bead slot management
- bd agent state for ZFC-compliant state reporting
- bd doctor --deep for full graph integrity validation
- Agent bead support (type=agent, type=role, migration 030)
- Computed .parent field in JSON output
- Auto-bypass daemon for wisp operations
- Pour warning for vapor-phase formulas
Performance:
- O(2^n) → O(V+E) cycle detection (GH#775)
Fixes:
- Import hash mismatch warnings
- Test updates for version tracking thresholds
- Migration test updated for new agent schema fields
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Now shows:
- Truncated title (40 chars max) after issue ID
- Assignee with @ prefix when present
- Format: 'bd-xxx completed · Title here... @assignee'
Also changed 'in_progress' to 'started' for cleaner output.
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Strip (bd-xxx), (gt-xxx) suffixes from code comments and changelog
entries. The descriptions remain meaningful without the ephemeral
issue IDs.
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Add a --deep flag to bd doctor that runs comprehensive graph integrity
checks on the beads database:
- Parent consistency: verify parent-child deps point to existing issues
- Dependency integrity: all dependencies reference valid issues
- Epic completeness: find epics ready to close (all children closed)
- Agent bead integrity: validate agent beads have valid state values
- Mail thread integrity: verify thread_id references exist
- Molecule integrity: check molecules have valid parent-child structures
The deep validation mode warns about potential slowness on large databases
and provides both human-readable and JSON output formats.
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Wisp operations (mol wisp *, mol burn, mol squash) and commands operating on
ephemeral issue IDs (bd-eph-*, gt-eph-*, eph-*) now auto-bypass the daemon.
Since wisps are ephemeral (Ephemeral=true) and never exported to JSONL,
the daemon cannot help with them anyway. This eliminates the need to manually
add --no-daemon for every wisp operation.
Changes:
- Add isWispOperation() helper to detect wisp commands and ephemeral IDs
- Add FallbackWispOperation constant for daemon status tracking
- Insert wisp detection in PersistentPreRunE daemon connection logic
- Update error messages in wisp.go, mol_burn.go, mol_squash.go
- Add comprehensive unit tests for isWispOperation()
Add agent commands for self-reporting state:
- bd agent state <agent> <state>: Update agent state and last_activity
- bd agent heartbeat <agent>: Update last_activity timestamp only
- bd agent show <agent>: Display agent bead details
States: idle, spawning, running, working, stuck, done, stopped, dead
Also adds AgentState and LastActivity fields to UpdateArgs in RPC protocol.
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Add Phase field to Formula type to indicate recommended instantiation phase
- Add warning in 'bd mol pour' when formula has phase="vapor"
- Improve pour/wisp help text with clear comparison of when to use each
- Add CheckPersistentMolIssues doctor check to detect mol- issues in JSONL
- Update beads-release.formula.json with phase="vapor"
This helps prevent accidental persistence of ephemeral workflow issues.
- Add CheckReadonly calls to create/remove commands
- Add cleanup on partial failure (remove worktree if beads setup fails)
- Prevent removing main repository as worktree
- Fix gitignore entry to use relative path from repo root
- Remove misleading stash check (stashes are repo-wide, not per-worktree)
- Populate Name field in WorktreeInfo struct
- Add #nosec comments for exec.Command and file reads
🤖 Generated with Claude Code
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Adds user-facing worktree management commands:
- bd worktree create <name> - creates worktree with beads redirect
- bd worktree list - shows all worktrees and their beads state
- bd worktree remove <name> - removes worktree with safety checks
- bd worktree info - shows current worktree info
The create command automatically sets up .beads/redirect to point to
the main repos .beads directory, ensuring all worktrees share
the same issue database. This enables parallel development with
multiple agents or features.
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Add slot management commands:
- bd slot set <agent> <slot> <bead> - set slot (error if occupied)
- bd slot clear <agent> <slot> - clear slot
- bd slot show <agent> - show all slots
These enforce cardinality constraints for agent bead slots.
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Update ParseIssueType to use canonical types.IsValid() (includes agent, role, gate, message)
- Add ValidateAgentID function to validate gt-<role>[-<rig>[-<name>]] pattern
- Wire up validation in create.go when --type=agent with explicit ID
- Update --type flag help text to include agent and role types
- Add comprehensive test coverage for agent ID validation
The import command was only updating jsonl_content_hash, not jsonl_file_hash.
After sync imports JSONL but skips re-export (because DB matches JSONL),
the jsonl_file_hash remained stale, causing validateJSONLIntegrity() to
emit spurious "JSONL file hash mismatch" warnings on subsequent operations.
Now import also calls SetJSONLFileHash with the same hash value, keeping
both hashes in sync and eliminating the false warnings.
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
The limit wasn't enforced by init/create, so users could create issues
with longer prefixes but couldn't use rename-prefix to consolidate them.
Since the DB handles longer prefixes fine, just remove the limit.
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Allows reparenting issues to a different epic/parent:
bd update bd-xyz --parent=bd-epic
Implementation:
- Add Parent field to UpdateArgs in protocol.go
- Handle reparenting in RPC handler (server_issues_epics.go)
- Add --parent flag to updateCmd with both daemon and direct mode support
- Remove old parent-child dependency before adding new one
- Pass empty string to remove parent entirely
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
When beads is redirected (e.g., in Gas Town crew clones), bd prime now
shows a notice about the redirect. This helps agents understand why
they share issues with other clones.
CLI mode shows:
> ⚠️ **Redirected**: Local .beads → /path/to/target/.beads
> You share issues with other clones using this redirect.
MCP mode shows:
**Note**: Beads redirected to /path/to/target/.beads (shared with other clones)
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Adds a new command that shows the active .beads directory path,
including redirect information for debugging. Supports --json output.
Example:
bd where
→ /Users/stevey/gt/beads/mayor/rig/.beads
(via redirect from /Users/stevey/gt/beads/crew/emma/.beads)
prefix: bd
database: /Users/stevey/gt/beads/mayor/rig/.beads/beads.db
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Extended bd-tvus fix to all doctor check functions that access .beads/
directory. In Gas Town multi-clone setups, crew/polecat clones use
.beads/redirect files to point to the shared mayor/rig beads directory.
Doctor checks now use resolveBeadsDir() to follow these redirects:
- daemon.go: CheckDaemonStatus
- git.go: CheckSyncBranchConfig, FindOrphanedIssues, CheckOrphanedIssues
- installation.go: CheckMultipleDatabases, CheckPermissions
- integrity.go: CheckIDFormat, CheckDependencyCycles, CheckTombstones,
CheckDeletionsManifest, CheckRepoFingerprint
- jsonl_integrity.go: CheckJSONLIntegrity
- legacy.go: CheckFreshClone
- maintenance.go: CheckStaleClosedIssues, CheckExpiredTombstones,
CheckCompactionCandidates
- perf.go: RunPerformanceDiagnostics, CollectPlatformInfo
- validation.go: CheckMergeArtifacts, CheckOrphanedDependencies,
CheckDuplicateIssues, CheckTestPollution, CheckChildParentDependencies,
CheckGitConflicts
- version.go: CheckMetadataVersionTracking
Intentionally NOT changed (check local files):
- CheckInstallation: checks local .beads/ exists
- CheckUntrackedBeadsFiles: checks git tracking of local files
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
The bug was that doctor's database checks used the local .beads/beads.db
file directly, while import followed the redirect to the actual database.
This caused confusing output showing 0 issues when the actual database
had hundreds. Fixed by using resolveBeadsDir() in all database checks.
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Add nolint:unparam for readOnly param in sqlite_open.go
- Handle cmd.Help() error in wisp.go
- Handle rows.Close() error in migration 028
- Handle targetStore.Close() error in create.go
- Update Nix vendorHash for current dependencies
Cherry-picked from PR #769
Implements the 'bd orphans' command to identify issues referenced in commits
but still open in the database, and refactors to eliminate code duplication.
- Creates cmd/bd/orphans.go with Cobra command structure
- Identifies orphaned issues (referenced in git commits but still open/in_progress)
- Supports multiple output formats (human, JSON, detailed)
- Auto-close with --fix flag
DRY refactoring:
- Extracted FindOrphanedIssues() to cmd/bd/doctor/git.go as shared core logic
- Moved OrphanIssue type to cmd/bd/doctor/types.go
- Refactored CheckOrphanedIssues() to use FindOrphanedIssues()
Cherry-picked from PR #767
Co-authored-by: Amp <amp@ampcode.com>
Move cleanup, compact, and reset commands under `bd admin` namespace.
Creates hidden aliases for backwards compatibility that show deprecation
notice when used.
- Create cmd/bd/admin.go with parent command
- Create cmd/bd/admin_aliases.go for hidden backwards-compat aliases
- Update cleanup.go, compact.go, reset.go to remove rootCmd.AddCommand
- Update all documentation to use `bd admin <cmd>` syntax
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Add --check flag to doctor for specific check modes
- Add --check=pollution to run detailed pollution detection
- Add --clean flag to delete detected test issues
- Mark detect-pollution command as hidden (deprecated)
- Update fix messages to point to new doctor --check=pollution
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Add --thanks flag to bd info command
- Make bd thanks a hidden command (deprecated but still works)
- Part of CLI consolidation effort (bd-9115)
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Analysis found these commands are dead code:
- gt never calls `bd pin` - uses `bd update --status=pinned` instead
- Beads.Pin() wrapper exists but is never called
- bd hook functionality duplicated by gt mol status
- Code comment says "pinned field is cosmetic for bd hook visibility"
Removed:
- cmd/bd/pin.go
- cmd/bd/unpin.go
- cmd/bd/hook.go
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Add TestSpawnMoleculeEphemeralFlag: verifies DB-based spawn
- Add TestSpawnMoleculeFromFormulaEphemeral: verifies formula-based spawn
- Both tests confirm Ephemeral flag is set correctly
- Tests also verify ephemeral issues excluded from ready work
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Delete mol_catalog.go (duplicate functionality)
- Update mol.go help text to point to bd formula list
- Update CLI_REFERENCE.md and MOLECULES.md docs
- Update deprecated template.go references
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Adds --prefix as a forgiving alias to --rig flag. Accepts:
- Exact prefix: bd-, gt-
- Prefix without hyphen: bd, gt
- Rig name: beads, gastown
All resolve to the correct rig via routes.jsonl lookup.
This matches agents' mental model of prefix-based routing.
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Adds --rig flag to bd create that allows creating issues in a different
rig without having to cd to that directory.
Example: bd create --rig beads --title='Bug report'
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
When `bd dep add` fails to resolve the dependency ID locally, it now
checks routes.jsonl for a matching prefix and auto-converts to an
external reference format (external:<project>:<id>).
This allows simpler syntax like:
bd dep add gt-xyz bd-abc
Instead of the verbose:
bd dep add gt-xyz external:beads:bd-abc
New functions in routing package:
- ExtractProjectFromPath: Gets project name from route path
- ResolveToExternalRef: Converts foreign ID to external ref using routes
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
The verb 'wisp' fits the chemistry metaphor (pour, bond, burn, squash)
while 'ephemeral' is an adjective. The internal API field remains
'Ephemeral' but the CLI command is now 'bd mol wisp'.
Commands:
bd mol wisp <proto> - create ephemeral wisp
bd mol wisp list - list wisps
bd mol wisp gc - garbage collect old wisps
For consistency, all molecule operations are now under bd mol:
- bd mol pour <proto> - create persistent mol
- bd mol ephemeral <proto> - create ephemeral mol
- bd mol ephemeral list - list ephemeral issues
- bd mol ephemeral gc - garbage collect old ephemeral issues
This aligns with existing mol subcommands: bond, squash, burn, etc.
The `bd comment --no-db` command was failing because
initializeNoDbMode() set the global `store` but never set
`storeActive = true`. When comments.go called ensureStoreActive(),
the guard check failed and it tried to find a SQLite database,
returning an ironic error telling the user to use --no-db.
Why only `comment` was affected:
- Commands like `create`, `update`, `close` use `store` directly
- The `comment` command calls `ensureStoreActive()` first as a safety check
- That function guards on `storeActive && store != nil`
- Since `storeActive` was never set, the guard failed and it looked for SQLite
The fix aligns no-db mode with what ensureStoreActive() expects.
