- Add explicit error checking for fmt.Fprintf/Fprintln in claude.go
- Add gosec nolint for safe exec.CommandContext calls in sync_git.go
- Remove unused error return from findTownRoutes in routes.go
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
The --cascade flag was documented but not working for single-issue
deletes. The bug had two causes:
1. CLI direct mode: Single-issue deletes bypassed the batch path where
cascade expansion actually happens. Fixed by routing cascade deletes
through deleteBatch() regardless of issue count.
2. Daemon/RPC mode: handleDelete() iterated through IDs individually
without expanding dependents. Fixed by using DeleteIssues() with
cascade flag when SQLite storage is available.
Now `bd delete <id> --cascade --force` correctly deletes the target
issue plus all issues that depend on it (recursively).
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
The CheckSyncBranchHookCompatibility was checking core.hooksPath first,
while CheckGitHooks always uses .git/hooks/. This caused inconsistent
results when core.hooksPath was set globally.
Fix: Remove core.hooksPath check from CheckSyncBranchHookCompatibility
to match CheckGitHooks behavior. Both now consistently use .git/hooks/.
Note: A future improvement could make both respect core.hooksPath.
The negation patterns (!issues.jsonl, !interactions.jsonl, etc.) in
.beads/.gitignore had higher precedence than the fork protection
exclusion in .git/info/exclude, effectively defeating fork protection.
Contributors could accidentally stage and commit upstream issue
databases because:
1. Fork protection added .beads/issues.jsonl to .git/info/exclude
2. .beads/.gitignore had !issues.jsonl which overrode the exclusion
3. .gitignore files have higher precedence than .git/info/exclude
The negation patterns were unnecessary anyway since no pattern in
.beads/.gitignore matches those files. Added a comment explaining
why negations should not be added.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Solaris/illumos use Statvfs (POSIX standard) rather than Statfs.
Add daemon_health_solaris.go and exclude illumos/solaris from the
generic unix build constraint.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com>
bd has 70+ commands, which can be overwhelming for human users who just
want to track issues. The new `bd human` command displays a curated list
of ~15 essential commands organized by workflow:
- Working With Issues: create, list, show, update, close, reopen, comment
- Finding Work: ready, search, status, stats
- Dependencies: dep add/remove/tree, graph, blocked
- Setup & Sync: init, sync, doctor
- Getting Help: quickstart, help, --help
Also includes quick examples showing common workflows.
Changes:
- Add cmd/bd/human.go with curated help output
- Add "human" to noDbCommands list in main.go (no database needed)
Consolidated 5 duplicate IssueDetails struct definitions into a single
types.IssueDetails in internal/types/types.go:
- Removed 4 inline definitions from cmd/bd/show.go
- Removed 1 inline definition from internal/rpc/server_issues_epics.go
The shared type embeds types.Issue by value and includes:
Labels, Dependencies, Dependents, Comments, and Parent fields.
This improves maintainability and reduces risk of inconsistency.
bd config list now shows a warning when config.yaml or environment
variables override database settings. This addresses the confusion when
sync.branch from config.yaml takes precedence over the database value.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Rename followRedirect to FollowRedirect in internal/beads (export it)
- Update doctor/maintenance.go to use beads.FollowRedirect
- Update doctor/fix/common.go to use beads.FollowRedirect
- Remove 66 lines of duplicated code across 3 implementations
This ensures consistent redirect handling with path canonicalization,
chain prevention, and proper error warnings.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Add exitWithError helper to ensure JSON output is used when --json
flag is set during orphan detection errors.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Add resolveBeadsDir helper to fix/common.go to follow redirect files
- Update OrphanedDependencies, ChildParentDependencies, and MergeArtifacts
to use resolveBeadsDir instead of hardcoded .beads path
- Add --verbose/-v flag to bd doctor command
- Only print individual items if verbose or count < 20, always show summary
(bd-dq74, bd-v55y)
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Check comments table for orphaned issue_id references
- Check events table for orphaned issue_id references
- Delete orphaned comments/events in repair transaction
- Add --json flag for machine-readable output with:
- orphan_counts by type (dependencies, labels, comments, events)
- orphan_details with full reference info
- status (success, no_orphans, dry_run, error)
- backup_path when applicable
(bd-2wm2, bd-ie7j)
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Code review fixes for critical issues:
- Wrap all DELETEs in a transaction with rollback on error
- Create .pre-repair backup before any destructive operations
- Mark parent issues as dirty when deleting orphaned depends_on refs
- Fix misleading PreRun comment
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
When the database has orphaned dependencies or labels, the migration
invariant check fails and prevents the database from opening. This
creates a chicken-and-egg problem where bd doctor --fix cannot run.
The new bd repair command:
- Opens SQLite directly, bypassing invariant checks
- Deletes orphaned dependencies (issue_id or depends_on_id not in issues)
- Deletes orphaned labels (issue_id not in issues)
- Runs WAL checkpoint to persist changes
- Supports --dry-run to preview what would be cleaned
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Eliminate code duplication between importFromGit and importFromLocalJSONL
by extracting the common JSONL parsing and import logic.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Adds --from-jsonl flag that imports from the current working tree's
.beads/issues.jsonl file instead of scanning git history. This prevents
deleted issues from being resurrected during re-initialization.
Use case: After running bd compact --purge-tombstones and committing
the cleaned JSONL, a subsequent bd init would previously re-import
all historical issues from git, defeating the cleanup.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Unlike --prune which removes tombstones by age, --purge-tombstones removes
tombstones that have no open issues depending on them, regardless of age.
Also cleans stale deps from closed issues to tombstones.
Usage:
bd compact --purge-tombstones --dry-run # Preview what would be purged
bd compact --purge-tombstones # Actually purge
Note: Use --no-daemon to prevent daemon from re-exporting after cleanup.
- Add findExistingSwarm helper and duplicate swarm check with --force flag
- Add bd swarm list command for discovering swarm molecules with progress stats
- Fix empty coordinator display in swarm create output
- Allow swarm status to accept swarm molecule ID (follows relates-to link)
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Add EpicChildren struct and getEpicChildren() helper function
- Define SwarmStore interface for dependency injection
- Refactor analyzeEpicForSwarm to use shared helper
- Refactor getSwarmStatus to use shared helper
- Eliminates duplicate code for fetching epic children and building
dependency maps across both functions
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Displays each issue on a single line with format:
<id> [<status>] P<priority> <type>: <title>
Example:
bd show bd-nlzv --short
bd-nlzv [open] P2 feature: bd show --short flag for compact output
Useful for quick status checks of multiple issues. (bd-nlzv)
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Build status map upfront from childIssues instead of calling
GetIssue for each dependency. Reduces queries from O(issues * deps)
to O(issues).
Also removes unused GetIssue from the interface.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Implements `bd swarm create <epic-id>` to create a swarm molecule
that orchestrates parallel work on an epic.
Features:
- Creates molecule with mol_type=swarm for discovery
- Links to epic via relates-to dependency
- Validates epic structure before creation
- Auto-wraps single issues in an epic when needed
- Optional --coordinator flag to specify coordinator agent
- Supports JSON output for machine consumption
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Show current swarm status computed from beads:
- Completed: closed issues with timestamps
- Active: in_progress issues with assignees
- Ready: open issues with all deps satisfied
- Blocked: open issues waiting on deps
- Progress percentage
State is COMPUTED from beads, not stored separately.
Supports --json for programmatic use.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Add mol_type field to beads for swarm coordination:
- Values: 'swarm' (multi-polecat), 'patrol' (recurring ops), 'work' (default)
- Nullable, defaults to empty string (treated as 'work')
Changes:
- Add mol_type column to SQLite schema and migration 031
- Add MolType type with IsValid() validation in types.go
- Update insertIssue/GetIssue to handle mol_type
- Add --mol-type flag to create command
- Add mol_type filtering to list and ready commands
- Update RPC protocol for daemon mode support
- Update test schema in migrations_test.go
🤝 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Adds validation of epic structure for swarm execution:
- Computes ready fronts (waves of parallel work)
- Detects structural issues (cycles, orphans, missing deps)
- Reports estimated worker-sessions and max parallelism
- Warns about potential dependency inversions
- Returns exit code for CI integration
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Extract init.go into multiple focused files:
- init_git_hooks.go: Git hooks installation and merge driver setup (~480 lines)
- init_stealth.go: Stealth mode and fork/exclude configuration (~310 lines)
- init_agent.go: AGENTS.md and Claude settings setup (~170 lines)
- init_templates.go: config.yaml and README.md templates (~180 lines)
This reduces init.go from 1928 lines to 705 lines, meeting the <800 line target.
Each extracted file handles a cohesive set of functionality.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
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.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
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
🤖 Generated with [Claude Code](https://claude.com/claude-code)
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
🤖 Generated with [Claude Code](https://claude.com/claude-code)
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.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
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
🤖 Generated with [Claude Code](https://claude.com/claude-code)
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.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
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.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
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.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
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.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
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>
