Add Dolt server mode configuration to metadata.json for multi-writer access:
- Add DoltMode, DoltServerHost, DoltServerPort, DoltServerUser fields to Config
- Add helper methods with sensible defaults (127.0.0.1:3306, root user)
- Update factory to read server mode config and pass to dolt.Config
- Add --server, --server-host, --server-port, --server-user flags to bd init
- Validate that --server requires --backend dolt
- Add comprehensive tests for server mode configuration
Example metadata.json for server mode:
{
"backend": "dolt",
"database": "dolt",
"dolt_mode": "server",
"dolt_server_host": "192.168.1.100",
"dolt_server_port": 3306,
"dolt_server_user": "beads"
}
Password should be set via BEADS_DOLT_PASSWORD env var for security.
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Adds Dolt auto-commit functionality for write commands and sets explicit commit authors.
Includes fix for race condition in commandDidWrite (converted to atomic.Bool).
Original PR: #1267 by @coffeegoddd
Co-authored-by: Dustin Brown <dustin@dolthub.com>
The dolthub/gozstd dependency requires CGO. Several files were importing
the dolt package without build constraints, causing CI failures when
building with CGO_ENABLED=0 for Linux, FreeBSD, and Android.
Changes:
- Add //go:build cgo to federation.go and doctor/federation.go
- Create dolt_server_cgo.go/nocgo.go to abstract dolt.Server usage
- Create federation_nocgo.go with stub command explaining CGO requirement
- Create doctor/federation_nocgo.go with stub health checks
- Update daemon.go to use the dolt server abstraction
Federation and Dolt-specific features are unavailable in non-CGO builds.
Users are directed to pre-built binaries from GitHub releases.
Fixes v0.49.0 CI failure.
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
* fix(autoimport): auto-correct deleted status to tombstone for JSONL compatibility (GH#1223)
This fix addresses the 'Stuck in sync diversion loop' issue where v0.48.0
encountered validation errors during JSONL import. The issue occurs when
JSONL files from older versions have issues with status='deleted' but the
current code expects status='tombstone' for deleted issues.
Changes:
- Add migration logic in parseJSONL to auto-correct 'deleted' status to 'tombstone'
- Ensure tombstones always have deleted_at timestamp set
- Add debug logging for both migration operations
- Prevents users from being stuck in sync divergence when upgrading
Fixes GH#1223: Stuck in sync diversion loop
* fix(autoimport): comprehensively fix corrupted deleted_at on non-tombstone issues (GH#1223)
The initial fix for GH#1223 only caught issues with status='deleted', but the real
data in the wild had issues with status='closed' (or other statuses) but also
had deleted_at set, which violates the validation rule.
Changes:
- Add broader migration logic: any non-tombstone issue with deleted_at should become tombstone
- Apply fix in all three JSONL parsing locations:
- internal/autoimport/autoimport.go (parseJSONL for auto-import)
- cmd/bd/import.go (import command)
- cmd/bd/daemon_sync.go (daemon sync helper)
- Add comprehensive test case for corrupted closed issues with deleted_at
- Fixes the 'non-tombstone issues cannot have deleted_at timestamp' validation error
during fresh bd init or import
Fixes GH#1223: Stuck in sync diversion loop
* Add merge driver comment to .gitattributes
* fix: properly clean up .gitattributes during bd admin reset
Fixes GH#1223 - Stuck in sync diversion loop
The removeGitattributesEntry() function was not properly cleaning up
beads-related entries from .gitattributes. It only removed lines
containing "merge=beads" but left behind:
- The comment line "# Use bd merge for beads JSONL files"
- Empty lines following removed entries
This caused .gitattributes to remain in a modified state after
bd admin reset --force, triggering sync divergence warning loop.
The fix now:
- Skips lines containing "merge=beads" (existing behavior)
- Skips beads-related comment lines
- Skips empty lines that follow removed beads entries
- Properly cleans up file so it's either empty (and gets deleted)
or contains only non-beads content
---------
Co-authored-by: Amp <amp@example.com>
* fix(routing): auto-enable hydration and flush JSONL after routed create
Fixes split-brain bug where issues routed to different repos (via routing.mode=auto)
weren't visible in bd list because JSONL wasn't updated and hydration wasn't configured.
**Problem**: When routing.mode=auto routes issues to a separate repo (e.g., ~/.beads-planning),
those issues don't appear in 'bd list' because:
1. Target repo's JSONL isn't flushed after create
2. Multi-repo hydration (repos.additional) not configured automatically
3. No doctor warnings about the misconfiguration
**Changes**:
1. **Auto-flush JSONL after routed create** (cmd/bd/create.go)
- After routing issue to target repo, immediately flush to JSONL
- Tries target daemon's export RPC first (if daemon running)
- Falls back to direct JSONL export if no daemon
- Ensures hydration can read the new issue immediately
2. **Enable hydration in bd init --contributor** (cmd/bd/init_contributor.go)
- Wizard now automatically adds planning repo to repos.additional
- Users no longer need to manually run 'bd repo add'
- Routed issues appear in bd list immediately after setup
3. **Add doctor check for hydrated repo daemons** (cmd/bd/doctor/daemon.go)
- New CheckHydratedRepoDaemons() warns if daemons not running
- Without daemons, JSONL becomes stale and hydration breaks
- Suggests: cd <repo> && bd daemon start --local
4. **Add doctor check for routing+hydration mismatch** (cmd/bd/doctor/config_values.go)
- Validates routing targets are in repos.additional
- Catches split-brain configuration before users encounter it
- Suggests: bd repo add <routing-target>
**Testing**: Builds successfully. Unit/integration tests pending.
Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
* test(routing): add comprehensive tests for routing fixes
Add unit tests for all 4 routing/hydration fixes:
1. **create_routing_flush_test.go** - Test JSONL flush after routing
- TestFlushRoutedRepo_DirectExport: Verify direct JSONL export
- TestPerformAtomicExport: Test atomic file operations
- TestFlushRoutedRepo_PathExpansion: Test path handling
- TestRoutingWithHydrationIntegration: E2E routing+hydration test
2. **daemon_test.go** - Test hydrated repo daemon check
- TestCheckHydratedRepoDaemons: Test with/without daemons running
- Covers no repos, daemons running, daemons missing scenarios
3. **config_values_test.go** - Test routing+hydration validation
- Test routing without hydration (should warn)
- Test routing with correct hydration (should pass)
- Test routing target not in hydration list (should warn)
- Test maintainer="." edge case (should pass)
All tests follow existing patterns and use t.TempDir() for isolation.
Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
* fix(tests): fix test failures and refine routing validation logic
Fixes test failures and improves validation accuracy:
1. **Fix routing+hydration validation** (config_values.go)
- Exclude "." from hasRoutingTargets check (current repo doesn't need hydration)
- Prevents false warnings when maintainer="." or contributor="."
2. **Fix test ID generation** (create_routing_flush_test.go)
- Use auto-generated IDs instead of hard-coded "beads-test1"
- Respects test store prefix configuration (test-)
- Fixed json.NewDecoder usage (file handle, not os.Open result)
3. **Fix config validation tests** (config_values_test.go)
- Create actual directories for routing paths to pass path validation
- Tests now verify both routing+hydration AND path existence checks
4. **Fix daemon test expectations** (daemon_test.go)
- When database unavailable, check returns "No additional repos" not error
- This is correct behavior (graceful degradation)
All tests now pass:
- TestFlushRoutedRepo* (3 tests)
- TestPerformAtomicExport
- TestCheckHydratedRepoDaemons (3 subtests)
- TestCheckConfigValues routing tests (5 subtests)
Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
* docs: clarify when git config beads.role maintainer is needed
Clarify that maintainer role config is only needed in edge case:
- Using GitHub HTTPS URL without credentials
- But you have write access (are a maintainer)
In most cases, beads auto-detects correctly via:
- SSH URLs (git@github.com:owner/repo.git)
- HTTPS with credentials
This prevents confusion - users with SSH or credential-based HTTPS
don't need to manually configure their role.
Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
* fix(lint): address linter warnings in routing flush code
- Add missing sqlite import in daemon.go
- Fix unchecked client.Close() error return
- Fix unchecked tempFile.Close() error returns
- Mark unused parameters with _ prefix
- Add nolint:gosec for safe tempPath construction
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
---------
Co-authored-by: Roland Tritsch <roland@ailtir.com>
Co-authored-by: Claude Sonnet 4.5 <noreply@anthropic.com>
When bd create --id=pq-xxx is called with an ID prefix that does not
match the current database, automatically route to the correct database
based on routes.jsonl configuration.
Changes:
- Add auto-routing logic before explicit --rig/--prefix handling
- Extract prefix from explicit ID and look it up in routes.jsonl
- If prefix matches a different rig, call createInRig automatically
- Update createInRig to accept explicitID parameter
- Pass explicitID through to issue creation
This fixes the prefix mismatch error when creating issues with
explicit IDs across rigs in multi-repo setups like Gas Town.
Example:
cd ~/gt # Root with hq- prefix
bd create --id=pq-xxx --title="Test"
# Now automatically routes to pgqueue/.beads/beads.db
Fixes: gt doctor --fix failing to create agent beads
Closes: #1188
Cherry-picked from Team-Ailtir/beads PR #1188 with build fix.
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Move LocalProvider from cmd/bd/doctor/git.go to internal/storage/local_provider.go
where it belongs alongside StorageProvider. Both implement IssueProvider for
orphan detection - LocalProvider for direct SQLite access (--db flag),
StorageProvider for the global Storage interface.
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Users naturally try 'bd view <id>' when they want to see an issue.
Adding 'view' as an alias improves discoverability and UX.
Fixes bd-bpx35
Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com>
* fix(orphans): honor --db flag for cross-repo orphan detection
Problem:
- `bd orphans --db /path` ignored the --db flag entirely
- FindOrphanedIssues() hardcoded local .beads/ directory
Solution:
- Introduce IssueProvider interface for abstract issue lookup
- Add StorageProvider adapter wrapping Storage instances
- Update FindOrphanedIssues to accept provider instead of path
- Wire orphans command to create provider from --db flag
Closes: steveyegge/beads#1196
* test(orphans): add cross-repo and provider tests for --db flag fix
- Add TestFindOrphanedIssues_WithMockProvider (table-driven, UT-01 through UT-09)
- Add TestFindOrphanedIssues_CrossRepo (validates --db flag honored)
- Add TestFindOrphanedIssues_LocalProvider (backward compat RT-01)
- Add TestFindOrphanedIssues_ProviderError (error handling UT-07)
- Add TestFindOrphanedIssues_IntegrationCrossRepo (IT-02 full)
- Add TestLocalProvider_* unit tests
Coverage for IssueProvider interface and cross-repo orphan detection.
* docs: add bd orphans command to CLI reference
Document the orphan detection command including the cross-repo
workflow enabled by the --db flag fix in this PR.
- repair.go: Extract validateRepairPaths(), findAllOrphans(), printOrphansText()
- config_values.go: Extract findConfigPath(), validateDurationConfig(), etc.
- Target: CC < 20 for each extracted function
Implements configurable per-field merge strategies (hq-ew1mbr.11):
- Add FieldStrategy type with strategies: newest, max, union, manual
- Add conflict.fields config section for per-field overrides
- compaction_level defaults to "max" (highest value wins)
- estimated_minutes defaults to "manual" (flags for user resolution)
- labels defaults to "union" (set merge)
Manual conflicts are displayed during sync with resolution options:
bd sync --ours / --theirs, or bd resolve <id> <field> <value>
Config example:
conflict:
strategy: newest
fields:
compaction_level: max
estimated_minutes: manual
labels: union
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Add --message/-m as a hidden alias for --description on bd create,
matching the git commit -m convention for muscle memory.
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
* fix(ready): exclude molecule steps from bd ready by default (GH#1239)
Add ID prefix constants (IDPrefixMol, IDPrefixWisp) to types.go as single
source of truth. Update pour.go and wisp.go to use these constants.
GetReadyWork now excludes issues with -mol- in their ID when no explicit
type filter is specified. Users can still see mol steps with --type=task.
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
* feat(ready): config-driven ID pattern exclusion (GH#1239)
Add ready.exclude_id_patterns config for excluding IDs from bd ready.
Default patterns: -mol-, -wisp- (molecule steps and wisps).
Changes:
- Add IncludeMolSteps to WorkFilter for internal callers
- Update findGateReadyMolecules and getMoleculeCurrentStep to use it
- Make exclusion patterns config-driven via ready.exclude_id_patterns
- Remove hardcoded MolStepIDPattern() in favor of config
- Add test for custom patterns (e.g., gastown's -role-)
Usage: bd config set ready.exclude_id_patterns "-mol-,-wisp-,-role-"
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
* docs: remove -role- example from ready.go comments
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
* docs: remove GH#1239 references from code comments
Issue references belong in commit messages, not code.
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
---------
Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com>
Fixes from code review:
1. **Data completeness**: Now migrates events (including comments)
and all config values, not just issues/labels/deps
2. **formatJSONArray**: Fixed to use JSON encoding for waiters field
to match Dolt schema (was using comma-separated format)
3. **Cleanup on failure**: Removes partial Dolt directory or SQLite
files if import fails mid-way
4. **Progress indicator**: Shows "Importing issues: N/M" for large
migrations (100+ issues)
5. **Code deduplication**: Extracted common logic into:
- migrationData struct
- storageReader interface
- extractFromStore() shared extraction
- Helper functions for output formatting
6. **Improved dry-run output**: Now shows event count and config
key count in migration plan
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
The daemon guard was blocking ALL daemon commands when using Dolt
backend, including read-only commands like `status`, `stop`, `logs`.
Changes:
- Rename guard to `guardDaemonStartForDolt` (more accurate)
- Remove `PersistentPreRunE` from `daemonCmd` and `daemonsCmd`
- Add `PreRunE` guard only to `daemonStartCmd` and `daemonsRestartCmd`
- Update test to use new function name and test start command
Now:
- `bd daemon status` works with Dolt backend
- `bd daemon start` blocked unless `--federation` flag
- `bd daemon start --federation` works (starts dolt sql-server)
Fixes: bd-n7o47
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Add `bd migrate --to-dolt` and `bd migrate --to-sqlite` commands for
migrating between SQLite and Dolt storage backends.
Features:
- `--to-dolt`: Migrate from SQLite to Dolt backend
- Creates backup of SQLite database before migration
- Imports all issues, labels, and dependencies
- Updates metadata.json to use Dolt backend
- Preserves JSONL export configuration
- `--to-sqlite`: Escape hatch to migrate back to SQLite
- Exports all data from Dolt to new SQLite database
- Updates metadata.json to use SQLite backend
Both commands support:
- `--dry-run` flag to preview changes
- `--yes` flag for automated/scripted usage
- `--json` flag for machine-readable output
- Non-cgo stub for builds without CGO support
This implements Part 7 (Migration Tooling) of DOLT-STORAGE-DESIGN.md.
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
* Fix sandboxed daemon autostart tests and lint cleanup (bd-1zo)
* Restore issues jsonl to main state (bd-1zo)
* Remove .beads changes from PR (bd-1zo)
* Fix Windows build for dolt SysProcAttr (bd-1zo)
* Reset .beads/issues.jsonl to upstream main (bd-1zo)
* Reset .beads/issues.jsonl to upstream main (bd-1zo)
* Reset .beads/issues.jsonl to upstream main (bd-1zo)
* Fix Windows password prompt fd type (bd-1zo)
* Reset .beads/issues.jsonl to upstream main (bd-1zo)
---------
Co-authored-by: Amp <amp@example.com>
Co-authored-by: beads/crew/darcy <steve.yegge@gmail.com>
Remove recursive tryAutoStartDaemon calls from handleStaleLock that
caused infinite recursion when daemon start lock cleanup looped.
The call chain was: acquireStartLock -> handleStaleLock ->
tryAutoStartDaemon -> acquireStartLock -> ... (unbounded)
Now handleStaleLock just cleans up stale locks and returns false,
letting the caller's bounded retry loop handle retries.
Co-authored-by: Nelson Melo <nmelo@users.noreply.github.com>
Remove Gas Town-specific type constants (TypeMolecule, TypeGate, TypeConvoy,
TypeMergeRequest, TypeSlot, TypeAgent, TypeRole, TypeRig, TypeEvent, TypeMessage)
from internal/types/types.go.
Beads now only has core work types built-in:
- bug, feature, task, epic, chore
All Gas Town types are now purely custom types with no special handling in beads.
Use string literals like "gate" or "molecule" when needed, and configure
types.custom in config.yaml for validation.
Changes:
- Remove Gas Town type constants from types.go
- Remove mr/mol aliases from Normalize()
- Update bd types command to only show core types
- Replace all constant usages with string literals throughout codebase
- Update tests to use string literals
This decouples beads from Gas Town, making it a generic issue tracker.
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Add CheckPatrolPollution to detect stale patrol beads:
- Patrol digests matching 'Digest: mol-*-patrol'
- Session ended beads matching 'Session ended: *'
Includes auto-fix via 'bd doctor --fix' to clean up pollution.
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Improve the federation status command to show more comprehensive
information similar to `git remote -v` with health info:
- Show peer URLs alongside peer names
- Display pending local changes count (uncommitted)
- Test connectivity to each peer (via fetch)
- Track and display last sync time in metadata table
- Show reachability status with error messages on failure
Changes:
- cmd/bd/federation.go: Enhanced status output with URLs, connectivity
checks, pending changes, and last sync time
- internal/storage/dolt/federation.go: Added getLastSyncTime/setLastSyncTime
methods using metadata table, record sync time on successful sync
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
For repos with 1000+ issues where less than 20% are dirty,
incremental export reads the existing JSONL, merges only
changed issues, and writes back - avoiding full re-export.
- Add exportToJSONLIncrementalDeferred as new default export path
- Add shouldUseIncrementalExport to check thresholds
- Add performIncrementalExport for merge-based export
- Add readJSONLToMap helper for fast JSONL parsing
- Falls back to full export when incremental is not beneficial
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Merge SQL user authentication with Emma federation sync implementation:
- Add federation_peers table for encrypted credential storage
- Add credentials.go with AES-256-GCM encryption, SHA-256 key derivation
- Extend FederatedStorage interface with credential methods
- Add --user, --password, --sovereignty flags to bd federation add-peer
- Integrate credentials into PushTo/PullFrom/Fetch via withPeerCredentials
- DOLT_REMOTE_USER/PASSWORD env vars protected by mutex for concurrency
Credentials automatically used when syncing with peers that have stored auth.
Continues: bd-wkumz.10, Closes: bd-4p67y
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Add --federation-port and --remotesapi-port flags (default 3306/8080)
- Fix log file leak in server.go - track and close on Stop()
- Add BEADS_DOLT_PASSWORD env var for server mode authentication
- Update DSN to include password when set
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Update guards to allow daemon commands when --federation is set.
Federation mode runs dolt sql-server which enables multi-writer
support, unlike embedded Dolt which is single-process only.
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Add --federation flag to bd daemon start that runs dolt sql-server
instead of the embedded driver. Enables multi-writer support and
exposes remotesapi on port 8080 for peer-to-peer push/pull.
Changes:
- Add --federation flag to daemon start command
- Create dolt server manager (internal/storage/dolt/server.go)
- Update DoltStore to support server mode via MySQL protocol
- Integrate server lifecycle into daemon (auto-start/stop)
- Add tests for server management and server mode connections
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Add peer-to-peer synchronization for Dolt-backed beads databases:
- New FederatedStorage interface with PushTo, PullFrom, Fetch, ListRemotes,
RemoveRemote, and SyncStatus methods
- DoltStore implementation using DOLT_PUSH, DOLT_PULL, DOLT_FETCH
- Full bd federation command with subcommands:
- sync: bidirectional sync with conflict resolution (--strategy ours|theirs)
- status: show ahead/behind counts and conflict state
- add-peer/remove-peer/list-peers: manage federation remotes
- Comprehensive tests for all federation APIs
Closes: bd-wkumz.4
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
When running `bd init` from a directory with a .beads/redirect file
pointing to a canonical .beads/ that already has a database, init
now errors instead of silently overwriting the existing database.
This prevents accidental data loss when:
- A project uses redirect to share a canonical database
- Someone runs `bd init` from the redirected location
- The canonical database was already initialized
The error message clearly explains:
- What happened (redirect target already has database)
- Where the redirect points to
- How to use the existing database (just run bd commands normally)
- How to reinitialize if needed (rm the database first)
Adds test: TestInitWithRedirectToExistingDatabase
Part of GH#bd-0qel
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
When bd runs with --no-daemon or during init in a directory that has a
.beads/redirect file, it now correctly follows the redirect to create
the database in the target location instead of locally.
The bug occurred because:
1. init.go hardcoded .beads/beads.db without checking for redirects
2. main.go's fallback path for auto-bootstrap also used local .beads
Both code paths now call beads.FollowRedirect() to resolve the correct
.beads directory before constructing the database path.
Added TestInitWithRedirect to verify the fix.
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Add jsonlFilePaths constant to eliminate duplicate file list definitions
- Update all usages in hook.go and hooks.go to use the shared constant
- Include beads.jsonl for backwards compatibility with older installations
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Add detection and hook support for jujutsu repositories:
- IsJujutsuRepo(): detects .jj directory
- IsColocatedJJGit(): detects colocated jj+git repos
- GetJujutsuRoot(): finds jj repo root
For colocated repos (jj git init --colocate):
- Install simplified hooks without staging (jj auto-commits working copy)
- Worktree handling preserved for git worktrees in colocated repos
For pure jj repos (no git):
- Print alias instructions since jj doesn't have native hooks yet
Closes: hq-ew1mbr.12
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Replace polling with filesystem watching for near-instant wake-up
(<50ms vs 250ms avg). Watches .beads/dolt/.dolt/noms for Dolt commits.
Falls back to polling if fsnotify unavailable.
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Convenience alias for 'bd list --parent <id>'. Lists all child beads
of a specified parent, supporting all standard list flags (--json,
--pretty, etc.).
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Add new `bd rename <old-id> <new-id>` command that:
- Updates the issue's primary ID
- Updates text references in other issues (title, description, etc.)
- Handles dependencies via storage layer's UpdateIssueID
Also fix sync.go build error where hasSyncBranchConfig/syncBranchName
were referenced but not defined - should use sbc.IsConfigured()/sbc.Branch.
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
* Fix doctor DB-JSONL sync check to exclude ephemeral wisps
The DB-JSONL Sync check was showing a false positive warning when wisps
(ephemeral issues) existed in the database. Wisps are intentionally
excluded from JSONL exports, so they shouldn't be counted when comparing
database and JSONL issue counts.
Changes:
- Updated CheckDatabaseJSONLSync to exclude ephemeral issues from count
using 'WHERE ephemeral = 0 OR ephemeral IS NULL'
- Added 'ephemeral' column to test database schema
- Added test case to verify ephemeral issues are excluded from count
- Updated TestCheckDatabaseJSONLSync_MoleculePrefix to include ephemeral column
This prevents false warnings like 'database has 92 issues, JSONL has 30'
when the difference is entirely due to wisps that should not be exported.
* feat(mol): add 'bd mol seed --patrol' command
Adds `bd mol seed` command to verify formula accessibility before
patrols attempt to spawn work.
## Problem
Gas Town's `gt rig add` calls `bd mol seed --patrol` but this command
didn't exist in beads, causing the call to always fail and fall back
to creating non-functional placeholder beads.
## Solution
Implemented `bd mol seed` with two modes:
1. **With --patrol flag**: Verifies all three patrol formulas are accessible
- mol-deacon-patrol
- mol-witness-patrol
- mol-refinery-patrol
2. **Without --patrol**: Verifies a specific formula is accessible
## Implementation
The command uses `resolveAndCookFormulaWithVars` to verify formulas:
- Checks formula search paths (.beads/formulas/, ~/.beads/formulas/, $GT_ROOT/.beads/formulas/)
- Validates formula syntax and resolution
- Confirms formula can be cooked to subgraph
## Usage
```bash
bd mol seed --patrol # Verify all patrol formulas
bd mol seed mol-feature # Verify specific formula
bd mol seed mol-review --var name=test # With variable substitution
```
## Testing
- ✅ Command compiles without errors
- ✅ Help text displays correctly
- ✅ `--patrol` succeeds when formulas accessible (town level)
- ✅ `--patrol` fails with clear error when formulas missing (rig level)
- ✅ Follows existing beads command patterns (cobra, flags, error handling)
## Impact
- Enables Gas Town's intended patrol formula verification flow
- Eliminates creation of unnecessary placeholder beads
- Provides health check command for formula accessibility
- Foundation for future seed commands (data initialization, etc.)
Fixes the missing command referenced in steveyegge/gastown#715
Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
---------
Co-authored-by: Roland Tritsch <roland@ailtir.com>
Co-authored-by: Claude Sonnet 4.5 <noreply@anthropic.com>
When running in gastown multi-workspace mode, two checks produce false
positives that are expected behavior:
1. routes.jsonl is a valid configuration file (maps issue prefixes to
rig directories), not a duplicate JSONL file
2. Duplicate issues are expected (ephemeral wisps from patrol cycles)
and normal up to ~1000, with GC cleaning them up automatically
This commit adds flags to bd doctor for gastown-specific checks:
- --gastown: Skip routes.jsonl warning and enable duplicate threshold
- --gastown-duplicates-threshold=N: Set duplicate tolerance (default 1000)
Fixes false positive warnings:
Multiple JSONL files found: issues.jsonl, routes.jsonl
70 duplicate issue(s) in 30 group(s)
Changes:
- Add --gastown flag to bd doctor command
- Add --gastown-duplicates-threshold flag (default: 1000)
- Update CheckLegacyJSONLFilename to skip routes.jsonl when gastown mode active
- Update CheckDuplicateIssues to use configurable threshold when gastown mode active
- Add test cases for gastown mode behavior with various thresholds
Co-authored-by: Roland Tritsch <roland@ailtir.com>
Co-authored-by: Claude Sonnet 4.5 <noreply@anthropic.com>
