Add support for template molecules (is_template field and TypeMolecule type):
- Add IsTemplate field to Issue type with JSON support
- Add TypeMolecule constant to IssueType constants
- Add IsTemplate filter to IssueFilter for querying
- Update all SQL queries to include is_template column
- Add migration 024 for is_template column
- Add FindMoleculesJSONLInDir helper for molecules.jsonl path detection
This enables treating certain issues as read-only templates that can be
instantiated to create work items. The template flag allows separating
template molecules from regular work items in queries and exports.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Add pinned column to the issues table to support persistent context markers
that should not be treated as work items (bd-7h5).
Changes:
- Add pinned column to schema.go CREATE TABLE
- Add migration 023_pinned_column.go for existing databases
- Update all issue queries to include pinned column
- Update scanIssues and scanIssuesWithDependencyType to handle pinned field
- Add Pinned field to types.Issue struct with JSON serialization
- Fix migrations_test.go to include pinned in legacy schema test
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Fixes 5 linting issues to allow PR checks to pass:
1. hooks.go: Explicitly ignore error in async goroutine
2. 022_drop_edge_columns.go: Handle deferred PRAGMA error
3. flags.go: Add nosec comment for validated file path
4. create_form.go: Fix American spelling (canceled vs cancelled)
5. create_form.go: Explicitly mark cmd parameter as required by cobra
These are pre-existing issues in the codebase, fixed here to
enable clean CI for the import deduplication fix.
🤖 Generated with Claude Code
This is the final phase of the Edge Schema Consolidation. It removes
the deprecated edge fields (RepliesTo, RelatesTo, DuplicateOf, SupersededBy)
from the Issue struct and all related code.
Changes:
- Remove edge fields from types.Issue struct
- Remove edge field scanning from queries.go and transaction.go
- Update graph_links_test.go to use dependency API exclusively
- Update relate.go to use AddDependency/RemoveDependency
- Update show.go with helper functions for thread traversal via deps
- Update mail_test.go to verify thread links via dependencies
- Add migration 022 to drop columns from issues table
- Fix cycle detection to allow bidirectional relates-to links
- Fix migration 022 to disable foreign keys before table recreation
All edge relationships now use the dependencies table exclusively.
The old Issue fields are fully removed.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Add migration to convert existing issue fields to dependency edges:
- replies_to -> replies-to dependency with thread_id
- relates_to -> relates-to dependencies (JSON array)
- duplicate_of -> duplicates dependency
- superseded_by -> supersedes dependency
The migration is idempotent (INSERT OR IGNORE) so it does not duplicate
edges that were already created by Phase 2 dual-write.
Generated with Claude Code
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Add metadata and thread_id columns to dependencies table to support:
- Edge metadata: JSON blob for type-specific data (similarity scores, etc.)
- Thread queries: O(1) conversation threading via thread_id
Changes:
- New migration 020_edge_consolidation.go
- Updated Dependency struct with Metadata and ThreadID fields
- Added new entity types: authored-by, assigned-to, approved-by
- Relaxed DependencyType validation (any non-empty string ≤50 chars)
- Added IsWellKnown() and AffectsReadyWork() methods
- Updated SQL queries to include new columns
- Updated tests for new behavior
This enables HOP knowledge graph requirements and Reddit-style threading.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
No point warning about orphaned issues that are already closed or
tombstoned - they're dead either way.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Orphan detection was reporting tombstoned issues (already deleted) as
orphans, causing repeated warnings during sync. Filter out status='tombstone'
from the orphan query.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Add TypeMessage issue type for inter-agent communication
- Add 6 new Issue fields: Sender, Ephemeral, RepliesTo, RelatesTo,
DuplicateOf, SupersededBy
- Add 4 new dependency types: replies-to, relates-to, duplicates, supersedes
- Create migration 019_messaging_fields with indexes
- Update all CRUD operations across storage layer
- Fix reset_test.go to use correct function names
- Fix redundant newline lint error in sync.go
Closes: bd-kwro.1
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
The orphan detection was incorrectly flagging issues with dots in their
prefix (e.g., "my.project-abc123") as orphans because it was looking for
any dot in the ID, treating everything before the first dot as the
parent ID.
The fix:
- Add IsHierarchicalID() helper that correctly detects hierarchical IDs
by checking if the ID ends with .{digits} (e.g., "bd-abc.1")
- Update SQL query in orphan detection migration to use GLOB patterns
that only match IDs ending with numeric suffixes
- Update all Go code that checks for hierarchical IDs to use the new
helper function
Test cases added:
- Unit tests for IsHierarchicalID covering normal, dotted prefix, and
edge cases
- Integration test verifying dotted prefixes do not trigger false
positives
Fixes: #508
Phase 1 of tombstone migration: bd delete now creates tombstones instead
of hard-deleting issues.
Key changes:
- Add CreateTombstone() method to SQLiteStorage for soft-delete
- Modify executeDelete() to create tombstones instead of removing rows
- Add IsExpired() method with 30-day default TTL and clock skew grace
- Fix deleted_at schema from TEXT to DATETIME for proper time scanning
- Update delete.go to call CreateTombstone (single issue path)
- Still writes to deletions.jsonl for backward compatibility (dual-write)
- Dependencies are removed when creating tombstones
- Tombstones are excluded from normal searches (bd-1bu)
TTL constants:
- DefaultTombstoneTTL: 30 days
- MinTombstoneTTL: 7 days (safety floor)
- ClockSkewGrace: 1 hour
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
- Add partial index on deleted_at for efficient TTL queries
- Exclude tombstones from SearchIssues by default (new IncludeTombstones filter)
- Report tombstone count separately in GetStatistics
- Display tombstone count in bd stats output
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
- Add migration 017_close_reason_column.go to create the column
- Update all INSERT statements to include close_reason
- Update all SELECT statements to include close_reason
- Update doctor.go to check for close_reason in schema validation
- Remove workaround code that batch-loaded close reasons from events table
- Fix migrations_test.go to include close_reason in test table schema
This fixes sync loops where close_reason values were silently dropped
because the DB lacked the column despite the struct having the field.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Creates migration to detect orphaned child issues and logs them for user
action. Orphaned children are issues with hierarchical IDs (e.g., "parent.child")
where the parent issue no longer exists in the database.
The migration:
- Queries for issues with IDs like '%.%' where parent doesn't exist
- Logs detected orphans with suggested actions (delete, convert, or restore)
- Does NOT automatically delete or convert orphans
- Is idempotent and safe to run multiple times
Test coverage:
- Detects orphaned child issues correctly
- Handles clean databases with no orphans
- Verifies idempotency
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Introduces a materialized cache table to store blocked issue IDs,
replacing the expensive recursive CTE computation that was causing
~752ms query times on 10K databases (bd-5qim).
The cache is maintained via invalidation on dependency and status
changes, reducing GetReadyWork from O(n²) recursive traversal to
O(1) cache lookup.
Technical details:
- New blocked_issues_cache table with single issue_id column
- ON DELETE CASCADE ensures automatic cleanup
- Migration populates cache using existing recursive CTE logic
- rebuildBlockedCache() fully rebuilds cache on invalidation
- execer interface allows both *sql.DB and *sql.Tx usage
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
- Force single connection for all in-memory databases (including file::memory:)
- Close rows before executing statements in external_ref migration
- Prevents connection pool deadlock with MaxOpenConns(1)
- Fixes test failures in syncbranch_test.go
The schema initialization was trying to create an index on the external_ref
column before the migration that adds the column runs. This caused 'no such
column: external_ref' errors when opening very old databases (pre-0.17.5).
Solution: Move the index creation into the migration that adds the column.
Fixes#284
Amp-Thread-ID: https://ampcode.com/threads/T-2744d5a7-168f-4ef6-bcab-926db846de20
Co-authored-by: Amp <amp@ampcode.com>
- Created migrations/ subdirectory with 14 individual migration files
- Reduced migrations.go from 680 to 98 lines (orchestration only)
- Updated test imports to use migrations package
- Updated MULTI_REPO_HYDRATION.md documentation
- All tests passing
