Commit Graph

67 Commits

Author SHA1 Message Date
Marco Del Pin
dba9bb91c3 fix(import): handle duplicate issue IDs in JSONL files gracefully
Implements three-layer deduplication strategy to prevent UNIQUE
constraint errors during import:
1. Early deduplication during processing (importer.go)
2. Pre-batch deduplication (importer.go)
3. INSERT OR IGNORE with explicit error handling (issues.go)
**Problem:**
JSONL files with duplicate issue IDs caused import failures:
  Import failed: UNIQUE constraint failed: issues.id
**Root Cause:**
- Go SQLite driver returns errors even with INSERT OR IGNORE
- Only content hash was deduplicated, not IDs
- Multiple code paths affected (insertIssue, insertIssues)
**Solution:**
Layer 1: Early deduplication by ID in upsertIssues (lines 489-502)
Layer 2: Pre-batch deduplication (lines 713-726)
Layer 3: INSERT OR IGNORE + isUniqueConstraintError() helper
**Testing:**
- Multiple production databases tested
- 9 duplicates handled successfully
- 100% success rate on v0.30.5 databases
- Zero UNIQUE constraint errors
**Impact:**
- Enables importing JSONL with duplicate IDs
- Duplicate count shown in import statistics
- No breaking changes, backward compatible
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2025-12-18 19:26:29 +01:00
Steve Yegge
0ce039429d fix: tombstone/deletion overhaul for bd-4q8
- IsExpired(): Negative TTL means immediately expired (for --hard mode)
- IsExpired(): ClockSkewGrace only added for TTLs > 1 hour
- bd cleanup --hard: Use negative TTL to prune freshly created tombstones
- bd delete --hard: New flag to immediately prune tombstones from JSONL
- Import: Add early tombstone check before all phases to prevent resurrection

The early tombstone check prevents ghost issues from being created when
tombstones exist in the DB. However, a deeper git merge issue (bd-ncwo)
can still cause resurrection when remote's status:closed wins the merge.

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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
2025-12-16 22:01:31 -08:00
Steve Yegge
d3b0cbb8b8 chore: bump version to 0.30.2
- Update version in version.go, default.nix, hook templates
- Add CHANGELOG.md entry for v0.30.2
- Add v0.30.1 and v0.30.2 to versionChanges in info.go
- Remove stale internal/deletions import from integration test
  (fixes CI failure from bd-fom refactor)

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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
2025-12-16 16:47:43 -08:00
Steve Yegge
9f76cfda01 refactor: remove all deletions.jsonl code (bd-fom)
Complete removal of the legacy deletions.jsonl manifest system.
Tombstones are now the sole deletion mechanism.

Removed:
- internal/deletions/ - entire package
- cmd/bd/deleted.go - deleted command
- cmd/bd/doctor/fix/deletions.go - HydrateDeletionsManifest
- Tests for all removed functionality

Cleaned:
- cmd/bd/sync.go - removed sanitize, auto-compact
- cmd/bd/delete.go - removed dual-writes
- cmd/bd/doctor.go - removed checkDeletionsManifest
- internal/importer/importer.go - removed deletions checks
- internal/syncbranch/worktree.go - removed deletions merge
- cmd/bd/integrity.go - updated validation (warn-only on decrease)

Files removed: 12
Lines removed: ~7500

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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
2025-12-16 14:20:49 -08:00
Steve Yegge
2c86404d65 fix: resolve P2 sync noise and cleanup issues
- bd-6pni: Auto-filter tombstoned issues with mismatched prefixes during
  import instead of failing. Tombstones from contributor PRs with different
  test prefixes are pollution and safe to ignore.

- bd-ffr9: Stop recreating deletions.jsonl after tombstone migration.
  Added IsTombstoneMigrationComplete() check to all code paths that write
  to the legacy deletions manifest.

- bd-admx: Fix perpetual "JSONL file hash mismatch" warning. Now clears
  both export_hashes AND jsonl_file_hash when mismatch detected, so the
  warning doesn't repeat.

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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
2025-12-16 00:56:06 -08:00
Steve Yegge
8c45069228 fix(doctor,sync): clean up deletions manifest and reduce sync noise
- bd-8v5o: When doctor --fix hydrates issues from git history, also
  remove them from the deletions manifest to prevent perpetual skip
  warnings during sync

- bd-wsqt: Remove verbose per-issue "Skipping bd-xxx" messages during
  sync. Caller already shows summary of skipped issues.

Added RemoveDeletions() function to deletions package with tests.

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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
2025-12-16 00:42:36 -08:00
Ryan Snodgrass
627ac1afb8 fix(import): skip cross-prefix content matches instead of triggering rename
When importing issues, if an incoming issue has the same content hash as an
existing issue but a DIFFERENT prefix, this should not be treated as a rename.
Cross-prefix content matches occur when importing issues from other projects
that happen to have identical content.

Previously, the importer would call handleRename which tries to create an issue
with the incoming prefix, failing prefix validation ("does not match configured
prefix" error).

The fix checks if prefixes differ before calling handleRename:
- Same prefix, different ID suffix → true rename, call handleRename
- Different prefix → skip incoming issue, keep existing unchanged

Added test: TestImportCrossPrefixContentMatch reproduces the bug scenario
where alpha-* issues exist but beta-* issues are imported with same content.
2025-12-16 00:29:19 -08:00
Ryan Snodgrass
421d41dfa0 docs: add detailed comments explaining ID formats and merge deletion logic
Document the intent and nuances of recent fixes:

internal/importer/utils.go:
- RenameImportedIssuePrefixes: explain the three ID formats (sequential,
  hash-based, hierarchical) and how prefix renaming preserves identity
- isValidIDSuffix: document why dots are allowed (hierarchical parent-child
  relationships) and what characters are rejected

cmd/bd/deletion_tracking.go:
- isIssueNotFoundError: explain why "not found" is success during merge
  (issue may be tombstoned, never existed locally, or manually deleted)
- Deletion loop: document what "accepted deletions" means and why we
  tolerate missing issues during the pruning phase
2025-12-16 00:17:40 -08:00
Ryan Snodgrass
c7b45a8a40 fix(import): support hierarchical hash IDs in --rename-on-import
The isNumeric function was rejecting valid hierarchical hash IDs like
'6we.2' that contain dots for parent.child notation. This caused
`bd import --rename-on-import` to fail with "non-numeric suffix" errors.

Changes:
- Rename isNumeric to isValidIDSuffix for clarity
- Accept dots (.) in addition to alphanumeric for hierarchical IDs
- Update test cases to cover hierarchical ID formats
2025-12-16 00:12:10 -08:00
matt wilkie
cd3b0e30be bd-ckej: fix orphan skip count mismatch on fresh import (#572)
* bd-ckej: fix orphan skip count mismatch on fresh import

When OrphanSkip mode is used during import and a child issue's parent doesn't
exist, the issue ID was cleared to '' but then regenerated anyway in
GenerateBatchIssueIDs, causing it to be created in the database. This resulted
in a count mismatch: JSONL had 824 issues but only 823 were in the database (one
orphan was counted but not created).

Fix: Filter out orphaned issues with empty IDs before batch creation and track
them in result.Skipped so the count stays accurate.

* test: add TestImportOrphanSkip_CountMismatch for bd-ckej

Adds comprehensive test that verifies orphaned issues are properly skipped
during import when orphan_handling=OrphanSkip and parent doesn't exist.

Also improves the fix to pre-filter orphaned issues before batch creation,
ensuring they're not inserted then have IDs cleared (preventing count
mismatches).

---------

Co-authored-by: Amp <amp@example.com>
2025-12-15 21:17:32 -08:00
Steve Yegge
8e58c306a7 fix(sync,blocked): add safety guards for issue deletion and include status=blocked in bd blocked
GH#464: Add safety guards to prevent deletion of open/in_progress issues during sync:
- Safety guard in git-history-backfill (importer.go)
- Safety guard in deletions manifest processing
- Warning when uncommitted changes detected before pull (daemon_sync.go)
- Enhanced repo ID mismatch error message

GH#545: Fix bd blocked to show status=blocked issues (sqlite/ready.go):
- Changed from INNER JOIN to LEFT JOIN to include issues without dependencies
- Added WHERE clause to include both status=blocked AND dependency-blocked issues

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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
2025-12-14 23:07:54 -08:00
Steve Yegge
a612c575f9 fix(sync): include tombstones when building ID map during import
The importer was not seeing tombstones when building the dbByID map,
causing it to treat tombstone IDs as "new" issues. This led to UNIQUE
constraint violations during INSERT.

- Include tombstones in SearchIssues call (IncludeTombstones: true)
- Skip tombstones when matching by ID instead of trying to update them

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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
2025-12-13 10:20:22 -08:00
Rod Davenport
6985ea94e5 fix(sync): protect local issues from git-history-backfill during sync (#485)
Fix sync bug where newly created issues were incorrectly tombstoned during bd sync.

The root cause was git-history-backfill finding issues in local commits on the sync branch, then tombstoning them when they weren't in the merged JSONL. The fix protects issues from the left snapshot (local export) from git-history-backfill.

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2025-12-12 13:28:48 -08:00
Steve Yegge
24917f27c2 fix(importer): use zero for unknown priority in convertDeletionToTombstone (bd-9auw)
Changed Priority from hardcoded 2 to 0 (unset) to distinguish legacy tombstones
from user-set values. IssueType remains TypeTask as empty fails validation.

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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
2025-12-07 21:20:00 +11:00
Steve Yegge
711dd9ccd4 feat(importer): add ConvertedToTombstone counter (bd-wucl)
Track legacy deletions.jsonl entries converted to tombstones during import:
- Add Result.ConvertedToTombstone counter
- Add Result.ConvertedTombstoneIDs for the converted IDs
- Update test to verify the new counter

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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
2025-12-07 21:18:17 +11:00
Steve Yegge
32f646a303 test(tombstones): add unit tests for tombstone functionality (bd-fmo, bd-hp0m)
- Add TestIsExpiredTombstone with edge cases for merge package
- Add TestImportIssues_LegacyDeletionsConvertedToTombstones for importer

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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
2025-12-07 21:16:23 +11:00
Steve Yegge
f4864c9cc4 feat(import/export): add tombstone support (bd-dve)
Update import/export to handle tombstones for deletion sync propagation:

Exporter:
- Include tombstones in JSONL output by setting IncludeTombstones: true
- Both single-repo and multi-repo exports now include tombstones

Importer:
- Tombstones from JSONL are imported as-is (they're issues with status=tombstone)
- Legacy deletions.jsonl entries are converted to tombstones via convertDeletionToTombstone()
- Non-tombstone issues in deletions manifest are still skipped (backward compat)
- purgeDeletedIssues() now creates tombstones instead of hard-deleting

This is Phase 2 of the tombstone implementation (bd-dli design), enabling
inline soft-delete tracking for cross-clone deletion synchronization.

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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
2025-12-07 20:34:02 +11:00
Steve Yegge
8d19e75431 fix: add safety guard to prevent git-history-backfill mass deletion (bd-t5m)
When a clone gets reset (git reset --hard origin/main), the
git-history-backfill logic was incorrectly marking ALL issues as
deleted since they appeared in git history but not in the current
JSONL. This caused the entire database to be purged.

Fix:
- Add 50% threshold check: abort if git-history-backfill would delete
  more than 50% of issues (likely a reset scenario, not deletions)
- Add warning when >10 issues would be deleted via backfill
- Print helpful message about manual deletion if needed

Test:
- Added TestMassDeletionSafetyGuard that simulates JSONL reset and
  verifies the safety guard prevents mass deletion

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Co-Authored-By: Claude <noreply@anthropic.com>
2025-11-30 21:26:16 -08:00
Steve Yegge
f7dea354d8 fix(import): add warning when issues are skipped due to deletions manifest
When importing JSONL that contains issues in the deletions manifest,
import now:
- Filters out deleted issues before import
- Prints per-issue warning with deletion details (date, actor)
- Shows count of skipped issues in summary
- Suggests --ignore-deletions flag to force import

The new --ignore-deletions flag allows importing issues that are in the
deletions manifest, useful for recovering accidentally deleted issues.

Fixes bd-4zy

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Co-Authored-By: Claude <noreply@anthropic.com>
2025-11-30 21:23:04 -08:00
Steve Yegge
774a57684c Fix auto-import git history backfill bug (bd-4pv)
Auto-import was allowing git history backfill to run, which could
incorrectly purge issues. The fix adds NoGitHistory=true to all
auto-import code paths:
- autoimport.go (importFromGit)
- autoflush.go (autoImportIfNewer)
- daemon_sync.go (importToJSONLWithStore)

Git history backfill is designed to detect deletions that happened
after a local DB was created. During auto-import, there is no local
work to protect - we are importing from the authoritative JSONL source.

Also adds comprehensive tests for NoGitHistory behavior.

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Co-Authored-By: Claude <noreply@anthropic.com>
2025-11-27 22:51:39 -08:00
Steve Yegge
22d34a22dc Fix bd migrate loop: skip prefix validation during auto-import
When auto-importing issues from JSONL, issues with different prefixes
(e.g., gt-1 vs gastown-) would fail validation and cause an infinite
loop of failed migrations.

The fix adds SkipPrefixValidation option to CreateIssuesWithFullOptions
which propagates through EnsureIDs to skip prefix validation for issues
that already have IDs during import. This allows importing issues with
any prefix while still validating new issues created interactively.

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Co-Authored-By: Claude <noreply@anthropic.com>
2025-11-27 21:45:42 -08:00
Steve Yegge
5506486dc5 feat(import,sync): add --no-git-history flag to prevent spurious deletions
Fixes bd-0b2: The git history backfill mechanism was causing data loss
during JSONL filename migrations (beads.jsonl → issues.jsonl). When issues
existed in the old filename's git history, the backfill incorrectly treated
them as "deleted" and purged them from the database.

Changes:
- Add NoGitHistory field to importer.Options and ImportOptions structs
- Modify purgeDeletedIssues() to skip git history check when flag is set
- Add --no-git-history flag to bd import command
- Add --no-git-history flag to bd sync command
- Update purge_test.go to pass Options argument

Usage:
  bd import -i .beads/issues.jsonl --no-git-history
  bd sync --no-git-history

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Co-Authored-By: Claude <noreply@anthropic.com>
2025-11-26 23:10:43 -08:00
Steve Yegge
ff3352ab23 bd-6xd: Standardize on issues.jsonl as canonical filename
- Change default JSONL filename from beads.jsonl to issues.jsonl
- Add bd doctor check and fix to auto-migrate legacy beads.jsonl configs
- Update FindJSONLPath to prefer issues.jsonl over beads.jsonl
- Add CheckLegacyJSONLConfig and CheckLegacyJSONLFilename checks
- Add LegacyJSONLConfig fix to rename files and update config
- Update .gitattributes to reference issues.jsonl
- Fix tests to expect new canonical filename
- Add bd-6xd to v0.25.1 release notes

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Co-Authored-By: Claude <noreply@anthropic.com>
2025-11-26 22:02:59 -08:00
Steve Yegge
4088e68da7 feat(deletions): complete deletions manifest epic with integration tests
Completes the deletion propagation epic (bd-imj) with all 9 subtasks:
- Cross-clone deletion propagation via deletions.jsonl
- bd deleted command for audit trail
- Auto-compact during sync (opt-in)
- Git history fallback with timeout and regex escaping
- JSON output for pruning results
- Integration tests for deletion scenarios
- Documentation in AGENTS.md, README.md, and docs/DELETIONS.md

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Co-Authored-By: Claude <noreply@anthropic.com>
2025-11-25 16:36:46 -08:00
Steve Yegge
4898c424aa feat(deletions): auto-compact during sync and git history fallback fixes
- Add Count function to deletions package for fast line counting
- Add maybeAutoCompactDeletions to sync (opt-in via deletions.auto_compact config)
- Fix regex escaping in batchCheckGitHistory (bd-bgs)
- Add 30s timeout to git history commands (bd-f0n)
- Use git rev-parse --show-toplevel for proper repo root detection (bd-bhd)
- Add tests for Count and auto-compact functionality

Closes: bd-qsm, bd-bgs, bd-f0n, bd-bhd
2025-11-25 15:08:12 -08:00
Steve Yegge
3f84ec3774 feat(deletions): add pruning and git history fallback
Implements two P1 tasks for the deletions manifest epic:

bd-v2x: Add deletions pruning to bd compact
- PruneDeletions function removes records older than retention period
- Default retention: 7 days (configurable via metadata.json)
- CLI --retention flag for override
- Atomic file rewrite prevents corruption
- Called automatically during all compact operations

bd-pnm: Add git history fallback for pruned deletions
- Catches deletions where manifest entry was pruned
- Uses git log -S to search for ID in JSONL history
- Batches multiple IDs for efficiency (git -G regex)
- Self-healing: backfills manifest on hit
- Conservative: keeps issue if git check fails (shallow clone)

Tests added for both features with edge cases covered.

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Co-Authored-By: Claude <noreply@anthropic.com>
2025-11-25 12:41:36 -08:00
Steve Yegge
be784a0b4b bd sync: 2025-11-25 11:46:06 2025-11-25 11:46:06 -08:00
Steve Yegge
d45cff5085 feat: Handle FOREIGN KEY constraint violations gracefully during import (bd-koab)
When importing JSONL after merges that include deletions, FK constraint
violations can occur if an issue references a deleted issue. Previously,
import would fail completely. Now it continues and reports skipped dependencies.

Changes:
- Add SkippedDependencies field to Result/ImportResult structs
- Update importDependencies() to detect FK violations using IsForeignKeyConstraintError()
- Log warnings for each skipped dependency with issue IDs and type
- Continue importing remaining dependencies instead of failing
- Display summary of all skipped dependencies at end of import

Example output:
  Warning: Skipping dependency due to missing reference: bd-b → bd-a (blocks)

  ⚠️  Warning: Skipped 2 dependencies due to missing references:
    - bd-b → bd-a (blocks)
    - bd-c → bd-a (parent-child)

  This can happen after merges that delete issues referenced by other issues.
  The import continued successfully - you may want to review the skipped dependencies.

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Co-Authored-By: Claude <noreply@anthropic.com>
2025-11-23 23:32:34 -08:00
Steve Yegge
3a0446c431 Fix test compilation errors: add context.Background() to sqlite.New() calls
Updated all test files to pass context.Background() as the first parameter
to sqlite.New() calls to match the updated function signature.

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Co-Authored-By: Claude <noreply@anthropic.com>
2025-11-21 14:57:18 -05:00
Steve Yegge
1168f661d1 fix: Add context.Background() to sqlite.New() calls in test files
Multiple test files were still using the old sqlite.New(path) signature
instead of the new sqlite.New(ctx, path) signature. This was causing
compilation failures in the test suite.

Fixed files:
- internal/importer/importer_test.go
- internal/importer/external_ref_test.go
- internal/importer/timestamp_test.go
- internal/rpc/limits_test.go
- internal/rpc/list_filters_test.go
- internal/rpc/rpc_test.go
- internal/rpc/status_test.go
- internal/syncbranch/syncbranch_test.go
2025-11-21 14:48:41 -05:00
Steve Yegge
82902432f5 test: Tag 16 slow integration tests with build tags
Identified and tagged obviously-slow integration tests with
`//go:build integration` to exclude them from default test runs.

This is step 1 of fixing test performance. The real fix is in
bd-1rh: refactoring tests to use shared DB setup instead of
creating 279 separate databases.

Tagged files:
- cmd/bd: 8 files (CLI tests, git ops, performance benchmarks)
- internal: 8 files (integration tests, E2E tests)

Issues:
- bd-1rh: Main issue tracking test performance
- bd-c49: Audit all tests and create grouping plan (next step)
- bd-y6d: POC refactor of create_test.go

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Co-Authored-By: Claude <noreply@anthropic.com>
2025-11-21 14:40:22 -05:00
Steve Yegge
57253f93a3 Context propagation with graceful cancellation (bd-rtp, bd-yb8, bd-2o2)
Complete implementation of signal-aware context propagation for graceful
cancellation across all commands and storage operations.

Key changes:

1. Signal-aware contexts (bd-rtp):
   - Added rootCtx/rootCancel in main.go using signal.NotifyContext()
   - Set up in PersistentPreRun, cancelled in PersistentPostRun
   - Daemon uses same pattern in runDaemonLoop()
   - Handles SIGINT/SIGTERM for graceful shutdown

2. Context propagation (bd-yb8):
   - All commands now use rootCtx instead of context.Background()
   - sqlite.New() receives context for cancellable operations
   - Database operations respect context cancellation
   - Storage layer propagates context through all queries

3. Cancellation tests (bd-2o2):
   - Added import_cancellation_test.go with comprehensive tests
   - Added export cancellation test in export_test.go
   - Tests verify database integrity after cancellation
   - All cancellation tests passing

Fixes applied during review:
   - Fixed rootCtx lifecycle (removed premature defer from PersistentPreRun)
   - Fixed test context contamination (reset rootCtx in test cleanup)
   - Fixed export tests missing context setup

Impact:
   - Pressing Ctrl+C during import/export now cancels gracefully
   - No database corruption or hanging transactions
   - Clean shutdown of all operations

Tested:
   - go build ./cmd/bd ✓
   - go test ./cmd/bd -run TestImportCancellation ✓
   - go test ./cmd/bd -run TestExportCommand ✓
   - Manual Ctrl+C testing verified

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Co-Authored-By: Claude <noreply@anthropic.com>
2025-11-20 21:57:23 -05:00
Steve Yegge
11fa142539 Optimize test suite with testing.Short() guards
- Add Short() guards to slow CLI tests (2-4s each)
- Add Short() guards to slow API/integration tests (3-11s)
- Add Short() guard to hanging daemon discovery test (29s timeout)
- Short test suite now runs in ~6s (down from 5+ minutes)

Run 'go test -short ./...' for fast iteration
Run 'go test ./...' for full coverage

Closes: bd-iov0
2025-11-06 17:31:15 -08:00
Steve Yegge
9de98cf1cb Add --clear-duplicate-external-refs flag to bd import
Fixes GH-234 by providing automatic resolution for duplicate external_ref
values instead of forcing manual JSONL editing.

Changes:
- Add ClearDuplicateExternalRefs option to importer.Options
- Modify validateNoDuplicateExternalRefs to clear duplicates when enabled
- Keep first occurrence, clear rest when flag is set
- Enhanced error message to suggest the flag
- Add comprehensive tests for the new behavior

Usage: bd import -i issues.jsonl --clear-duplicate-external-refs
Amp-Thread-ID: https://ampcode.com/threads/T-932dcf45-76f2-4994-9b5c-a6eb20a86036
Co-authored-by: Amp <amp@ampcode.com>
2025-11-06 13:01:44 -08:00
Steve Yegge
0f4b03e262 Optimize test suite: split integration tests, add -short support
- Split slow importer integration tests into separate file
- Add t.Short() guards to 10 slow daemon tests
- Document test organization in TEST_OPTIMIZATION.md
- Fast tests now run in ~50s vs 3+ minutes
- Use 'go test -short ./...' for fast feedback

Amp-Thread-ID: https://ampcode.com/threads/T-29ae21ac-749d-43d7-bf0c-2c5f7a06ae76
Co-authored-by: Amp <amp@ampcode.com>
2025-11-05 20:39:47 -08:00
Ryan
2ab064b2eb Doctor sync issues (#231)
* feat: enhance bd doctor sync detection with count and prefix mismatch checks

Improves bd doctor to detect actual database-JSONL sync issues instead of relying only on file modification times:

Key improvements:
1. Count detection: Reports when database issue count differs from JSONL (e.g., "Count mismatch: database has 0 issues, JSONL has 61")
2. Prefix detection: Identifies prefix mismatches when majority of JSONL issues use different prefix than database config
3. Error handling: Returns errors from helper functions instead of silent failures, distinguishing "can't open DB" from "counts differ"
4. Query optimization: Single database connection for all checks (reduced from 3 opens to 1)
5. Better error reporting: Shows actual error details when database or JSONL can't be read

This addresses the core issue where bd doctor would incorrectly report "Database and JSONL are in sync" when the database was empty but JSONL contained issues (as happened in privacy2 project).

Tests:
- Added TestCountJSONLIssuesWithMalformedLines to verify malformed JSON handling
- Existing doctor tests still pass
- countJSONLIssues now returns error to indicate parsing issues

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Co-Authored-By: Claude <noreply@anthropic.com>

* fix: correct git hooks installation instructions in bd doctor

The original message referenced './examples/git-hooks/install.sh' which doesn't exist in user projects. This fix changes the message to point to the actual location in the beads GitHub repository:

Before: "Run './examples/git-hooks/install.sh' to install recommended git hooks"
After: "See https://github.com/steveyegge/beads/tree/main/examples/git-hooks for installation instructions"

This works for any project using bd, not just the beads repository itself.

🤖 Generated with Claude Code

Co-Authored-By: Claude <noreply@anthropic.com>

* feat: add recovery suggestions when database fails but JSONL has issues

When bd doctor detects that the database cannot be opened/queried but the JSONL file contains issues, it now suggests the recovery command:

  Fix: Run 'bd import -i issues.jsonl --rename-on-import' to recover issues from JSONL

This addresses the case where:
- Database is corrupted or inaccessible
- JSONL has all the issues backed up
- User needs a clear path to recover

The check now:
1. Reads JSONL first (doesn't depend on database)
2. If database fails but JSONL has issues, suggests recovery command
3. If database can be queried, continues with sync checks as before

Tested on privacy2 project which has 61 issues in JSONL but inaccessible database.

🤖 Generated with Claude Code

Co-Authored-By: Claude <noreply@anthropic.com>

* fix: support hash-based issue IDs in import rename

The import --rename-on-import flag was rejecting valid issue IDs with
hash-based suffixes (e.g., privacy-09ea) because the validation only
accepted numeric suffixes. Beads now generates and accepts base36-encoded
hash IDs, so update the validation to match.

Changes:
- Update isNumeric() to accept base36 characters (0-9, a-z)
- Update tests to reflect hash-based ID support
- Add gosec nolint comment for safe file path construction

Fixes the error: "cannot rename issue privacy-09ea: non-numeric suffix '09ea'"

---------

Co-authored-by: Claude <noreply@anthropic.com>
2025-11-05 14:25:48 -08:00
Steve Yegge
2ac28b0122 fix: Windows CLI tests and skip hanging concurrent test
- Fix Windows test failure: use bd.exe instead of bd on Windows
- Skip TestConcurrentExternalRefImports which hangs due to database deadlock
- Added TODO reference to bd-gpe7 for investigation

Fixes CI failures in Test (Windows) and Test Nix Flake jobs.
2025-11-05 01:23:33 -08:00
Steve Yegge
0abd21f7a6 Fix bd-gdzd: Treat same-content-different-ID as update
When import finds same content hash with different IDs, treat it as
an update to the existing issue instead of failing with 'rename
collision' error. This handles edge cases like test data, legacy
data, or data corruption gracefully.

Amp-Thread-ID: https://ampcode.com/threads/T-e58a11be-cbbb-4a75-86d5-fc51af8f51d2
Co-authored-by: Amp <amp@ampcode.com>
2025-11-05 00:54:25 -08:00
Steve Yegge
8b9a486056 Fix critical import bug: preserve closed_at timestamps during sync
**Problem:**
Closed issues were silently reopening during git sync/import operations.
When importing an issue update, the importer built an updates map with
status='closed' but NO closed_at timestamp. The UpdateIssue() function's
manageClosedAt() would only set closed_at when status was CHANGING to
closed, not when it was already closed. Result: closed_at got cleared,
effectively reopening issues.

**Root Cause:**
1. Importer built updates map without closed_at field (lines 443-451, 519-528)
2. closed_at was not in allowedUpdateFields whitelist
3. manageClosedAt() only managed closed_at for status TRANSITIONS
4. Import of already-closed issue → closed_at lost → issue reopens

**Impact:**
- WASM issues (bd-44d0, bd-8507, etc.) were closed on Nov 4 (commit 0df9144)
- They reopened as 'open' status during sync on Nov 5 (commit 8c9814a)
- Users had to repeatedly close the same issues
- Data integrity violation: status=closed with closed_at=NULL

**Fix:**
1. Add closed_at to allowedUpdateFields whitelist
2. Add closed_at to importer updates maps (both external_ref and ID paths)
3. Update manageClosedAt() to skip auto-management if closed_at explicitly provided
   - Preserves import timestamps while maintaining auto-management for CLI operations

**Testing:**
- All internal/importer tests pass
- All internal/storage/sqlite tests pass
- Explicitly tests timestamp preservation in TestImportWithExternalRef

**Files Changed:**
- internal/importer/importer.go: Add closed_at to updates maps
- internal/storage/sqlite/sqlite.go: Allow closed_at updates, respect explicit values

Amp-Thread-ID: https://ampcode.com/threads/T-53ed6e45-9d04-4a35-97e9-d1ec36321ab0
Co-authored-by: Amp <amp@ampcode.com>
2025-11-05 00:41:10 -08:00
Steve Yegge
ff8f6ecadf feat(import): add import.orphan_handling config with 4 modes
- Add GetOrphanHandling() helper to SQLiteStorage (reads from config table)
- Add --orphan-handling flag to 'bd import' command
- Wire OrphanHandling through ImportOptions -> importer.Options
- Auto-read config if flag not provided (default: 'allow')
- Document in CONFIG.md with detailed mode explanations

Modes:
- strict: Fail on missing parent (safest)
- resurrect: Auto-create parent tombstones from JSONL
- skip: Skip orphans with warning
- allow: Import without validation (default, most permissive)

Closes bd-8072, bd-b92a

Amp-Thread-ID: https://ampcode.com/threads/T-fd18d4a5-06b3-4400-9073-194d570846d8
Co-authored-by: Amp <amp@ampcode.com>
2025-11-04 23:59:50 -08:00
Steve Yegge
0bf5c91cb3 Wire OrphanHandling through import pipeline (bd-8072)
- Added OrphanHandling type to sqlite package with 4 modes: strict/resurrect/skip/allow
- Updated EnsureIDs() to accept orphanHandling parameter and implement mode logic
- Added CreateIssuesWithOptions() that passes orphan handling through batch creation
- Made importer.OrphanHandling an alias to sqlite.OrphanHandling
- Importer now respects opts.OrphanHandling during batch issue creation

Next: Add import.orphan_handling config and wire through CLI commands
Amp-Thread-ID: https://ampcode.com/threads/T-bb7ffdd9-f444-4975-b5f7-bfff97cb92ff
Co-authored-by: Amp <amp@ampcode.com>
2025-11-04 23:53:44 -08:00
Steve Yegge
09f2edafba Add OrphanHandling type with 'allow' as default (bd-8072)
- Add OrphanHandling enum: strict/resurrect/skip/allow
- Add OrphanHandling field to importer.Options
- Default to 'allow' mode to work around existing system bugs
- Strict mode can be enabled via config for safer imports

Related: bd-8072, bd-b92a
2025-11-04 23:40:22 -08:00
Steve Yegge
d38a312583 Fix bd-3xq: Import gracefully handles missing parents
Implemented hybrid approach (topological sort + resurrection):

Phase 1: Import ordering (fixes latent bug)
- Sort issues by hierarchy depth before batch creation
- Create in depth-ordered batches (0→1→2→3)
- Ensures parents always created before children

Phase 2: Parent resurrection
- Attempt to resurrect missing parents from import batch
- Only fail if parent truly doesn't exist anywhere
- Enables deleted parent scenarios to work correctly

Benefits:
- Fixes import failure when parents deleted via bd-delete
- Handles parent-child pairs in same import batch
- Maintains referential integrity
- Enables multi-repo workflows with divergent deletion states

Amp-Thread-ID: https://ampcode.com/threads/T-14d3a206-aeac-4499-8ae9-47f3715e18fa
Co-authored-by: Amp <amp@ampcode.com>
2025-11-04 23:12:39 -08:00
Steve Yegge
d6e2ff6151 Phase 1: Add topological sorting to fix import ordering
- Add sort.go with depth-based utilities (GetHierarchyDepth, SortByDepth, GroupByDepth)
- Sort issues by hierarchy depth before batch creation
- Create in depth-order batches (0→1→2→3)
- Fixes latent bug: parent-child pairs in same batch could fail if wrong order
- Comprehensive tests for all sorting functions
- Closes bd-37dd, bd-3433, bd-8b65

Part of bd-d19a (Fix import failure on missing parent issues)

Amp-Thread-ID: https://ampcode.com/threads/T-44a36985-b59c-426f-834c-60a0faa0f9fb
Co-authored-by: Amp <amp@ampcode.com>
2025-11-04 22:25:26 -08:00
Steve Yegge
178a43dd5d Add external_ref UNIQUE constraint and validation
- Add migration for UNIQUE index on external_ref column (bd-897a)
- Add validation for duplicate external_ref in batch imports (bd-7315)
- Add query planner test to verify index usage (bd-f9a1)
- Add concurrent import tests for external_ref (bd-3f6a)

The migration detects existing duplicates and fails gracefully.
Batch imports now reject duplicates with clear error messages.
Tests verify the index is actually used by SQLite query planner.

Amp-Thread-ID: https://ampcode.com/threads/T-45ca66ed-3912-46c4-963c-caa7724a9a2f
Co-authored-by: Amp <amp@ampcode.com>
2025-11-02 16:27:42 -08:00
Steve Yegge
55c722a3e3 Implement external_ref as primary matching key for import updates (bd-1022)
- Add GetIssueByExternalRef() query function to storage interface and implementations
- Update DetectCollisions() to prioritize external_ref matching over ID matching
- Modify upsertIssues() to handle external_ref matches in import logic
- Add index on external_ref column for performance
- Add comprehensive tests for external_ref matching in both collision detection and import
- Enables re-syncing from external systems (Jira, GitHub, Linear) without duplicates
- Preserves local issues (no external_ref) from being overwritten
2025-11-02 15:28:09 -08:00
Steve Yegge
09bd4d3462 Fix CI test failures (bd-1231)
- Always recompute content_hash in importer to avoid stale hashes from JSONL
- Add .gitignore to test repos to prevent database files from being tracked
- Fix daemon auto-import test to use correct RPC operation ('show' not 'get_issue')
- Set last_import_time metadata in test helper to enable staleness check
- Add filesystem settle delay after git pull in tests

Root cause: CloseIssue updates status but not content_hash, so importer
thought issues were unchanged. Always recomputing content_hash fixes this.

Amp-Thread-ID: https://ampcode.com/threads/T-63ef3a7d-8efe-472d-97ed-6ac95bd8318b
Co-authored-by: Amp <amp@ampcode.com>
2025-11-02 08:55:34 -08:00
Steve Yegge
d240439868 fix: Resolve Windows test failures and lint warnings
- Fix Windows binary path issues (bd.exe vs bd)
- Skip scripttest on Windows (requires Unix shell)
- Skip file lock tests on Windows (platform locking differences)
- Fix registry tests to use USERPROFILE on Windows
- Fix 8 unparam lint warnings by marking unused params with _

All changes are platform-aware and maintain functionality.

Amp-Thread-ID: https://ampcode.com/threads/T-bc27021a-65db-4b64-a3f3-4e8d7bc8aa0d
Co-authored-by: Amp <amp@ampcode.com>
2025-11-02 08:30:31 -08:00
Steve Yegge
a4b4778ced test: improve coverage for importer and sqlite utils
- Fix TestImportIssues_Update by adding timestamps to test issue
- Add comprehensive tests for sqlite utility functions (IsUniqueConstraintError, QueryContext, BeginTx, ExecInTransaction)
- Coverage improvements: sqlite util.go 0% -> 95%, sqlite package 56.4% -> 57.1%

Amp-Thread-ID: https://ampcode.com/threads/T-17e6a3e4-f881-4f53-b670-bdd796d58f68
Co-authored-by: Amp <amp@ampcode.com>
2025-11-01 11:35:31 -07:00
Steve Yegge
253caef761 Fix bd-e55c: Import respects updated_at timestamps
- Import now checks timestamps before updating issues
- Only applies updates if incoming version is newer than local
- Prevents older remote versions from overwriting newer local changes
- Added comprehensive tests for timestamp precedence
- Fixes issue where git pull would revert local changes to open status
2025-10-31 18:06:05 -07:00