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1e20d702f2aaa0b2137877570187a5e32630e357
beads/cmd/bd
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Steve Yegge 1e20d702f2 fix(doctor): include tombstones in getCurrentJSONLIDs to prevent corruption (#552) 
The previous bd-in7q fix had backwards logic - by EXCLUDING tombstones
from currentIDs, they appeared missing when compared to historicalIDs,
causing HydrateDeletionsManifest to erroneously add them to deletions.jsonl.

This corruption manifested when:
1. Issues were migrated to tombstones via migrate-tombstones
2. Doctor hydration ran (directly or via sync)
3. Tombstones were seen as deleted and re-added to deletions.jsonl
4. Next import skipped thousands of issues with in deletions manifest

Fix: Include ALL issues (including tombstones) in currentIDs. Tombstones
represent migrated deletions that ARE accounted for - they should not
trigger new deletion records.

Generated with Claude Code

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
2025-12-14 17:33:07 -08:00
..
doctor
fix(doctor): include tombstones in getCurrentJSONLIDs to prevent corruption (#552)
2025-12-14 17:33:07 -08:00
setup
feat: add Git worktree compatibility (PR #478)
2025-12-13 12:50:33 -08:00
templates
fix: improve JSONL-only mode detection and error messages (GH #534)
2025-12-13 12:50:33 -08:00
testdata
…
autoflush.go
fix(memory): implement GetReadyWork/GetBlockedIssues + child counters
2025-12-13 23:22:10 -08:00
autoimport_test.go
fix: use proper YAML parsing for no-db mode detection (bd-r6k2)
2025-12-07 21:09:32 +11:00
autoimport.go
feat: add Git worktree compatibility (PR #478)
2025-12-13 12:50:33 -08:00
autostart_test.go
…
clean_security_test.go
test: Add security and error handling tests for lint warnings
2025-11-21 19:30:48 -05:00
clean.go
bd-6xd: Standardize on issues.jsonl as canonical filename
2025-11-26 22:02:59 -08:00
cleanup.go
fix(cleanup): resolve CHECK constraint failure and add tombstone pruning
2025-12-14 00:37:54 -08:00
cli_fast_test.go
fix(storage): persist close_reason to issues table on close (#551)
2025-12-14 14:18:01 -08:00
comments_test.go
…
comments.go
feat: add --readonly flag for worker sandboxes (gt-ymo)
2025-12-02 23:44:22 -08:00
compact_test.go
feat(tombstones): add migrate-tombstones command and compact pruning
2025-12-07 21:34:35 +11:00
compact.go
fix(cleanup): resolve CHECK constraint failure and add tombstone pruning
2025-12-14 00:37:54 -08:00
config_test.go
…
config.go
feat(bd-1pj6): Add custom status states via config
2025-11-28 23:19:21 -08:00
count.go
feat: Add 'bd count' command for counting and grouping issues
2025-11-21 19:21:05 -05:00
create_test.go
…
create.go
feat: add --estimate flag to bd create/update commands (GH #443)
2025-12-03 15:55:35 -08:00
daemon_autoimport_test.go
…
daemon_autostart.go
feat(cli): add 'bd thanks' command to thank contributors
2025-12-14 12:40:32 -08:00
daemon_config.go
refactor: remove deprecated global daemon support
2025-11-24 23:39:54 -08:00
daemon_crash_test.go
…
daemon_debouncer_test.go
fix: CI test failures on Windows
2025-11-26 20:59:07 -08:00
daemon_debouncer.go
…
daemon_event_loop.go
refactor: rename last_import_hash to jsonl_content_hash (bd-39o)
2025-11-28 23:14:12 -08:00
daemon_health_unix.go
fix(ci): more changes to fix failing CI (#415)
2025-11-29 22:24:29 -08:00
daemon_health_wasm.go
feat: implement health checks in daemon event loop (bd-gqo)
2025-11-28 23:10:44 -08:00
daemon_health_windows.go
feat: implement health checks in daemon event loop (bd-gqo)
2025-11-28 23:10:44 -08:00
daemon_lifecycle.go
feat(daemon): add --foreground flag for systemd/supervisord integration
2025-12-01 21:09:00 -08:00
daemon_local_test.go
feat(daemon): add --local flag for git-free daemon operation (#433)
2025-12-01 17:37:56 -08:00
daemon_lock_test.go
…
daemon_lock_unix.go
…
daemon_lock_wasm.go
…
daemon_lock_windows.go
…
daemon_lock.go
…
daemon_logger.go
Increase daemon log rotation limits for production use
2025-11-23 21:33:00 -08:00
daemon_parent_test.go
Fix integration test compilation errors in cmd/bd
2025-12-11 07:11:15 -05:00
daemon_rotation_test.go
Increase daemon log rotation limits for production use
2025-11-23 21:33:00 -08:00
daemon_server.go
refactor: remove deprecated global daemon support
2025-11-24 23:39:54 -08:00
daemon_sync_branch_test.go
Update pre-commit hook regression test for proper isolation
2025-12-11 07:11:42 -05:00
daemon_sync_branch.go
feat: add Git worktree compatibility (PR #478)
2025-12-13 12:50:33 -08:00
daemon_sync_test.go
refactor: rename last_import_hash to jsonl_content_hash (bd-39o)
2025-11-28 23:14:12 -08:00
daemon_sync.go
feat: add Git worktree compatibility (PR #478)
2025-12-13 12:50:33 -08:00
daemon_test.go
Fix integration test compilation errors in cmd/bd
2025-12-11 07:11:15 -05:00
daemon_unix_test.go
feat: Complete GH #353 follow-up phases (bd-9nw, bd-u3t, bd-e0o)
2025-11-21 19:32:45 -05:00
daemon_unix.go
feat: Complete GH #353 follow-up phases (bd-9nw, bd-u3t, bd-e0o)
2025-11-21 19:32:45 -05:00
daemon_wasm.go
…
daemon_watcher_platform_test.go
…
daemon_watcher_test.go
…
daemon_watcher.go
feat: add Git worktree compatibility (PR #478)
2025-12-13 12:50:33 -08:00
daemon_windows.go
…
daemon.go
feat(daemon): add --foreground flag for systemd/supervisord integration
2025-12-01 21:09:00 -08:00
daemons_test.go
…
daemons.go
…
delete_recording_test.go
bd sync: 2025-11-25 11:46:06
2025-11-25 11:46:06 -08:00
delete_test.go
…
delete.go
Enable daemon RPC support for delete operations to trigger auto-sync, Fix for issue #527 (#528)
2025-12-12 13:19:31 -08:00
deleted.go
feat(deletions): complete deletions manifest epic with integration tests
2025-11-25 16:36:46 -08:00
deletion_propagation_test.go
bd sync: 2025-11-25 12:03:21
2025-11-25 12:03:21 -08:00
deletion_tracking_test.go
fix(multi-repo): filter issues by prefix when flushing from non-primary repos (GH #437)
2025-12-01 21:17:56 -08:00
deletion_tracking.go
…
dep_test.go
bd sync: 2025-11-25 19:32:04
2025-11-25 19:32:05 -08:00
dep.go
feat: add --readonly flag for worker sandboxes (gt-ymo)
2025-12-02 23:44:22 -08:00
detect_pollution.go
feat: Complete command set standardization (bd-au0)
2025-11-23 20:33:31 -08:00
direct_mode_test.go
fix(test): Complete rootCtx initialization fix for all hanging tests (issue #355)
2025-11-21 23:09:47 -08:00
direct_mode.go
fix: improve JSONL-only mode detection and error messages (GH #534)
2025-12-13 12:50:33 -08:00
docs.md
docs: Add comprehensive documentation for version reporting changes
2025-12-13 10:04:01 +11:00
doctor_test.go
fix(doctor): detect sync-branch hook incompatibility (#532)
2025-12-13 18:05:49 -08:00
doctor.go
fix(doctor): detect sync-branch hook incompatibility (#532)
2025-12-13 18:05:49 -08:00
duplicates_test.go
Implement auto-merge functionality for duplicates command
2025-11-27 22:39:13 -08:00
duplicates.go
feat: add --readonly flag for worker sandboxes (gt-ymo)
2025-12-02 23:44:22 -08:00
epic_test.go
…
epic.go
feat: add --readonly flag for worker sandboxes (gt-ymo)
2025-12-02 23:44:22 -08:00
errors.go
feat: add --readonly flag for worker sandboxes (gt-ymo)
2025-12-02 23:44:22 -08:00
export_import_test.go
test(export): add test for tombstone inclusion in JSONL export (bd-yk8w)
2025-12-07 21:14:13 +11:00
export_integrity_integration_test.go
fix: replace string(rune()) with strconv.Itoa in tests (bd-fmc)
2025-12-02 22:41:07 -08:00
export_mtime_test.go
…
export_staleness_test.go
…
export_test.go
…
export.go
chore: sync changes from beads-sync
2025-12-07 20:57:58 +11:00
flags.go
feat: Add --body flag as alias for --description
2025-11-21 20:08:55 -05:00
flush_manager_test.go
Fix linter issues and test failures
2025-11-22 00:11:45 -08:00
flush_manager.go
Fix linter issues and test failures
2025-11-22 00:11:45 -08:00
git_sync_test.go
…
helpers_test.go
fix: support multi-part prefixes in issue ID extraction (#398)
2025-11-26 17:42:14 -08:00
hooks_test.go
feat: add Git worktree compatibility (PR #478)
2025-12-13 12:50:33 -08:00
hooks.go
feat: add Git worktree compatibility (PR #478)
2025-12-13 12:50:33 -08:00
import_bug_test.go
…
import_cancellation_test.go
…
import_idempotent_test.go
fix(test): Complete rootCtx initialization fix for all hanging tests (issue #355)
2025-11-21 23:09:47 -08:00
import_mtime_test.go
…
import_multipart_id_test.go
…
import_profile_test.go
…
import_shared.go
fix(sync): protect local issues from git-history-backfill during sync (#485)
2025-12-12 13:28:48 -08:00
import_uncommitted_test.go
…
import.go
fix(sync): protect local issues from git-history-backfill during sync (#485)
2025-12-12 13:28:48 -08:00
info_test.go
…
info.go
docs: update changelog and info.go for v0.29.0 release
2025-12-03 16:24:24 -08:00
init_contributor.go
feat: configure sync.remote for contributor fork workflows
2025-11-29 23:22:52 -08:00
init_hooks_test.go
feat: add Git worktree compatibility (PR #478)
2025-12-13 12:50:33 -08:00
init_team.go
fix: Auto-configure sync.branch during bd init (bd-flil)
2025-11-23 19:42:21 -08:00
init_test.go
feat: add Git worktree compatibility (PR #478)
2025-12-13 12:50:33 -08:00
init.go
feat: add Git worktree compatibility (PR #478)
2025-12-13 12:50:33 -08:00
integrity_content_test.go
…
integrity_test.go
refactor: rename last_import_hash to jsonl_content_hash (bd-39o)
2025-11-28 23:14:12 -08:00
integrity.go
fix(bd-53c): Add reverse ZFC check to prevent stale DB from corrupting JSONL
2025-11-29 17:01:36 -08:00
jira_test.go
test: add unit tests for Jira integration
2025-11-30 15:35:30 -08:00
jira.go
fix: resolve CI lint errors and Windows test timeout
2025-12-03 17:50:23 -08:00
jsonl_integrity_test.go
…
label_test.go
…
label.go
feat: add --readonly flag for worker sandboxes (gt-ymo)
2025-12-02 23:44:22 -08:00
list_test.go
…
list.go
Add --sort and --reverse flags to bd list command
2025-11-24 20:16:07 -08:00
main_test.go
fix(ci): more changes to fix failing CI (#415)
2025-11-29 22:24:29 -08:00
main.go
fix: bd onboard hangs on Windows (GH #531)
2025-12-13 18:09:34 -08:00
markdown_test.go
…
markdown.go
…
merge_security_test.go
fix: skip /etc/passwd check on Windows in security test (#363)
2025-11-22 16:49:29 -08:00
merge.go
docs(UX): improve daemon and merge documentation (bd-bt6y)
2025-11-28 23:11:24 -08:00
message.go
…
migrate_hash_ids_test.go
…
migrate_hash_ids.go
feat: add --readonly flag for worker sandboxes (gt-ymo)
2025-12-02 23:44:22 -08:00
migrate_issues.go
feat: add --readonly flag for worker sandboxes (gt-ymo)
2025-12-02 23:44:22 -08:00
migrate_sync_test.go
test: replace manual os.Chdir with t.Chdir in tests (#457)
2025-12-04 11:21:43 -08:00
migrate_sync.go
feat: add Git worktree compatibility (PR #478)
2025-12-13 12:50:33 -08:00
migrate_test.go
…
migrate_tombstones_test.go
Fix bd-in7q: prevent migrate-tombstones from corrupting deletions manifest (#554)
2025-12-14 14:11:27 -08:00
migrate_tombstones.go
feat: add Git worktree compatibility (PR #478)
2025-12-13 12:50:33 -08:00
migrate.go
feat: add --readonly flag for worker sandboxes (gt-ymo)
2025-12-02 23:44:22 -08:00
nodb_test.go
test: replace manual os.Chdir with t.Chdir in tests (#457)
2025-12-04 11:21:43 -08:00
nodb.go
fix: support multi-part prefixes in issue ID extraction (#398)
2025-11-26 17:42:14 -08:00
onboard_test.go
fix: make bd onboard output generic, not beads-specific (#465)
2025-12-05 13:20:51 -08:00
onboard.go
fix: make bd onboard output generic, not beads-specific (#465)
2025-12-05 13:20:51 -08:00
output_test.go
…
prime_test.go
feat(prime): add --stealth flag for flush-only workflow
2025-12-03 18:08:33 -08:00
prime.go
feat(prime): add --stealth flag for flush-only workflow
2025-12-03 18:08:33 -08:00
quickstart.go
…
readonly_test.go
feat: add --readonly flag for worker sandboxes (gt-ymo)
2025-12-02 23:44:22 -08:00
ready_test.go
feat(ready): add --unassigned filter for bd ready
2025-11-30 00:38:57 -08:00
ready.go
feat(tombstone): add P2 code review improvements (bd-saa, bd-1bu, bd-nyt)
2025-12-05 15:48:46 -08:00
reinit_test.go
fix(init): bootstrap from sync-branch when configured (bd-0is)
2025-12-05 14:47:02 -08:00
rename_prefix_repair_test.go
…
rename_prefix_test.go
…
rename_prefix.go
feat: add --readonly flag for worker sandboxes (gt-ymo)
2025-12-02 23:44:22 -08:00
reopen_test.go
…
reopen.go
feat: add --readonly flag for worker sandboxes (gt-ymo)
2025-12-02 23:44:22 -08:00
repair_deps_test.go
…
repair_deps.go
feat: add --readonly flag for worker sandboxes (gt-ymo)
2025-12-02 23:44:22 -08:00
repo.go
…
restore_test.go
test: replace manual os.Chdir with t.Chdir in tests (#457)
2025-12-04 11:21:43 -08:00
restore.go
…
sandbox_test.go
feat: Complete GH #353 follow-up phases (bd-9nw, bd-u3t, bd-e0o)
2025-11-21 19:32:45 -05:00
sandbox_unix.go
feat: Complete GH #353 follow-up phases (bd-9nw, bd-u3t, bd-e0o)
2025-11-21 19:32:45 -05:00
sandbox_windows.go
feat: Complete GH #353 follow-up phases (bd-9nw, bd-u3t, bd-e0o)
2025-11-21 19:32:45 -05:00
scripttest_test.go
…
search_test.go
feat: Add date and priority filters to bd search (bd-au0.5)
2025-11-21 22:46:12 -05:00
search.go
bd sync: 2025-11-24 21:16:44
2025-11-24 21:16:44 -08:00
setup.go
feat(setup claude): add --stealth flag
2025-12-03 18:10:35 -08:00
show.go
feat: add --estimate flag to bd create/update commands (GH #443)
2025-12-03 15:55:35 -08:00
simple_helpers_test.go
…
snapshot_manager.go
Fix bd-pq5k: merge conflicts now prefer closed>open and deletion>modification
2025-11-23 21:42:43 -08:00
stale_test.go
fix: replace string(rune()) with strconv.Itoa in tests (bd-fmc)
2025-12-02 22:41:07 -08:00
stale.go
…
staleness.go
bd-6xd: Standardize on issues.jsonl as canonical filename
2025-11-26 22:02:59 -08:00
status_test.go
Fix: TestGetAssignedStatus - Missing rootCtx initialization
2025-11-21 23:22:12 -08:00
status.go
bd-6xd: Standardize on issues.jsonl as canonical filename
2025-11-26 22:02:59 -08:00
sync_local_only_test.go
test: replace manual os.Chdir with t.Chdir in tests (#457)
2025-12-04 11:21:43 -08:00
sync_merge_test.go
Fix: Change default JSONL filename from beads.jsonl to issues.jsonl
2025-11-21 23:34:22 -08:00
sync_test.go
fix(sync): protect locally exported issues from sanitization (bd-3ee1)
2025-12-14 00:55:55 -08:00
sync.go
fix(sync): protect locally exported issues from sanitization (bd-3ee1)
2025-12-14 00:55:55 -08:00
template_security_test.go
…
template_test.go
test: replace manual os.Chdir with t.Chdir in tests (#457)
2025-12-04 11:21:43 -08:00
template.go
…
test_helpers_test.go
feat: add Git worktree compatibility (PR #478)
2025-12-13 12:50:33 -08:00
test_wait_helper.go
fix: CI test failures and lint errors
2025-11-24 00:21:01 -08:00
thanks.go
feat(cli): add 'bd thanks' command to thank contributors
2025-12-14 12:40:32 -08:00
tips_example_test.go
Add tip system infrastructure (bd-d4i)
2025-11-24 10:56:14 -08:00
tips_test.go
bd sync: 2025-11-24 11:28:32
2025-11-24 11:28:32 -08:00
tips.go
feat: add Git worktree compatibility (PR #478)
2025-12-13 12:50:33 -08:00
upgrade.go
fix: Code review fixes for bd-loka
2025-11-23 17:16:27 -08:00
validate_test.go
fix: add test parallelism and increase Windows CI timeout
2025-12-03 18:30:53 -08:00
validate.go
feat: add --readonly flag for worker sandboxes (gt-ymo)
2025-12-02 23:44:22 -08:00
version_test.go
fix: Add commit and branch to bd version output (github #503)
2025-12-13 10:04:01 +11:00
version_tracking_test.go
test: replace manual os.Chdir with t.Chdir in tests (#457)
2025-12-04 11:21:43 -08:00
version_tracking.go
fix: store version in gitignored .local_version to prevent notification spam (bd-tok)
2025-12-02 23:38:20 -08:00
version.go
chore: Bump version to 0.29.0
2025-12-03 16:24:46 -08:00
worktree_test.go
…
worktree.go
feat: add Git worktree compatibility (PR #478)
2025-12-13 12:50:33 -08:00