Steve Yegge 1facf7fb83 feat: Add bd repair command for orphaned foreign key refs (hq-2cchm) ...

When the database has orphaned dependencies or labels, the migration
invariant check fails and prevents the database from opening. This
creates a chicken-and-egg problem where bd doctor --fix cannot run.

The new bd repair command:
- Opens SQLite directly, bypassing invariant checks
- Deletes orphaned dependencies (issue_id or depends_on_id not in issues)
- Deletes orphaned labels (issue_id not in issues)
- Runs WAL checkpoint to persist changes
- Supports --dry-run to preview what would be cleaned

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

2025-12-29 12:43:22 -08:00

..

doctor

test: add git helper and guard annotations

2025-12-28 20:48:37 -08:00

setup

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templates/hooks

chore: Bump version to 0.39.1

2025-12-27 22:33:05 -08:00

testdata

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.gitattributes

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@AGENTS.md

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activity_test.go

test: add git helper and guard annotations

2025-12-28 20:48:37 -08:00

activity.go

Improve activity feed with title and assignee context

2025-12-28 10:06:08 -08:00

admin_aliases.go

docs: Document deprecation timeline and add removal warnings (bd-pndo)

2025-12-28 16:40:43 -08:00

admin.go

feat: add bd admin parent command for cleanup/compact/reset (bd-3u8m)

2025-12-27 16:21:08 -08:00

agent_test.go

feat: add bd agent state command for ZFC-compliant state reporting (bd-uxlb)

2025-12-28 01:56:53 -08:00

agent.go

chore: remove issue ID references from comments and changelogs

2025-12-28 10:05:16 -08:00

AGENTS.md

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audit.go

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autoflush.go

refactor: Break up 280-line flushToJSONLWithState into focused helpers (bd-9hc9)

2025-12-28 16:23:45 -08:00

autoimport_test.go

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autoimport.go

refactor: Extract shared importFromJSONLData function

2025-12-29 12:38:02 -08:00

autostart_test.go

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cleanup.go

chore: remove issue ID references from comments and changelogs

2025-12-28 10:05:16 -08:00

cli_coverage_show_test.go

refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)

2025-12-27 16:02:15 -08:00

cli_fast_test.go

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close.go

refactor: Split large cmd/bd files to meet 800-line limit (bd-xtf5)

2025-12-28 18:43:09 -08:00

comments_test.go

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comments.go

docs: Document deprecation timeline and add removal warnings (bd-pndo)

2025-12-28 16:40:43 -08:00

compact_rpc.go

refactor: Split large cmd/bd files to meet 800-line limit (bd-xtf5)

2025-12-28 18:43:09 -08:00

compact_test.go

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compact_tombstone.go

feat: Add bd compact --purge-tombstones for dependency-aware cleanup (hq-n19iv)

2025-12-28 23:46:22 -08:00

compact.go

feat: Add bd compact --purge-tombstones for dependency-aware cleanup (hq-n19iv)

2025-12-28 23:46:22 -08:00

config_test.go

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config.go

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cook_test.go

feat: Compile-time vs runtime cooking (gt-8tmz.23)

2025-12-25 18:40:15 -08:00

cook.go

refactor: Break up 275-line runCook into focused helpers (bd-8zbo)

2025-12-28 16:37:30 -08:00

count.go

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create_form_test.go

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create_form.go

refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)

2025-12-27 16:02:15 -08:00

create_test.go

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create.go

feat: Add mol_type schema field for molecule type classification (bd-oxgi)

2025-12-28 19:52:51 -08:00

daemon_autoimport_test.go

refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)

2025-12-27 16:02:15 -08:00

daemon_autostart_unit_test.go

feat: auto-bypass daemon for wisp operations (bd-ta4r)

2025-12-28 02:11:13 -08:00

daemon_autostart.go

refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)

2025-12-27 16:02:15 -08:00

daemon_basics_test.go

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daemon_config.go

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daemon_crash_test.go

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daemon_debouncer_test.go

refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)

2025-12-27 16:02:15 -08:00

daemon_debouncer.go

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daemon_event_loop.go

chore: remove issue ID references from comments and changelogs

2025-12-28 10:05:16 -08:00

daemon_health_freebsd.go

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daemon_health_unix.go

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daemon_health_wasm.go

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daemon_health_windows.go

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daemon_integration_test.go

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daemon_lifecycle.go

chore: remove issue ID references from comments and changelogs

2025-12-28 10:05:16 -08:00

daemon_local_test.go

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daemon_lock_test.go

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daemon_lock_unix.go

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daemon_lock_wasm.go

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daemon_lock_windows.go

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daemon_lock.go

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daemon_logger.go

chore: Convert scattered TODOs to tracked issues (bd-lrj8)

2025-12-28 16:34:24 -08:00

daemon_parent_test.go

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daemon_rotation_test.go

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daemon_server.go

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daemon_sync_branch_test.go

refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)

2025-12-27 16:02:15 -08:00

daemon_sync_branch.go

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daemon_sync_state.go

refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)

2025-12-27 16:02:15 -08:00

daemon_sync_test.go

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daemon_sync.go

chore: remove issue ID references from comments and changelogs

2025-12-28 10:05:16 -08:00

daemon_test.go

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daemon_unix_test.go

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daemon_unix.go

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daemon_wasm.go

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daemon_watcher_platform_test.go

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daemon_watcher_test.go

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daemon_watcher.go

chore: remove issue ID references from comments and changelogs

2025-12-28 10:05:16 -08:00

daemon_windows.go

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daemon.go

refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)

2025-12-27 16:02:15 -08:00

daemons_test.go

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daemons.go

docs: Document deprecation timeline and add removal warnings (bd-pndo)

2025-12-28 16:40:43 -08:00

defer.go

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delete_rpc_test.go

refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)

2025-12-27 16:02:15 -08:00

delete_test.go

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delete.go

feat: Add --reason flag to bd delete for audit trail

2025-12-29 12:40:03 -08:00

deletion_tracking_test.go

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deletion_tracking.go

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dep_test.go

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dep.go

chore: remove issue ID references from comments and changelogs

2025-12-28 10:05:16 -08:00

detect_pollution.go

docs: Document deprecation timeline and add removal warnings (bd-pndo)

2025-12-28 16:40:43 -08:00

direct_mode_test.go

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direct_mode.go

chore: remove issue ID references from comments and changelogs

2025-12-28 10:05:16 -08:00

docs.md

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doctor_fix.go

refactor: Split large cmd/bd files to meet 800-line limit (bd-xtf5)

2025-12-28 18:43:09 -08:00

doctor_health.go

refactor: Split large cmd/bd files to meet 800-line limit (bd-xtf5)

2025-12-28 18:43:09 -08:00

doctor_pollution.go

fix: resolve golangci-lint errors (errcheck, gosec, unparam)

2025-12-28 20:50:54 -08:00

doctor_repair_chaos_test.go

test: add git helper and guard annotations

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doctor_repair_test.go

test: add git helper and guard annotations

2025-12-28 20:48:37 -08:00

doctor_test.go

test: add git helper and guard annotations

2025-12-28 20:48:37 -08:00

doctor.go

refactor: Split large cmd/bd files to meet 800-line limit (bd-xtf5)

2025-12-28 18:43:09 -08:00

duplicate.go

chore: remove issue ID references from comments and changelogs

2025-12-28 10:05:16 -08:00

duplicates_test.go

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duplicates.go

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edit.go

fix: resolve golangci-lint errors (errcheck, gosec, unparam)

2025-12-28 20:50:54 -08:00

epic_test.go

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epic.go

fix: Use FatalErrorRespectJSON across all commands (bd-28sq)

2025-12-25 13:56:19 -08:00

errors.go

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export_import_test.go

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export_integrity_integration_test.go

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export_mtime_test.go

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export_staleness_test.go

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export_test.go

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export.go

chore: remove issue ID references from comments and changelogs

2025-12-28 10:05:16 -08:00

external_ref_test.go

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flags.go

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flush_manager_test.go

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flush_manager.go

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fork_protection_test.go

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fork_protection.go

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formula.go

refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)

2025-12-27 16:02:15 -08:00

gate.go

chore: remove issue ID references from comments and changelogs

2025-12-28 10:05:16 -08:00

git_sync_test.go

refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)

2025-12-27 16:02:15 -08:00

git_test_helpers.go

test: add git helper and guard annotations

2025-12-28 20:48:37 -08:00

graph_test.go

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graph.go

refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)

2025-12-27 16:02:15 -08:00

helpers_test.go

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hooks_test.go

test: add git helper and guard annotations

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hooks.go

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import_bug_test.go

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import_cancellation_test.go

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import_helpers_test.go

refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)

2025-12-27 16:02:15 -08:00

import_idempotent_test.go

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import_mtime_test.go

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import_multipart_id_test.go

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import_profile_test.go

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import_shared.go

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import_uncommitted_test.go

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import.go

chore: remove issue ID references from comments and changelogs

2025-12-28 10:05:16 -08:00

info_test.go

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info.go

chore: remove issue ID references from comments and changelogs

2025-12-28 10:05:16 -08:00

init_agent.go

refactor: Split init.go from 1928 to 705 lines (bd-xtf5)

2025-12-28 18:43:09 -08:00

init_contributor.go

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init_git_hooks.go

refactor: Split init.go from 1928 to 705 lines (bd-xtf5)

2025-12-28 18:43:09 -08:00

init_hooks_test.go

test: add git helper and guard annotations

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init_stealth.go

refactor: Split init.go from 1928 to 705 lines (bd-xtf5)

2025-12-28 18:43:09 -08:00

init_team.go

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init_templates.go

refactor: Split init.go from 1928 to 705 lines (bd-xtf5)

2025-12-28 18:43:09 -08:00

init_test.go

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init.go

feat: Add bd init --from-jsonl for preserving manual cleanups

2025-12-29 12:34:57 -08:00

integrity_content_test.go

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integrity_test.go

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integrity.go

chore: remove issue ID references from comments and changelogs

2025-12-28 10:05:16 -08:00

jira_test.go

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jira.go

chore: Convert scattered TODOs to tracked issues (bd-lrj8)

2025-12-28 16:34:24 -08:00

jsonl_integrity_test.go

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label_test.go

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label.go

chore: remove issue ID references from comments and changelogs

2025-12-28 10:05:16 -08:00

linear_conflict.go

refactor: Split large cmd/bd files to meet 800-line limit (bd-xtf5)

2025-12-28 18:43:09 -08:00

linear_sync.go

refactor: Split large cmd/bd files to meet 800-line limit (bd-xtf5)

2025-12-28 18:43:09 -08:00

linear_test.go

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linear.go

refactor: Split large cmd/bd files to meet 800-line limit (bd-xtf5)

2025-12-28 18:43:09 -08:00

list_helpers_test.go

refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)

2025-12-27 16:02:15 -08:00

list_test.go

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list.go

feat: Add mol_type schema field for molecule type classification (bd-oxgi)

2025-12-28 19:52:51 -08:00

mail.go

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main_daemon.go

refactor: Split large cmd/bd files to meet 800-line limit (bd-xtf5)

2025-12-28 18:43:09 -08:00

main_errors.go

refactor: Split large cmd/bd files to meet 800-line limit (bd-xtf5)

2025-12-28 18:43:09 -08:00

main_help.go

refactor: Split large cmd/bd files to meet 800-line limit (bd-xtf5)

2025-12-28 18:43:09 -08:00

main_test.go

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main.go

feat: Add bd repair command for orphaned foreign key refs (hq-2cchm)

2025-12-29 12:43:22 -08:00

markdown_test.go

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markdown.go

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merge_security_test.go

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merge.go

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migrate_hash_ids_test.go

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migrate_hash_ids.go

docs: Document deprecation timeline and add removal warnings (bd-pndo)

2025-12-28 16:40:43 -08:00

migrate_issues.go

docs: Document deprecation timeline and add removal warnings (bd-pndo)

2025-12-28 16:40:43 -08:00

migrate_sync_test.go

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migrate_sync.go

docs: Document deprecation timeline and add removal warnings (bd-pndo)

2025-12-28 16:40:43 -08:00

migrate_test.go

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migrate_tombstones.go

docs: Document deprecation timeline and add removal warnings (bd-pndo)

2025-12-28 16:40:43 -08:00

migrate.go

chore: Convert scattered TODOs to tracked issues (bd-lrj8)

2025-12-28 16:34:24 -08:00

mol_bond.go

chore: remove issue ID references from comments and changelogs

2025-12-28 10:05:16 -08:00

mol_burn.go

feat: auto-bypass daemon for wisp operations (bd-ta4r)

2025-12-28 02:11:13 -08:00

mol_current.go

refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)

2025-12-27 16:02:15 -08:00

mol_distill.go

refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)

2025-12-27 16:02:15 -08:00

mol_show.go

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mol_squash.go

feat: auto-bypass daemon for wisp operations (bd-ta4r)

2025-12-28 02:11:13 -08:00

mol_stale.go

chore: Convert scattered TODOs to tracked issues (bd-lrj8)

2025-12-28 16:34:24 -08:00

mol_test.go

refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)

2025-12-27 16:02:15 -08:00

mol.go

refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)

2025-12-27 16:02:15 -08:00

nodb_test.go

refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)

2025-12-27 16:02:15 -08:00

nodb.go

chore: remove issue ID references from comments and changelogs

2025-12-28 10:05:16 -08:00

onboard_test.go

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onboard.go

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orphans_test.go

feat: Add 'bd orphans' command with DRY refactoring of orphan detection

2025-12-27 17:23:45 -08:00

orphans.go

fix: resolve golangci-lint errors (errcheck, gosec, unparam)

2025-12-28 20:50:54 -08:00

output_test.go

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periodic_remote_sync_test.go

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pour.go

chore: remove issue ID references from comments and changelogs

2025-12-28 10:05:16 -08:00

prime_test.go

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prime.go

feat: show redirect info in bd prime output (bd-kblo)

2025-12-27 21:33:01 -08:00

quick.go

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quickstart.go

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readonly_test.go

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ready_test.go

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ready.go

feat: Add mol_type schema field for molecule type classification (bd-oxgi)

2025-12-28 19:52:51 -08:00

reinit_test.go

refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)

2025-12-27 16:02:15 -08:00

relate_test.go

refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)

2025-12-27 16:02:15 -08:00

relate.go

docs: Document deprecation timeline and add removal warnings (bd-pndo)

2025-12-28 16:40:43 -08:00

rename_prefix_repair_test.go

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rename_prefix_test.go

fix: remove arbitrary 8-char prefix limit from rename-prefix (GH#770)

2025-12-27 22:24:19 -08:00

rename_prefix.go

fix: remove arbitrary 8-char prefix limit from rename-prefix (GH#770)

2025-12-27 22:24:19 -08:00

reopen_test.go

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reopen.go

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repair_deps_test.go

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repair_orphans_test.go

feat: Add bd repair command for orphaned foreign key refs (hq-2cchm)

2025-12-29 12:43:22 -08:00

repair.go

feat: Add bd repair command for orphaned foreign key refs (hq-2cchm)

2025-12-29 12:43:22 -08:00

repo.go

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reset_test.go

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reset.go

feat: add bd admin parent command for cleanup/compact/reset (bd-3u8m)

2025-12-27 16:21:08 -08:00

restore_test.go

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restore.go

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routed.go

refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)

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sandbox_test.go

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sandbox_unix.go

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sandbox_windows.go

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scripttest_test.go

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search_test.go

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search.go

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setup.go

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ship.go

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show_thread.go

refactor: Split large cmd/bd files to meet 800-line limit (bd-xtf5)

2025-12-28 18:43:09 -08:00

show_unit_helpers_test.go

refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)

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show_unit_helpers.go

refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)

2025-12-27 16:02:15 -08:00

show.go

Add --short flag to bd show for compact output

2025-12-28 21:35:30 -08:00

simple_helpers_test.go

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slot.go

chore: remove issue ID references from comments and changelogs

2025-12-28 10:05:16 -08:00

snapshot_manager.go

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stale_test.go

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stale.go

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staleness.go

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status_test.go

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status.go

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swarm.go

feat: swarm commands improvements (bd-2ubv)

2025-12-28 22:07:39 -08:00

sync_branch_priority_test.go

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sync_branch.go

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sync_check.go

chore: remove issue ID references from comments and changelogs

2025-12-28 10:05:16 -08:00

sync_export.go

chore: remove issue ID references from comments and changelogs

2025-12-28 10:05:16 -08:00

sync_git.go

fix: resolve golangci-lint errors (errcheck, gosec, unparam)

2025-12-28 20:50:54 -08:00

sync_helpers_more_test.go

refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)

2025-12-27 16:02:15 -08:00

sync_import.go

chore: remove issue ID references from comments and changelogs

2025-12-28 10:05:16 -08:00

sync_local_only_test.go

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sync_merge_test.go

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sync_test.go

chore: Convert scattered TODOs to tracked issues (bd-lrj8)

2025-12-28 16:34:24 -08:00

sync.go

refactor: Split large cmd/bd files to meet 800-line limit (bd-xtf5)

2025-12-28 18:43:09 -08:00

template_test.go

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template.go

docs: Document deprecation timeline and add removal warnings (bd-pndo)

2025-12-28 16:40:43 -08:00

test_guard_helpers.go

test: add git helper and guard annotations

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test_helpers_test.go

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test_repo_beads_guard_test.go

refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)

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test_wait_helper.go

refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)

2025-12-27 16:02:15 -08:00

thanks.go

refactor: relocate thanks command to bd info --thanks (bd-wb9g)

2025-12-27 16:08:34 -08:00

thread_test.go

refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)

2025-12-27 16:02:15 -08:00

tips_example_test.go

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tips_test.go

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tips.go

refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)

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undefer.go

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update.go

refactor: Split large cmd/bd files to meet 800-line limit (bd-xtf5)

2025-12-28 18:43:09 -08:00

upgrade.go

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version_test.go

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version_tracking_test.go

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version_tracking.go

chore: remove issue ID references from comments and changelogs

2025-12-28 10:05:16 -08:00

version.go

Release v0.40.0

2025-12-28 10:59:02 -08:00

where.go

feat: add 'bd where' command to show active beads location (bd-8x43)

2025-12-27 21:27:44 -08:00

wisp.go

chore: remove issue ID references from comments and changelogs

2025-12-28 10:05:16 -08:00

worktree_cmd.go

fix: resolve golangci-lint errors (errcheck, gosec, unparam)

2025-12-28 20:50:54 -08:00

worktree_daemon_test.go

refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)

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worktree_test.go

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worktree.go

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