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beads/cmd/bd
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Steve Yegge f3c663d31c feat: add bd doctor --deep for full graph integrity validation (bd-cwpl) 
Add a --deep flag to bd doctor that runs comprehensive graph integrity
checks on the beads database:

- Parent consistency: verify parent-child deps point to existing issues
- Dependency integrity: all dependencies reference valid issues
- Epic completeness: find epics ready to close (all children closed)
- Agent bead integrity: validate agent beads have valid state values
- Mail thread integrity: verify thread_id references exist
- Molecule integrity: check molecules have valid parent-child structures

The deep validation mode warns about potential slowness on large databases
and provides both human-readable and JSON output formats.

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

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
2025-12-28 02:13:34 -08:00
..
doctor
feat: add bd doctor --deep for full graph integrity validation (bd-cwpl)
2025-12-28 02:13:34 -08:00
setup
Add tests for setup package (28.4% → 53.8% coverage)
2025-12-23 22:40:16 -08:00
templates/hooks
chore: Bump version to 0.39.1
2025-12-27 22:33:05 -08:00
testdata
bd sync: 2025-12-23 23:38:57
2025-12-24 00:06:41 -08:00
.gitattributes
…
@AGENTS.md
…
activity_test.go
fix: emit rich mutation events for status changes (bd-313v)
2025-12-23 04:16:26 -08:00
activity.go
fix: emit rich mutation events for status changes (bd-313v)
2025-12-23 04:16:26 -08:00
admin_aliases.go
feat: add bd admin parent command for cleanup/compact/reset (bd-3u8m)
2025-12-27 16:21:08 -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
feat: add bd agent state command for ZFC-compliant state reporting (bd-uxlb)
2025-12-28 01:56:53 -08:00
AGENTS.md
…
audit.go
…
autoflush.go
refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)
2025-12-27 16:02:15 -08:00
autoimport_test.go
refactor: consolidate duplicate path-finding utilities (bd-74w1, bd-4nqq)
2025-12-22 21:15:41 -08:00
autoimport.go
Refactor duplicate JSONL-from-git parsing code (bd-y2v)
2025-12-23 22:41:05 -08:00
autostart_test.go
bd sync: 2025-12-23 23:38:57
2025-12-24 00:06:41 -08:00
cleanup.go
feat: add bd admin parent command for cleanup/compact/reset (bd-3u8m)
2025-12-27 16:21:08 -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
refactor: remove legacy autoflush code paths (bd-xsl9)
2025-12-23 01:56:19 -08:00
comments_test.go
…
comments.go
fix: Use FatalErrorRespectJSON across all commands (bd-28sq)
2025-12-25 13:56:19 -08:00
compact_test.go
feat(compact): Add --prune mode for standalone tombstone pruning (bd-c7y5)
2025-12-24 00:08:10 -08:00
compact.go
feat: add bd admin parent command for cleanup/compact/reset (bd-3u8m)
2025-12-27 16:21:08 -08:00
config_test.go
…
config.go
bd sync: 2025-12-23 23:38:57
2025-12-24 00:06:41 -08:00
cook_test.go
feat: Compile-time vs runtime cooking (gt-8tmz.23)
2025-12-25 18:40:15 -08:00
cook.go
feat: add pour warning for vapor-phase formulas, improve help text, add doctor check
2025-12-28 01:34:01 -08:00
count.go
feat: add gate issue type and CLI commands for async coordination (bd-udsi)
2025-12-23 12:06:42 -08:00
create_form_test.go
…
create_form.go
refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)
2025-12-27 16:02:15 -08:00
create_test.go
…
create.go
feat: add agent ID pattern validation for bd create --type=agent (gt-hlaaf)
2025-12-28 00:07:04 -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
…
daemon_config.go
…
daemon_crash_test.go
…
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
…
daemon_event_loop.go
feat(daemon): add auto_pull config parameter for periodic remote sync
2025-12-22 18:47:18 -05:00
daemon_health_freebsd.go
…
daemon_health_unix.go
…
daemon_health_wasm.go
…
daemon_health_windows.go
…
daemon_integration_test.go
bd sync: 2025-12-23 23:38:57
2025-12-24 00:06:41 -08:00
daemon_lifecycle.go
bd sync: 2025-12-23 23:38:57
2025-12-24 00:06:41 -08:00
daemon_local_test.go
bd sync: 2025-12-23 23:38:57
2025-12-24 00:06:41 -08:00
daemon_lock_test.go
…
daemon_lock_unix.go
…
daemon_lock_wasm.go
…
daemon_lock_windows.go
…
daemon_lock.go
chore: code health review - test fix and error comments (bd-9g1z, bd-ork0)
2025-12-22 21:30:57 -08:00
daemon_logger.go
bd sync: 2025-12-23 23:38:57
2025-12-24 00:06:41 -08:00
daemon_parent_test.go
…
daemon_rotation_test.go
…
daemon_server.go
bd sync: 2025-12-23 23:38:57
2025-12-24 00:06:41 -08:00
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
fix(sync): respect sync.remote config in daemon sync operations (#736)
2025-12-24 12:43:18 -08:00
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
bd sync: 2025-12-23 23:38:57
2025-12-24 00:06:41 -08:00
daemon_sync.go
refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)
2025-12-27 16:02:15 -08:00
daemon_test.go
…
daemon_unix_test.go
…
daemon_unix.go
…
daemon_wasm.go
…
daemon_watcher_platform_test.go
…
daemon_watcher_test.go
bd sync: 2025-12-23 23:38:57
2025-12-24 00:06:41 -08:00
daemon_watcher.go
fix(daemon): deduplicate file and git ref change log messages
2025-12-22 19:02:42 -05:00
daemon_windows.go
…
daemon.go
refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)
2025-12-27 16:02:15 -08:00
daemons_test.go
…
daemons.go
refactor(cmd): replace map[string]interface{} with typed JSON response structs (bd-u2sc.1)
2025-12-22 15:48:36 -08:00
defer.go
…
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
bd sync: 2025-12-23 23:38:57
2025-12-24 00:06:41 -08:00
delete.go
…
deletion_tracking_test.go
…
deletion_tracking.go
chore: remove dead deprecated wrapper functions
2025-12-21 15:50:10 -08:00
dep_test.go
feat(deps): detect/prevent child→parent dependency anti-pattern (bd-nim5)
2025-12-24 13:03:27 -08:00
dep.go
refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)
2025-12-27 16:02:15 -08:00
detect_pollution.go
feat: integrate detect-pollution into bd doctor --check=pollution (bd-kff0)
2025-12-27 16:20:12 -08:00
direct_mode_test.go
refactor: remove legacy autoflush code paths (bd-xsl9)
2025-12-23 01:56:19 -08:00
direct_mode.go
…
docs.md
…
doctor_repair_chaos_test.go
refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)
2025-12-27 16:02:15 -08:00
doctor_repair_test.go
refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)
2025-12-27 16:02:15 -08:00
doctor_test.go
fix(doctor): handle installed_plugins.json v2 format (GH#741)
2025-12-25 16:20:02 -08:00
doctor.go
feat: add bd doctor --deep for full graph integrity validation (bd-cwpl)
2025-12-28 02:13:34 -08:00
duplicate.go
chore: code health review - test fix and error comments (bd-9g1z, bd-ork0)
2025-12-22 21:30:57 -08:00
duplicates_test.go
…
duplicates.go
…
epic_test.go
…
epic.go
fix: Use FatalErrorRespectJSON across all commands (bd-28sq)
2025-12-25 13:56:19 -08:00
errors.go
fix(json): standardize JSON output for errors and empty arrays (bd-au0.7)
2025-12-24 00:07:52 -08:00
export_import_test.go
…
export_integrity_integration_test.go
…
export_mtime_test.go
bd sync: 2025-12-23 23:38:57
2025-12-24 00:06:41 -08:00
export_staleness_test.go
…
export_test.go
…
export.go
refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)
2025-12-27 16:02:15 -08:00
external_ref_test.go
feat: add cross-project dependency support - config and external: prefix (bd-66w1, bd-om4a)
2025-12-21 23:08:00 -08:00
flags.go
…
flush_manager_test.go
refactor: remove legacy autoflush code paths (bd-xsl9)
2025-12-23 01:56:19 -08:00
flush_manager.go
…
fork_protection_test.go
…
fork_protection.go
refactor: consolidate duplicate path-finding utilities (bd-74w1, bd-4nqq)
2025-12-22 21:15:41 -08:00
formula.go
refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)
2025-12-27 16:02:15 -08:00
gate.go
refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)
2025-12-27 16:02:15 -08:00
git_sync_test.go
refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)
2025-12-27 16:02:15 -08:00
graph_test.go
…
graph.go
refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)
2025-12-27 16:02:15 -08:00
helpers_test.go
…
hooks_test.go
…
hooks.go
…
import_bug_test.go
…
import_cancellation_test.go
…
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
…
import_mtime_test.go
…
import_multipart_id_test.go
bd sync: 2025-12-23 23:38:57
2025-12-24 00:06:41 -08:00
import_profile_test.go
…
import_shared.go
…
import_uncommitted_test.go
…
import.go
fix: update jsonl_file_hash on import to prevent hash mismatch warnings (bd-0vtq)
2025-12-27 23:22:18 -08:00
info_test.go
refactor: consolidate duplicate path-finding utilities (bd-74w1, bd-4nqq)
2025-12-22 21:15:41 -08:00
info.go
chore: Bump version to 0.39.1
2025-12-27 22:33:05 -08:00
init_contributor.go
…
init_hooks_test.go
…
init_team.go
…
init_test.go
…
init.go
refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)
2025-12-27 16:02:15 -08:00
integrity_content_test.go
…
integrity_test.go
…
integrity.go
refactor(cmd): migrate sort.Slice to slices.SortFunc (bd-u2sc.2)
2025-12-22 15:39:55 -08:00
jira_test.go
…
jira.go
refactor: consolidate duplicate path-finding utilities (bd-74w1, bd-4nqq)
2025-12-22 21:15:41 -08:00
jsonl_integrity_test.go
…
label_test.go
…
label.go
fix: Use FatalErrorRespectJSON across all commands (bd-28sq)
2025-12-25 13:56:19 -08:00
linear_test.go
…
linear.go
…
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
…
list.go
feat(list): add --pretty and --watch flags for built-in viewer (#729)
2025-12-24 12:35:57 -08:00
mail.go
fix(lint): add nosec for mail delegate exec.Command
2025-12-21 15:29:58 -08:00
main_test.go
refactor: remove legacy autoflush code paths (bd-xsl9)
2025-12-23 01:56:19 -08:00
main.go
feat: auto-bypass daemon for wisp operations (bd-ta4r)
2025-12-28 02:11:13 -08:00
markdown_test.go
…
markdown.go
fix: bd create -f now works with daemon mode (GH#719)
2025-12-22 23:30:08 -08:00
merge_security_test.go
…
merge.go
…
migrate_hash_ids_test.go
…
migrate_hash_ids.go
refactor(cmd): migrate sort.Slice to slices.SortFunc (bd-u2sc.2)
2025-12-22 15:39:55 -08:00
migrate_issues.go
chore: code health review - test fix and error comments (bd-9g1z, bd-ork0)
2025-12-22 21:30:57 -08:00
migrate_sync_test.go
…
migrate_sync.go
…
migrate_test.go
…
migrate_tombstones.go
refactor: consolidate duplicate path-finding utilities (bd-74w1, bd-4nqq)
2025-12-22 21:15:41 -08:00
migrate.go
bd sync: 2025-12-23 23:38:57
2025-12-24 00:06:41 -08:00
mol_bond.go
refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)
2025-12-27 16:02:15 -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
feat: add parallel step detection for molecules (bd-xo1o.4)
2025-12-23 03:57:08 -08:00
mol_squash.go
feat: auto-bypass daemon for wisp operations (bd-ta4r)
2025-12-28 02:11:13 -08:00
mol_stale.go
refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)
2025-12-27 16:02:15 -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
refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)
2025-12-27 16:02:15 -08:00
onboard_test.go
…
onboard.go
…
orphans_test.go
feat: Add 'bd orphans' command with DRY refactoring of orphan detection
2025-12-27 17:23:45 -08:00
orphans.go
feat: Add 'bd orphans' command with DRY refactoring of orphan detection
2025-12-27 17:23:45 -08:00
output_test.go
…
periodic_remote_sync_test.go
feat(daemon): add auto_pull config parameter for periodic remote sync
2025-12-22 18:47:18 -05:00
pour.go
feat: add pour warning for vapor-phase formulas, improve help text, add doctor check
2025-12-28 01:34:01 -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
…
quickstart.go
…
readonly_test.go
…
ready_test.go
…
ready.go
refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)
2025-12-27 16:02:15 -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
…
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
…
reopen.go
…
repair_deps_test.go
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repo.go
fix: bd repo commands write to YAML and cleanup on remove (#683)
2025-12-22 01:26:45 -08:00
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
…
routed.go
refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)
2025-12-27 16:02:15 -08:00
sandbox_test.go
…
sandbox_unix.go
…
sandbox_windows.go
…
scripttest_test.go
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search_test.go
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search.go
bd sync: 2025-12-23 23:38:57
2025-12-24 00:06:41 -08:00
setup.go
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ship.go
feat: add bd ship command for cross-project capabilities (bd-eijl)
2025-12-21 23:11:48 -08:00
show_unit_helpers_test.go
refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)
2025-12-27 16:02:15 -08:00
show_unit_helpers.go
refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)
2025-12-27 16:02:15 -08:00
show.go
feat: add --parent flag to bd update for reparenting issues (bd-cj2e)
2025-12-27 22:17:24 -08:00
simple_helpers_test.go
…
slot.go
feat: add bd slot commands for agent bead slot management (gt-h5sza)
2025-12-28 00:11:22 -08:00
snapshot_manager.go
chore: code health review - test fix and error comments (bd-9g1z, bd-ork0)
2025-12-22 21:30:57 -08:00
stale_test.go
fix(json): audit and standardize JSON output across commands (bd-au0.7)
2025-12-24 00:10:14 -08:00
stale.go
fix(json): audit and standardize JSON output across commands (bd-au0.7)
2025-12-24 00:10:14 -08:00
staleness.go
…
status_test.go
…
status.go
…
sync_branch_priority_test.go
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sync_branch.go
fix: Prevent bd sync from committing non-.beads files (bd-trgb)
2025-12-25 12:05:46 -08:00
sync_check.go
fix: address CI lint errors (gosec, errcheck, unparam, duplicate tests) (#730)
2025-12-24 12:35:32 -08:00
sync_export.go
refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)
2025-12-27 16:02:15 -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
fix: address CI lint errors (gosec, errcheck, unparam, duplicate tests) (#730)
2025-12-24 12:35:32 -08:00
sync_local_only_test.go
…
sync_merge_test.go
…
sync_test.go
…
sync.go
refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)
2025-12-27 16:02:15 -08:00
template_test.go
fix: mol run loads all hierarchical children + supports title lookup (bd-c8d5, bd-drcx)
2025-12-24 23:33:34 -08:00
template.go
feat: add pour warning for vapor-phase formulas, improve help text, add doctor check
2025-12-28 01:34:01 -08:00
test_helpers_test.go
…
test_repo_beads_guard_test.go
refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)
2025-12-27 16:02:15 -08:00
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
…
tips_test.go
…
tips.go
refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)
2025-12-27 16:02:15 -08:00
undefer.go
…
upgrade.go
…
version_test.go
…
version_tracking_test.go
…
version_tracking.go
…
version.go
chore: Bump version to 0.39.1
2025-12-27 22:33:05 -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
feat: auto-bypass daemon for wisp operations (bd-ta4r)
2025-12-28 02:11:13 -08:00
worktree_cmd.go
fix: address code review issues in bd worktree command
2025-12-28 01:07:38 -08:00
worktree_daemon_test.go
refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)
2025-12-27 16:02:15 -08:00
worktree_test.go
…
worktree.go
…