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e9be35e374c873d2e6e9efb06708dd048b7558c1
beads/cmd/bd
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Ryan e9be35e374 refactor(doctor): split doctor.go into modular package files (#653) 
* refactor(doctor): split doctor.go into modular package files

Split the 3,171-line doctor.go into logical sub-files within the
cmd/bd/doctor/ package, reducing the main file to 834 lines (74% reduction).

New package structure:
- types.go: DoctorCheck struct and status constants
- installation.go: CheckInstallation, CheckMultipleDatabases, CheckPermissions
- git.go: CheckGitHooks, CheckMergeDriver, CheckSyncBranch* checks
- database.go: CheckDatabaseVersion, CheckSchemaCompatibility, CheckDatabaseJSONLSync
- version.go: CheckCLIVersion, CheckMetadataVersionTracking, CompareVersions
- integrity.go: CheckIDFormat, CheckDependencyCycles, CheckTombstones
- daemon.go: CheckDaemonStatus, CheckVersionMismatch
- quick.go: Quick checks for sync-branch and hooks

Updated tests to use exported doctor.CheckXxx() functions and
doctor.StatusXxx constants.

* fix(doctor): suppress gosec G204 false positives

Add #nosec G204 comments to exec.Command calls in CheckSyncBranchHealth
where variables come from trusted sources (config files or hardcoded
values like "main"/"master"/"origin"), not untrusted user input.
2025-12-19 17:29:36 -08:00
..
doctor
refactor(doctor): split doctor.go into modular package files (#653)
2025-12-19 17:29:36 -08:00
setup
feat: add Factory.ai (Droid) support to bd setup command (#598)
2025-12-16 13:42:43 -08:00
templates/hooks
chore: Bump version to 0.30.6
2025-12-18 22:46:14 -08:00
testdata
…
.gitattributes
Fix tests (bd-6ss and sub-issues) (#626)
2025-12-18 18:23:30 -08:00
@AGENTS.md
Fix tests (bd-6ss and sub-issues) (#626)
2025-12-18 18:23:30 -08:00
AGENTS.md
Fix tests (bd-6ss and sub-issues) (#626)
2025-12-18 18:23:30 -08:00
autoflush.go
refactor: remove all deletions.jsonl code (bd-fom)
2025-12-16 14:20:49 -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
refactor: remove all deletions.jsonl code (bd-fom)
2025-12-16 14:20:49 -08:00
autostart_test.go
Fix tests (bd-6ss and sub-issues) (#626)
2025-12-18 18:23:30 -08:00
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
feat(cleanup): protect pinned issues from cleanup/compact (bd-b2k)
2025-12-19 00:42:35 -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
test: Refactor P1 test files to use shared DB pattern (bd-1rh)
2025-11-21 15:51:07 -05:00
comments.go
feat: add --readonly flag for worker sandboxes (gt-ymo)
2025-12-02 23:44:22 -08:00
compact_test.go
feat: add --hard flag to bd cleanup for bypassing tombstone TTL safety
2025-12-16 01:25:57 -08:00
compact.go
refactor: remove all deletions.jsonl code (bd-fom)
2025-12-16 14:20:49 -08:00
config_test.go
Context propagation with graceful cancellation (bd-rtp, bd-yb8, bd-2o2)
2025-11-20 21:57:23 -05:00
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_form_test.go
cleanup
2025-12-16 17:26:06 -08:00
create_form.go
fix(lint): resolve golangci-lint errors for clean CI
2025-12-18 20:06:41 +01:00
create_test.go
test: Refactor P1 test files to use shared DB pattern (bd-1rh)
2025-11-21 15:51:07 -05:00
create.go
feat: add merge-request issue type for refinery processing
2025-12-18 20:09:46 -08:00
daemon_autoimport_test.go
…
daemon_autostart.go
Auto-disable daemon in git worktrees for safety (#567)
2025-12-16 00:06:19 -08:00
daemon_basics_test.go
Fix tests (bd-6ss and sub-issues) (#626)
2025-12-18 18:23:30 -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_integration_test.go
Fix tests (bd-6ss and sub-issues) (#626)
2025-12-18 18:23:30 -08:00
daemon_lifecycle.go
Merge bd-cddj-nux: GH#519
2025-12-16 01:17:25 -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
refactor: remove all deletions.jsonl code (bd-fom)
2025-12-16 14:20:49 -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
Merge bd-cddj-nux: GH#519
2025-12-16 01:17:25 -08:00
daemons_test.go
…
daemons.go
fix: address critical resource leaks and error handling issues (#327)
2025-11-20 08:13:06 -08:00
delete_test.go
test: Tag 16 slow integration tests with build tags
2025-11-21 14:40:22 -05:00
delete.go
fix: tombstone/deletion overhaul for bd-4q8
2025-12-16 22:01:31 -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
docs: add detailed comments explaining ID formats and merge deletion logic
2025-12-16 00:17:40 -08:00
dep_test.go
Fix tests (bd-6ss and sub-issues) (#626)
2025-12-18 18:23:30 -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
refactor(doctor): split doctor.go into modular package files (#653)
2025-12-19 17:29:36 -08:00
doctor.go
refactor(doctor): split doctor.go into modular package files (#653)
2025-12-19 17:29:36 -08:00
duplicate.go
Fix daemon/direct mode inconsistency in graph commands (bd-fu83)
2025-12-18 01:34:14 -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
test: Refactor epic_test.go to use shared DB pattern (P2)
2025-11-21 16:14:30 -05:00
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
test: Tag 16 slow integration tests with build tags
2025-11-21 14:40:22 -05:00
export_staleness_test.go
…
export_test.go
Fix context propagation lifecycle bugs
2025-11-20 21:54:11 -05:00
export.go
chore: sync changes from beads-sync
2025-12-07 20:57:58 +11:00
flags.go
bd create: support --description=- for stdin input
2025-12-19 01:47:03 -08:00
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
fork_protection_test.go
feat: auto-protect forks from committing upstream issue database
2025-12-18 18:56:59 -08:00
fork_protection.go
feat: auto-protect forks from committing upstream issue database
2025-12-18 18:56:59 -08:00
git_sync_test.go
…
graph_test.go
feat(graph): use subgraph to display dependency counts
2025-12-18 20:35:00 -08:00
graph.go
feat(graph): use subgraph to display dependency counts
2025-12-18 20:35:00 -08:00
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
Context propagation with graceful cancellation (bd-rtp, bd-yb8, bd-2o2)
2025-11-20 21:57:23 -05:00
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
fix: Fix daemon export leaving JSONL newer than database (issues #301, #321)
2025-11-19 05:06:12 -05:00
import_multipart_id_test.go
…
import_profile_test.go
test: Tag 16 slow integration tests with build tags
2025-11-21 14:40:22 -05:00
import_shared.go
refactor: remove all deletions.jsonl code (bd-fom)
2025-12-16 14:20:49 -08:00
import_uncommitted_test.go
test: Tag 16 slow integration tests with build tags
2025-11-21 14:40:22 -05:00
import.go
fix: Resolve 3 P1 bugs and add --body-file flag to bd create
2025-12-17 17:29:33 -08:00
info_test.go
…
info.go
fix(merge): proper 3-way merge for dependencies - removals win (bd-ndye)
2025-12-18 23:20:49 -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
fix(init): update output to show hash-based ID format
2025-12-18 20:33:25 -08:00
init.go
fix(init): update output to show hash-based ID format
2025-12-18 20:33:25 -08:00
integrity_content_test.go
test: Tag 16 slow integration tests with build tags
2025-11-21 14:40:22 -05:00
integrity_test.go
refactor: remove all deletions.jsonl code (bd-fom)
2025-12-16 14:20:49 -08:00
integrity.go
fix: Include tombstones in DB count for stale check (bd-53c)
2025-12-18 00:41:49 -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
fix: resolve P2 sync noise and cleanup issues
2025-12-16 00:56:06 -08:00
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
test: Refactor P1 test files to use shared DB pattern (bd-1rh)
2025-11-21 15:51:07 -05:00
list.go
Merge remote-tracking branch 'origin/polecat/Doof'
2025-12-19 01:28:54 -08:00
mail_test.go
Phase 4: Remove deprecated edge fields from Issue struct (Decision 004)
2025-12-18 02:48:13 -08:00
mail.go
feat(mail): add --priority, --type, --thread-id, --reply-to flags
2025-12-19 12:07:13 -08:00
main_test.go
fix(ci): more changes to fix failing CI (#415)
2025-11-29 22:24:29 -08:00
main.go
feat: auto-protect forks from committing upstream issue database
2025-12-18 18:56:59 -08:00
markdown_test.go
…
markdown.go
Context propagation with graceful cancellation (bd-rtp, bd-yb8, bd-2o2)
2025-11-20 21:57:23 -05:00
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
migrate_hash_ids_test.go
Context propagation with graceful cancellation (bd-rtp, bd-yb8, bd-2o2)
2025-11-20 21:57:23 -05:00
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
Context propagation with graceful cancellation (bd-rtp, bd-yb8, bd-2o2)
2025-11-20 21:57:23 -05:00
migrate_tombstones.go
refactor: remove all deletions.jsonl code (bd-fom)
2025-12-16 14:20:49 -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
refactor(onboard): simplify to minimal snippet pointing to bd prime
2025-12-18 11:48:02 -08:00
onboard.go
Fix tests (bd-6ss and sub-issues) (#626)
2025-12-18 18:23:30 -08:00
output_test.go
…
pin.go
feat(cli): add bd pin/unpin commands (bd-iea)
2025-12-19 00:34:52 -08:00
prime_test.go
feat(prime): add --stealth flag for flush-only workflow
2025-12-03 18:08:33 -08:00
prime.go
feat: add no-push config to disable automatic git push
2025-12-18 00:49:07 -05:00
quick.go
feat: add silent quick-capture mode (bd q)
2025-12-16 01:08:40 -08:00
quickstart.go
fix(init): update output to show hash-based ID format
2025-12-18 20:33:25 -08:00
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(ready): add --type flag for filtering by issue type (gt-ktf3)
2025-12-19 15:09:30 -08:00
reinit_test.go
fix(init): bootstrap from sync-branch when configured (bd-0is)
2025-12-05 14:47:02 -08:00
relate_test.go
Add tests for Decision 004 Phase 4 edge schema consolidation
2025-12-18 11:25:17 -08:00
relate.go
Phase 4: Remove deprecated edge fields from Issue struct (Decision 004)
2025-12-18 02:48:13 -08:00
rename_prefix_repair_test.go
fix(rename-prefix): use hash IDs instead of sequential in --repair mode
2025-12-15 23:59:21 -08:00
rename_prefix_test.go
Context propagation with graceful cancellation (bd-rtp, bd-yb8, bd-2o2)
2025-11-20 21:57:23 -05:00
rename_prefix.go
fix(rename-prefix): use hash IDs instead of sequential in --repair mode
2025-12-15 23:59:21 -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
Context propagation with graceful cancellation (bd-rtp, bd-yb8, bd-2o2)
2025-11-20 21:57:23 -05:00
repair_deps.go
feat: add --readonly flag for worker sandboxes (gt-ymo)
2025-12-02 23:44:22 -08:00
repo.go
Context propagation with graceful cancellation (bd-rtp, bd-yb8, bd-2o2)
2025-11-20 21:57:23 -05:00
reset_test.go
feat(schema): add messaging fields for bd-kwro epic
2025-12-16 13:06:47 -08:00
reset.go
fix: resolve all golangci-lint errors
2025-12-16 17:50:25 -08:00
restore_test.go
test: replace manual os.Chdir with t.Chdir in tests (#457)
2025-12-04 11:21:43 -08:00
restore.go
Context propagation with graceful cancellation (bd-rtp, bd-yb8, bd-2o2)
2025-11-20 21:57:23 -05:00
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: add Factory.ai (Droid) support to bd setup command (#598)
2025-12-16 13:42:43 -08:00
show.go
feat(types): add StatusPinned for persistent beads (bd-6v2)
2025-12-18 21:55:54 -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
Context propagation with graceful cancellation (bd-rtp, bd-yb8, bd-2o2)
2025-11-20 21:57:23 -05:00
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
fix(docs): use consistent in_progress status naming (GH#444)
2025-12-16 01:07:33 -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
refactor: remove all deletions.jsonl code (bd-fom)
2025-12-16 14:20:49 -08:00
sync.go
feat: add no-push config to disable automatic git push
2025-12-18 00:49:07 -05:00
template_test.go
refactor: Remove YAML template system entirely
2025-12-18 00:18:37 -08:00
template.go
refactor: Remove YAML template system entirely
2025-12-18 00:18:37 -08:00
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
thread_test.go
Add tests for Decision 004 Phase 4 thread traversal functions
2025-12-18 11:30:26 -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
unpin.go
feat(cli): add bd pin/unpin commands (bd-iea)
2025-12-19 00:34:52 -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 0.30.6
2025-12-18 22:46:14 -08:00
worktree_daemon_test.go
Auto-disable daemon in git worktrees for safety (#567)
2025-12-16 00:06:19 -08:00
worktree_test.go
…
worktree.go
Auto-disable daemon in git worktrees for safety (#567)
2025-12-16 00:06:19 -08:00