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beads/cmd/bd
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Steve Yegge 87ee3a674e Improve bd doctor JSONL checks to focus on real problems 
Previously bd doctor warned about using beads.jsonl vs issues.jsonl, but
users should be free to configure any name they want. The real problems are:
1. Having multiple JSONL files (sync/merge conflicts)
2. Configuration not matching reality

Changes:
- Rewrote CheckLegacyJSONLFilename to scan for ALL .jsonl files
- Now filters out merge artifacts (backup, .orig, .bak, etc.)
- Warns only when multiple real JSONL files exist
- Added CheckDatabaseConfig to detect when configured paths do not match
  what actually exists on disk
- Updated tests to verify backup files are ignored
- Added test cases for custom JSONL filenames

🤖 Generated with Claude Code
Co-Authored-By: Claude <noreply@anthropic.com>
2025-11-21 23:44:26 -08:00
..
doctor
Improve bd doctor JSONL checks to focus on real problems
2025-11-21 23:44:26 -08:00
setup
feat: add context optimization features for AI agents (#297)
2025-11-12 10:48:36 -08:00
templates
chore: Bump version to 0.24.1
2025-11-21 22:06:07 -08:00
testdata
fix: Update dep_add test to match current show output format
2025-11-04 00:23:25 -08:00
autoflush.go
refactor: Delete 7 redundant tests from main_test.go (3x speedup)
2025-11-21 21:29:43 -05:00
autoimport_test.go
Context propagation with graceful cancellation (bd-rtp, bd-yb8, bd-2o2)
2025-11-20 21:57:23 -05:00
autoimport.go
Fix: Change default JSONL filename from beads.jsonl to issues.jsonl
2025-11-21 23:34:22 -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
test: Add security and error handling tests for lint warnings
2025-11-21 19:30:48 -05:00
cleanup.go
Context propagation with graceful cancellation (bd-rtp, bd-yb8, bd-2o2)
2025-11-20 21:57:23 -05:00
cli_fast_test.go
feat: Add label operations to bd update command
2025-11-21 22:17:26 -05:00
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
Context propagation with graceful cancellation (bd-rtp, bd-yb8, bd-2o2)
2025-11-20 21:57:23 -05:00
compact_test.go
test: Refactor compact_test.go to use shared DB pattern (bd-1rh)
2025-11-21 16:13:18 -05:00
compact.go
Context propagation with graceful cancellation (bd-rtp, bd-yb8, bd-2o2)
2025-11-20 21:57:23 -05:00
config_test.go
Context propagation with graceful cancellation (bd-rtp, bd-yb8, bd-2o2)
2025-11-20 21:57:23 -05:00
config.go
Context propagation with graceful cancellation (bd-rtp, bd-yb8, bd-2o2)
2025-11-20 21:57:23 -05:00
count.go
feat: Add 'bd count' command for counting and grouping issues
2025-11-21 19:21:05 -05:00
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 --body flag as alias for --description
2025-11-21 20:08:55 -05:00
daemon_autoimport_test.go
Optimize test suite: split integration tests, add -short support
2025-11-05 20:39:47 -08:00
daemon_autostart.go
Centralize BD_DEBUG logging into internal/debug package
2025-11-06 20:14:34 -08:00
daemon_config.go
Reorganize project structure: move Go files to internal/beads, docs to docs/
2025-11-05 21:04:00 -08:00
daemon_crash_test.go
bd-vcg5: Add daemon crash recovery with panic handler + socket cleanup
2025-11-07 21:17:24 -08:00
daemon_debouncer_test.go
Optimize test suite performance (15-18x speedup)
2025-11-05 10:26:58 -08:00
daemon_debouncer.go
Fix FileWatcher robustness issues (bd-71)
2025-10-29 22:55:13 -07:00
daemon_event_loop.go
feat: Complete GH #353 follow-up phases (bd-9nw, bd-u3t, bd-e0o)
2025-11-21 19:32:45 -05:00
daemon_lifecycle.go
Add RPC diagnostics with BD_RPC_DEBUG env var
2025-11-07 21:29:22 -08:00
daemon_lock_test.go
Optimize test suite: split integration tests, add -short support
2025-11-05 20:39:47 -08:00
daemon_lock_unix.go
…
daemon_lock_wasm.go
WIP: WASM port - switch to ncruces/go-sqlite3, add WASM stubs
2025-11-02 22:17:08 -08:00
daemon_lock_windows.go
…
daemon_lock.go
Fix daemon orphaning: track parent PID and exit when parent dies
2025-11-07 18:57:43 -08:00
daemon_logger.go
Refactor daemon.go for testability and maintainability (bd-2b34)
2025-11-01 19:20:01 -07:00
daemon_parent_test.go
test: Tag 16 slow integration tests with build tags
2025-11-21 14:40:22 -05:00
daemon_rotation_test.go
…
daemon_server.go
Context propagation with graceful cancellation (bd-rtp, bd-yb8, bd-2o2)
2025-11-20 21:57:23 -05:00
daemon_sync_branch_test.go
Context propagation with graceful cancellation (bd-rtp, bd-yb8, bd-2o2)
2025-11-20 21:57:23 -05:00
daemon_sync_branch.go
Remove legacy issues.jsonl and update defaults to beads.jsonl
2025-11-20 19:00:36 -05:00
daemon_sync_test.go
Close bd-ar2.8: Add edge case tests for export metadata updates
2025-11-21 14:57:01 -05:00
daemon_sync.go
Complete bd-ar2 P2 tasks: metadata, resurrection, and testing improvements
2025-11-21 11:40:37 -05:00
daemon_test.go
Context propagation with graceful cancellation (bd-rtp, bd-yb8, bd-2o2)
2025-11-20 21:57:23 -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
WIP: WASM port - switch to ncruces/go-sqlite3, add WASM stubs
2025-11-02 22:17:08 -08:00
daemon_watcher_platform_test.go
Optimize test suite: split integration tests, add -short support
2025-11-05 20:39:47 -08:00
daemon_watcher_test.go
Optimize test suite: split integration tests, add -short support
2025-11-05 20:39:47 -08:00
daemon_watcher.go
fix: address critical resource leaks and error handling issues (#327)
2025-11-20 08:13:06 -08:00
daemon_windows.go
…
daemon.go
Context propagation with graceful cancellation (bd-rtp, bd-yb8, bd-2o2)
2025-11-20 21:57:23 -05:00
daemons_test.go
Improve test coverage for cmd/bd
2025-10-31 18:40:32 -07:00
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
Context propagation with graceful cancellation (bd-rtp, bd-yb8, bd-2o2)
2025-11-20 21:57:23 -05:00
deletion_tracking_test.go
Fix: Change default JSONL filename from beads.jsonl to issues.jsonl
2025-11-21 23:34:22 -08:00
deletion_tracking.go
Fix lint errors: handle error return values
2025-11-15 12:52:34 -08:00
dep_test.go
test: Refactor P1 test files to use shared DB pattern (bd-1rh)
2025-11-21 15:51:07 -05:00
dep.go
Context propagation with graceful cancellation (bd-rtp, bd-yb8, bd-2o2)
2025-11-20 21:57:23 -05:00
detect_pollution.go
Context propagation with graceful cancellation (bd-rtp, bd-yb8, bd-2o2)
2025-11-20 21:57:23 -05:00
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
Context propagation with graceful cancellation (bd-rtp, bd-yb8, bd-2o2)
2025-11-20 21:57:23 -05:00
doctor_test.go
Fix doctor incorrectly diagnosing hash IDs as sequential (issue #322)
2025-11-18 05:20:11 -05:00
doctor.go
Improve bd doctor JSONL checks to focus on real problems
2025-11-21 23:44:26 -08:00
duplicates_test.go
feat: Add sandbox escape hatches for daemon lock issues (GH #353 Phase 1)
2025-11-21 18:53:34 -05:00
duplicates.go
feat: Add issue IDs to TODO comments
2025-11-21 19:01:42 -05:00
epic_test.go
test: Refactor epic_test.go to use shared DB pattern (P2)
2025-11-21 16:14:30 -05:00
epic.go
Context propagation with graceful cancellation (bd-rtp, bd-yb8, bd-2o2)
2025-11-20 21:57:23 -05:00
export_import_test.go
Optimize test suite performance (15-18x speedup)
2025-11-05 10:26:58 -08:00
export_integrity_integration_test.go
Context propagation with graceful cancellation (bd-rtp, bd-yb8, bd-2o2)
2025-11-20 21:57:23 -05:00
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
Fix bd-srwk: Add ID-based staleness detection to bd export
2025-11-07 20:07:59 -08:00
export_test.go
Fix context propagation lifecycle bugs
2025-11-20 21:54:11 -05:00
export.go
Context propagation with graceful cancellation (bd-rtp, bd-yb8, bd-2o2)
2025-11-20 21:57:23 -05:00
flags.go
feat: Add --body flag as alias for --description
2025-11-21 20:08:55 -05:00
flush_manager_test.go
test: Add security and error handling tests for lint warnings
2025-11-21 19:30:48 -05:00
flush_manager.go
Improve FlushManager: constants, error logging, and functional tests
2025-11-20 21:38:31 -05:00
git_sync_test.go
Optimize test suite: split integration tests, add -short support
2025-11-05 20:39:47 -08:00
helpers_test.go
bd sync: 2025-11-09 14:53:59
2025-11-09 14:53:59 -08:00
hooks_test.go
Fix CI regressions and stabilize tests
2025-11-17 10:06:35 -07:00
hooks.go
Annotate gosec-safe file accesses
2025-11-17 10:12:46 -07:00
import_bug_test.go
Remove vestigial --resolve-collisions flag
2025-10-31 01:07:42 -07:00
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
bd sync: 2025-11-09 14:53:59
2025-11-09 14:53:59 -08:00
import_profile_test.go
test: Tag 16 slow integration tests with build tags
2025-11-21 14:40:22 -05:00
import_shared.go
Add --clear-duplicate-external-refs flag to bd import
2025-11-06 13:01:44 -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
feat: Add sandbox escape hatches for daemon lock issues (GH #353 Phase 1)
2025-11-21 18:53:34 -05:00
info_test.go
feat: Add bd info --whats-new for agent version awareness (bd-eiz9)
2025-11-08 02:28:54 -08:00
info.go
Context propagation with graceful cancellation (bd-rtp, bd-yb8, bd-2o2)
2025-11-20 21:57:23 -05:00
init_contributor.go
Annotate gosec-safe file accesses
2025-11-17 10:12:46 -07:00
init_hooks_test.go
Fix CI regressions and stabilize tests
2025-11-17 10:06:35 -07:00
init_team.go
feat: Add bd init --contributor and --team wizards
2025-11-05 19:04:14 -08:00
init_test.go
Fix: Change default JSONL filename from beads.jsonl to issues.jsonl
2025-11-21 23:34:22 -08:00
init.go
Fix: Change default JSONL filename from beads.jsonl to issues.jsonl
2025-11-21 23:34:22 -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
test: Refactor integrity_test.go to use shared DB pattern (bd-1rh P2)
2025-11-21 16:11:56 -05:00
integrity.go
Complete bd-ar2 P2 tasks: metadata, resurrection, and testing improvements
2025-11-21 11:40:37 -05:00
jsonl_integrity_test.go
Context propagation with graceful cancellation (bd-rtp, bd-yb8, bd-2o2)
2025-11-20 21:57:23 -05:00
label_test.go
…
label.go
Context propagation with graceful cancellation (bd-rtp, bd-yb8, bd-2o2)
2025-11-20 21:57:23 -05:00
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
feat: Accept both integer and P-format for priority flags in bd list
2025-11-21 21:57:23 -05:00
main_test.go
Fix: Change default JSONL filename from beads.jsonl to issues.jsonl
2025-11-21 23:34:22 -08:00
main.go
feat: Complete GH #353 follow-up phases (bd-9nw, bd-u3t, bd-e0o)
2025-11-21 19:32:45 -05:00
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: Change default JSONL filename from beads.jsonl to issues.jsonl
2025-11-21 23:34:22 -08:00
merge.go
Fix: Change default JSONL filename from beads.jsonl to issues.jsonl
2025-11-21 23:34:22 -08:00
message.go
Fix lint errors: handle error return values
2025-11-15 12:52:34 -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
Context propagation with graceful cancellation (bd-rtp, bd-yb8, bd-2o2)
2025-11-20 21:57:23 -05:00
migrate_issues.go
Context propagation with graceful cancellation (bd-rtp, bd-yb8, bd-2o2)
2025-11-20 21:57:23 -05:00
migrate_test.go
Context propagation with graceful cancellation (bd-rtp, bd-yb8, bd-2o2)
2025-11-20 21:57:23 -05:00
migrate.go
Context propagation with graceful cancellation (bd-rtp, bd-yb8, bd-2o2)
2025-11-20 21:57:23 -05:00
nodb_test.go
bd sync: 2025-11-09 14:53:59
2025-11-09 14:53:59 -08:00
nodb.go
Context propagation with graceful cancellation (bd-rtp, bd-yb8, bd-2o2)
2025-11-20 21:57:23 -05:00
onboard_test.go
Handle formatting errors in onboard renderer
2025-11-17 11:32:37 -07:00
onboard.go
feat: Add GitHub Copilot support with .github/copilot-instructions.md
2025-11-21 20:52:18 -05:00
output_test.go
…
prime.go
Annotate gosec-safe file accesses
2025-11-17 10:12:46 -07:00
quickstart.go
…
ready_test.go
test: Refactor P1 test files to use shared DB pattern (bd-1rh)
2025-11-21 15:51:07 -05:00
ready.go
Context propagation with graceful cancellation (bd-rtp, bd-yb8, bd-2o2)
2025-11-20 21:57:23 -05:00
reinit_test.go
Fix: Change default JSONL filename from beads.jsonl to issues.jsonl
2025-11-21 23:34:22 -08:00
rename_prefix_repair_test.go
Context propagation with graceful cancellation (bd-rtp, bd-yb8, bd-2o2)
2025-11-20 21:57:23 -05:00
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
Context propagation with graceful cancellation (bd-rtp, bd-yb8, bd-2o2)
2025-11-20 21:57:23 -05:00
reopen_test.go
…
reopen.go
feat: Add issue IDs to TODO comments
2025-11-21 19:01:42 -05:00
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
Context propagation with graceful cancellation (bd-rtp, bd-yb8, bd-2o2)
2025-11-20 21:57:23 -05:00
repo.go
Context propagation with graceful cancellation (bd-rtp, bd-yb8, bd-2o2)
2025-11-20 21:57:23 -05:00
restore_test.go
Improve cmd/bd test coverage from 21% to 23.1% (bd-27ea)
2025-10-31 19:44:43 -07:00
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
Optimize test suite performance - 45% reduction in integration tests
2025-11-04 11:25:36 -08:00
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
feat: Add date and priority filters to bd search (bd-au0.5)
2025-11-21 22:46:12 -05:00
setup.go
feat: add context optimization features for AI agents (#297)
2025-11-12 10:48:36 -08:00
show.go
feat: Add label operations to bd update command
2025-11-21 22:17:26 -05:00
simple_helpers_test.go
bd-211: Remove deprecated rename functions from import_shared.go
2025-10-27 20:38:13 -07:00
snapshot_manager.go
Annotate gosec-safe file accesses
2025-11-17 10:12:46 -07:00
stale_test.go
test: Refactor P1 test files to use shared DB pattern (bd-1rh)
2025-11-21 15:51:07 -05:00
stale.go
Context propagation with graceful cancellation (bd-rtp, bd-yb8, bd-2o2)
2025-11-20 21:57:23 -05:00
staleness.go
feat: Add sandbox escape hatches for daemon lock issues (GH #353 Phase 1)
2025-11-21 18:53:34 -05:00
status_test.go
Fix: TestGetAssignedStatus - Missing rootCtx initialization
2025-11-21 23:22:12 -08:00
status.go
Context propagation with graceful cancellation (bd-rtp, bd-yb8, bd-2o2)
2025-11-20 21:57:23 -05:00
sync_local_only_test.go
test: Tag 16 slow integration tests with build tags
2025-11-21 14:40:22 -05:00
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
Add git hooks check to bd doctor
2025-11-02 17:09:39 -08:00
sync.go
fix: Correct git merge driver placeholders from %L/%R to %A/%B
2025-11-21 20:40:18 -05:00
template_security_test.go
Add template support for issue creation (bd-164b)
2025-11-03 20:31:11 -08:00
template_test.go
Add template support for issue creation (bd-164b)
2025-11-03 20:31:11 -08:00
template.go
fix: CI failures - performance thresholds, test eligibility, Nix hash, lint errors
2025-11-03 22:01:37 -08:00
test_helpers_test.go
Context propagation with graceful cancellation (bd-rtp, bd-yb8, bd-2o2)
2025-11-20 21:57:23 -05:00
test_wait_helper.go
test: add waitFor helper for event-driven testing
2025-11-04 01:10:18 -08:00
validate_test.go
test: Refactor validate_test.go - remove ALL DB setup (P2)
2025-11-21 16:14:30 -05:00
validate.go
Context propagation with graceful cancellation (bd-rtp, bd-yb8, bd-2o2)
2025-11-20 21:57:23 -05:00
version_test.go
Add support for bd --version flag
2025-11-05 17:37:53 -08:00
version.go
chore: Bump version to 0.24.1
2025-11-21 22:06:07 -08:00
worktree_test.go
Improve cmd/bd test coverage from 20.2% to 23.3%
2025-11-08 18:22:28 -08:00
worktree.go
Reorganize project structure: move Go files to internal/beads, docs to docs/
2025-11-05 21:04:00 -08:00