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beads/cmd/bd
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Steve Yegge a40b27a03d Add repair commands: bd repair-deps, bd detect-pollution, bd validate 
Implements Phase 1 of bd-56 (Repair Commands & AI-Assisted Tooling):

New commands:
- bd repair-deps: Find and fix orphaned dependency references
- bd detect-pollution: Detect test issues using pattern matching
- bd validate: Comprehensive health check (orphans, duplicates, pollution)

Features:
- JSON output support for all commands
- Safe deletion with backup for detect-pollution
- Auto-fix support for orphaned dependencies
- Direct storage access (requires BEADS_NO_DAEMON=1)

Closes bd-56 (Phase 1 complete)
Related: bd-103, bd-105, bd-106

Amp-Thread-ID: https://ampcode.com/threads/T-5822c6d2-d645-4043-9a8d-3c51ac93bbb7
Co-authored-by: Amp <amp@ampcode.com>
2025-10-28 19:46:12 -07:00
..
testdata
Add config.json support for database path configuration (bd-163)
2025-10-26 18:44:27 -07:00
autoflush.go
Fix bd-159: Apply timestamp-only dedup to auto-flush exports
2025-10-27 20:21:34 -07:00
autoimport_collision_test.go
Fix autoimport tests for content-hash collision scoring (bd-100)
2025-10-28 19:19:06 -07:00
autoimport.go
Add rename-prefix --repair flag and consolidate issue ID parsing
2025-10-27 18:31:01 +00:00
autostart_test.go
Fix failing tests
2025-10-27 20:08:50 -07:00
comments_test.go
Fix all test failures from bd-166 (missing issue_prefix)
2025-10-26 22:31:24 -07:00
comments.go
Fix variable shadowing in author detection
2025-10-27 22:30:36 -07:00
compact_test.go
Fix failing tests
2025-10-27 20:08:50 -07:00
compact.go
Fix revive style issues (bd-56)
2025-10-25 18:13:49 -07:00
config_test.go
Fix bd-166: Prevent duplicate issues with wrong prefix
2025-10-26 21:55:01 -07:00
config.go
Fix revive style issues (bd-56)
2025-10-25 18:13:49 -07:00
create.go
Add two-clone collision test proving beads multi-agent workflow failure
2025-10-28 11:34:27 -07:00
daemon_autostart.go
Fix failing tests
2025-10-27 20:08:50 -07:00
daemon_debouncer.go
Add event-driven daemon architecture (Phase 1 foundation)
2025-10-28 13:12:37 -07:00
daemon_event_loop.go
Add event-driven daemon architecture (Phase 1 foundation)
2025-10-28 13:12:37 -07:00
daemon_lock_test.go
Implement stricter daemon lock file validation (bd-161)
2025-10-26 18:37:25 -07:00
daemon_lock_unix.go
…
daemon_lock_windows.go
…
daemon_lock.go
Address gosec security warnings (bd-102)
2025-10-26 22:48:19 -07:00
daemon_rotation_test.go
…
daemon_test.go
Fix bd-166: Prevent duplicate issues with wrong prefix
2025-10-26 21:55:01 -07:00
daemon_unix.go
…
daemon_watcher.go
Fix bd-66: Add robust polling fallback for file watcher
2025-10-28 19:27:56 -07:00
daemon_windows.go
…
daemon.go
Add event-driven daemon architecture (Phase 1 foundation)
2025-10-28 13:12:37 -07:00
daemons.go
Address gosec security warnings (bd-102)
2025-10-26 22:48:19 -07:00
delete_test.go
Improve test coverage to 57.7% (+13.5%)
2025-10-24 00:56:18 -07:00
delete.go
Address gosec security warnings (bd-102)
2025-10-26 22:48:19 -07:00
dep_test.go
Fix remaining test database initialization errors (bd-207)
2025-10-27 20:00:49 -07:00
dep.go
feat: add --reverse flag to bd dep tree command
2025-10-27 09:25:57 +00:00
detect_pollution.go
Add repair commands: bd repair-deps, bd detect-pollution, bd validate
2025-10-28 19:46:12 -07:00
direct_mode_test.go
Fix all test failures from bd-166 (missing issue_prefix)
2025-10-26 22:31:24 -07:00
direct_mode.go
…
duplicates_test.go
Add bd duplicates command for automated duplicate detection (bd-203)
2025-10-24 13:45:04 -07:00
duplicates.go
Fix revive style issues (bd-56)
2025-10-25 18:13:49 -07:00
epic.go
Fix lint errors: handle errors, use fmt.Fprintf, apply De Morgan's law, use switch statements
2025-10-24 12:27:07 -07:00
export_import_test.go
Fix remaining test database initialization errors (bd-207)
2025-10-27 20:00:49 -07:00
export_test.go
Fix export test failures with ClearAllExportHashes for test isolation
2025-10-26 23:06:03 -07:00
export.go
Fix bd-159: Apply timestamp-only dedup to auto-flush exports
2025-10-27 20:21:34 -07:00
git_sync_test.go
Remove unreachable utility functions (bd-224, bd-214)
2025-10-27 20:45:59 -07:00
helpers_test.go
Resolve merge conflicts: use importer package
2025-10-27 22:44:40 -07:00
import_bug_test.go
Fix remaining test database initialization errors (bd-207)
2025-10-27 20:00:49 -07:00
import_collision_regression_test.go
Make DetectCollisions read-only (bd-96)
2025-10-28 19:16:51 -07:00
import_collision_test.go
Remove skipped tests and unreachable RPC methods (bd-212, bd-213)
2025-10-27 20:52:52 -07:00
import_idempotent_test.go
Fix remaining test database initialization errors (bd-207)
2025-10-27 20:00:49 -07:00
import_profile_test.go
…
import_shared.go
Remove unreachable functions from import_shared.go (bd-18)
2025-10-28 14:20:04 -07:00
import.go
Address gosec security warnings (bd-102)
2025-10-26 22:48:19 -07:00
info_test.go
Add bd info command to show database path and daemon status
2025-10-25 16:43:44 -07:00
info.go
Add bd info command to show database path and daemon status
2025-10-25 16:43:44 -07:00
init_test.go
Fix failing tests
2025-10-27 20:08:50 -07:00
init.go
Merge PR #149: Add --no-db mode for JSONL-only operation
2025-10-27 10:45:01 -07:00
integrity_test.go
Fix remaining test database initialization errors (bd-207)
2025-10-27 20:00:49 -07:00
integrity.go
bd-162: Add database integrity checks with oracle review fixes
2025-10-26 20:17:48 -07:00
label_test.go
Fix all test failures from bd-166 (missing issue_prefix)
2025-10-26 22:31:24 -07:00
label.go
Fix 15 lint errors: dupl, gosec, revive, staticcheck, unparam
2025-10-24 12:40:56 -07:00
list_test.go
Fix all test failures from bd-166 (missing issue_prefix)
2025-10-26 22:31:24 -07:00
list.go
Add two-clone collision test proving beads multi-agent workflow failure
2025-10-28 11:34:27 -07:00
main_test.go
Fix bd-159: Apply timestamp-only dedup to auto-flush exports
2025-10-27 20:21:34 -07:00
main.go
Fix failing tests
2025-10-27 20:08:50 -07:00
markdown_test.go
…
markdown.go
Fix failing tests
2025-10-27 20:08:50 -07:00
merge_test.go
Fix remaining test database initialization errors (bd-207)
2025-10-27 20:00:49 -07:00
merge.go
Fix revive style issues (bd-56)
2025-10-25 18:13:49 -07:00
migrate_test.go
Add bd migrate command for database upgrades (bd-164)
2025-10-26 19:20:59 -07:00
migrate.go
Add database fingerprinting and validation (bd-166)
2025-10-26 21:15:57 -07:00
nodb.go
Fix bd-159: Apply timestamp-only dedup to auto-flush exports
2025-10-27 20:21:34 -07:00
onboard.go
Fix syntax error in onboard.go from PR #154
2025-10-26 13:24:18 -07:00
output_test.go
…
quickstart.go
…
ready_test.go
Fix failing tests
2025-10-27 20:08:50 -07:00
ready.go
Add two-clone collision test proving beads multi-agent workflow failure
2025-10-28 11:34:27 -07:00
reinit_test.go
Fix goconst linter issues (bd-116)
2025-10-25 18:04:05 -07:00
rename_prefix_repair_test.go
Fix TestRepairMultiplePrefixes to bypass prefix validation
2025-10-27 22:59:19 -07:00
rename_prefix_test.go
…
rename_prefix.go
Add rename-prefix --repair flag and consolidate issue ID parsing
2025-10-27 18:31:01 +00:00
renumber_test.go
…
renumber.go
Enable errcheck linter and fix all production code warnings
2025-10-25 18:44:38 -07:00
reopen_test.go
Fix all test failures from bd-166 (missing issue_prefix)
2025-10-26 22:31:24 -07:00
reopen.go
Fix nil pointer crash in bd reopen command (bd-133)
2025-10-25 10:39:45 -07:00
repair_deps.go
Add repair commands: bd repair-deps, bd detect-pollution, bd validate
2025-10-28 19:46:12 -07:00
restore.go
Address gosec security warnings (bd-102)
2025-10-26 22:48:19 -07:00
scripttest_test.go
Fix Windows CI test failures (bd-99)
2025-10-24 10:07:05 -07:00
show.go
Fix failing tests
2025-10-27 20:08:50 -07:00
simple_helpers_test.go
bd-211: Remove deprecated rename functions from import_shared.go
2025-10-27 20:38:13 -07:00
stale_test.go
Improve test coverage to 57.7% (+13.5%)
2025-10-24 00:56:18 -07:00
stale.go
Enable errcheck linter and fix all production code warnings
2025-10-25 18:44:38 -07:00
sync.go
bd sync: 2025-10-28 17:19:28
2025-10-28 17:19:28 -07:00
test_helpers_test.go
Fix failing tests
2025-10-27 20:08:50 -07:00
validate.go
Add repair commands: bd repair-deps, bd detect-pollution, bd validate
2025-10-28 19:46:12 -07:00
version_test.go
Improve test coverage to 57.7% (+13.5%)
2025-10-24 00:56:18 -07:00
version.go
chore: Bump version to 0.17.7
2025-10-26 23:30:37 -07:00
worktree_test.go
…
worktree.go
Add warning for multiple databases in directory hierarchy (bd-75)
2025-10-24 15:28:23 -07:00