Steve Yegge a0f4a9cacd feat(doctor): add tombstone health checks (bd-s3v) ...

Add two new doctor checks for tombstone health:

1. Updated Deletions Manifest check:
   - Warns when legacy deletions.jsonl has entries (suggests migration)
   - Shows "Migrated to tombstones" when .migrated file exists
   - Shows "Using inline tombstones" for new repos

2. New Tombstones check:
   - Reports total tombstone count
   - Warns about expired tombstones (older than 30 days)
   - Shows tombstones expiring within 7 days
   - Suggests 'bd compact' to prune expired tombstones

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

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

2025-12-13 10:16:45 -08:00

..

doctor

fix(gitignore): switch to whitelist approach for .beads/.gitignore (#473)

2025-12-13 10:14:05 +11:00

setup

fix(setup): correct allowedTools pattern from "bd:*" to "bd *"

2025-12-13 09:46:38 +11:00

templates

chore: Bump version to 0.29.0

2025-12-03 16:24:46 -08:00

testdata

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autoflush.go

fix(multi-repo): filter issues by prefix when flushing from non-primary repos (GH #437)

2025-12-01 21:17:56 -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

fix: use proper YAML parsing for no-db mode detection (bd-r6k2)

2025-12-07 21:09:32 +11:00

autostart_test.go

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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

bd-6xd: Standardize on issues.jsonl as canonical filename

2025-11-26 22:02:59 -08:00

cli_fast_test.go

feat: Add label operations to bd update command

2025-11-21 22:17:26 -05:00

comments_test.go

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comments.go

feat: add --readonly flag for worker sandboxes (gt-ymo)

2025-12-02 23:44:22 -08:00

compact_test.go

feat(tombstones): add migrate-tombstones command and compact pruning

2025-12-07 21:34:35 +11:00

compact.go

fix: resolve golangci-lint warnings

2025-12-13 10:07:36 +11:00

config_test.go

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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_test.go

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create.go

feat: add --estimate flag to bd create/update commands (GH #443)

2025-12-03 15:55:35 -08:00

daemon_autoimport_test.go

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daemon_autostart.go

perf: fix stale startlock delay and add comprehensive benchmarks (#484)

2025-12-13 06:57:11 -08:00

daemon_config.go

refactor: remove deprecated global daemon support

2025-11-24 23:39:54 -08:00

daemon_crash_test.go

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daemon_debouncer_test.go

fix: CI test failures on Windows

2025-11-26 20:59:07 -08:00

daemon_debouncer.go

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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_lifecycle.go

feat(daemon): add --foreground flag for systemd/supervisord integration

2025-12-01 21:09:00 -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

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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

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

Fix daemon sync branch commit failing with pre-commit hooks

2025-12-09 22:17:23 -05:00

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

fix(sync): prevent daemon race condition from dirtying working directory

2025-12-13 06:54:46 -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

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daemon_watcher_platform_test.go

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daemon_watcher_test.go

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daemon_watcher.go

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daemon_windows.go

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daemon.go

feat(daemon): add --foreground flag for systemd/supervisord integration

2025-12-01 21:09:00 -08:00

daemons_test.go

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daemons.go

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delete_recording_test.go

bd sync: 2025-11-25 11:46:06

2025-11-25 11:46:06 -08:00

delete_test.go

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delete.go

Enable daemon RPC support for delete operations to trigger auto-sync, Fix for issue #527 (#528)

2025-12-12 13:19:31 -08:00

deleted.go

feat(deletions): complete deletions manifest epic with integration tests

2025-11-25 16:36:46 -08:00

deletion_propagation_test.go

bd sync: 2025-11-25 12:03:21

2025-11-25 12:03:21 -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

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dep_test.go

bd sync: 2025-11-25 19:32:04

2025-11-25 19:32:05 -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 fresh clone UX with friendly error messages (bd-dmb)

2025-11-27 22:40:57 -08:00

docs.md

docs: Add comprehensive documentation for version reporting changes

2025-12-13 10:04:01 +11:00

doctor_test.go

test(doctor): add tests for export diagnostics feature (bd-9cc)

2025-12-07 20:19:49 +11:00

doctor.go

feat(doctor): add tombstone health checks (bd-s3v)

2025-12-13 10:16:45 -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

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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

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export_staleness_test.go

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export_test.go

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export.go

chore: sync changes from beads-sync

2025-12-07 20:57:58 +11:00

flags.go

feat: Add --body flag as alias for --description

2025-11-21 20:08:55 -05:00

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

git_sync_test.go

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helpers_test.go

fix: support multi-part prefixes in issue ID extraction (#398)

2025-11-26 17:42:14 -08:00

hooks_test.go

fix: make hook tests worktree-aware by using getGitDir()

2025-12-13 08:42:26 +11:00

hooks.go

fix: support git worktrees in hooks installation

2025-11-29 23:19:57 -08:00

import_bug_test.go

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import_cancellation_test.go

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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

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import_multipart_id_test.go

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import_profile_test.go

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import_shared.go

fix(sync): protect local issues from git-history-backfill during sync (#485)

2025-12-12 13:28:48 -08:00

import_uncommitted_test.go

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import.go

fix(sync): protect local issues from git-history-backfill during sync (#485)

2025-12-12 13:28:48 -08:00

info_test.go

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info.go

docs: update changelog and info.go for v0.29.0 release

2025-12-03 16:24:24 -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

fix: make hook tests worktree-aware by using getGitDir()

2025-12-13 08:42:26 +11:00

init_team.go

fix: Auto-configure sync.branch during bd init (bd-flil)

2025-11-23 19:42:21 -08:00

init_test.go

feat(config): add BD_NO_INSTALL_HOOKS environment variable to disable git hook installation (#500)

2025-12-13 06:38:26 -08:00

init.go

feat(config): add BD_NO_INSTALL_HOOKS environment variable to disable git hook installation (#500)

2025-12-13 06:38:26 -08:00

integrity_content_test.go

…

integrity_test.go

refactor: rename last_import_hash to jsonl_content_hash (bd-39o)

2025-11-28 23:14:12 -08:00

integrity.go

fix(bd-53c): Add reverse ZFC check to prevent stale DB from corrupting JSONL

2025-11-29 17:01:36 -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

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label_test.go

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label.go

feat: add --readonly flag for worker sandboxes (gt-ymo)

2025-12-02 23:44:22 -08:00

list_test.go

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list.go

Add --sort and --reverse flags to bd list command

2025-11-24 20:16:07 -08:00

main_test.go

fix(ci): more changes to fix failing CI (#415)

2025-11-29 22:24:29 -08:00

main.go

fix: use proper YAML parsing for no-db mode detection (bd-r6k2)

2025-12-07 21:09:32 +11:00

markdown_test.go

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markdown.go

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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

message.go

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migrate_hash_ids_test.go

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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 bd migrate-sync command for sync.branch workflow setup (bd-epn)

2025-12-01 20:07:27 -08:00

migrate_test.go

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migrate_tombstones_test.go

feat(tombstones): add migrate-tombstones command and compact pruning

2025-12-07 21:34:35 +11:00

migrate_tombstones.go

fix: resolve golangci-lint warnings

2025-12-13 10:07:36 +11:00

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

fix: make bd onboard output generic, not beads-specific (#465)

2025-12-05 13:20:51 -08:00

onboard.go

fix: make bd onboard output generic, not beads-specific (#465)

2025-12-05 13:20:51 -08:00

output_test.go

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prime_test.go

feat(prime): add --stealth flag for flush-only workflow

2025-12-03 18:08:33 -08:00

prime.go

feat(prime): add --stealth flag for flush-only workflow

2025-12-03 18:08:33 -08:00

quickstart.go

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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(tombstone): add P2 code review improvements (bd-saa, bd-1bu, bd-nyt)

2025-12-05 15:48:46 -08:00

reinit_test.go

fix(init): bootstrap from sync-branch when configured (bd-0is)

2025-12-05 14:47:02 -08:00

rename_prefix_repair_test.go

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rename_prefix_test.go

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rename_prefix.go

feat: add --readonly flag for worker sandboxes (gt-ymo)

2025-12-02 23:44:22 -08:00

reopen_test.go

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reopen.go

feat: add --readonly flag for worker sandboxes (gt-ymo)

2025-12-02 23:44:22 -08:00

repair_deps_test.go

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repair_deps.go

feat: add --readonly flag for worker sandboxes (gt-ymo)

2025-12-02 23:44:22 -08:00

repo.go

…

reset_test.go

feat(reset): add integration tests and doctor reset suggestion

2025-12-13 10:20:31 +11:00

reset.go

fix: resolve golangci-lint warnings

2025-12-13 10:07:36 +11:00

restore_test.go

test: replace manual os.Chdir with t.Chdir in tests (#457)

2025-12-04 11:21:43 -08:00

restore.go

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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

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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(setup claude): add --stealth flag

2025-12-03 18:10:35 -08:00

show.go

feat: add --estimate flag to bd create/update commands (GH #443)

2025-12-03 15:55:35 -08:00

simple_helpers_test.go

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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

…

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

bd-6xd: Standardize on issues.jsonl as canonical filename

2025-11-26 22:02:59 -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

test: replace manual os.Chdir with t.Chdir in tests (#457)

2025-12-04 11:21:43 -08:00

sync.go

fix(sync): add multi-repo support to hash update after restore

2025-12-13 06:57:20 -08:00

template_security_test.go

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template_test.go

test: replace manual os.Chdir with t.Chdir in tests (#457)

2025-12-04 11:21:43 -08:00

template.go

…

test_helpers_test.go

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test_wait_helper.go

fix: CI test failures and lint errors

2025-11-24 00:21:01 -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

fix: resolve golangci-lint warnings

2025-12-13 10:07:36 +11:00

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 0.29.0

2025-12-03 16:24:46 -08:00

worktree_test.go

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worktree.go

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