Steve Yegge b4a6ee4f5f fix: Include tombstones in DB count for stale check (bd-53c) ...

The countDBIssuesFast() fallback path used SearchIssues without
IncludeTombstones, returning only live issues (161). Meanwhile
countIssuesInJSONL counts all lines including tombstones (221).

This mismatch caused false "stale DB detected" warnings on every
sync, even when DB and JSONL were in sync.

Fix: Set IncludeTombstones: true in the fallback SearchIssues call.

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

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

2025-12-18 00:41:49 -08:00

..

doctor

refactor: remove all deletions.jsonl code (bd-fom)

2025-12-16 14:20:49 -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 0.30.5

2025-12-18 00:27:59 -08:00

testdata

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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

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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

fix: tombstone/deletion overhaul for bd-4q8

2025-12-16 22:01:31 -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

cleanup

2025-12-16 17:26:06 -08:00

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

refactor: Remove YAML template system entirely

2025-12-18 00:18:37 -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_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_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

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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

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: 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

fix(doctor): remove circular error message in --fix mode

2025-12-16 01:08:20 -08:00

doctor.go

refactor: remove all deletions.jsonl code (bd-fom)

2025-12-16 14:20:49 -08:00

duplicate.go

feat: add graph links and hooks system (bd-kwro.2-5, bd-kwro.8)

2025-12-16 18:34:48 -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

fix: Resolve 3 P1 bugs and add --body-file flag to bd create

2025-12-17 17:29:33 -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

git_sync_test.go

…

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

…

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

chore: Bump version to 0.30.5

2025-12-18 00:27:59 -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

feat: add Git worktree compatibility (PR #478)

2025-12-13 12:50:33 -08:00

init.go

fix: resolve all golangci-lint errors

2025-12-16 17:50:25 -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

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

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

mail_test.go

feat: complete bd-kwro messaging & knowledge graph epic

2025-12-16 20:36:47 -08:00

mail.go

feat: Add --assignee flag to template instantiate, fix mail inbox --identity

2025-12-17 23:38:19 -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: add graph links and hooks system (bd-kwro.2-5, bd-kwro.8)

2025-12-16 18:34:48 -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

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

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

onboard.go

feat: Add dependency direction guidance to onboard

2025-12-17 18:46:46 -08:00

output_test.go

…

prime_test.go

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

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

prime.go

fix: align bd prime guidance with skill's hybrid TodoWrite approach

2025-12-16 16:11:30 -08:00

quick.go

feat: add silent quick-capture mode (bd q)

2025-12-16 01:08:40 -08:00

quickstart.go

…

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

fix(docs): use consistent in_progress status naming (GH#444)

2025-12-16 01:07:33 -08:00

reinit_test.go

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

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

relate.go

feat: add graph links and hooks system (bd-kwro.2-5, bd-kwro.8)

2025-12-16 18:34:48 -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

Revert "fix: Address workflow template issues from code review"

2025-12-17 22:44:23 -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

fix: daemon delete creates tombstones, export includes tombstones (bd-rp4o)

2025-12-17 01:15:40 -08:00

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

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

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 0.30.5

2025-12-18 00:27:59 -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