Steve Yegge e4f9c3556f feat(sync): prevent zombie resurrection from stale clones ...

Add JSONL sanitization after git pull to remove deleted issues that
git's 3-way merge may resurrect. Also add bd doctor check to hydrate
deletions.jsonl from git history for pre-v0.25.0 deletions.

Changes:
- Add sanitizeJSONLWithDeletions() in sync.go (Step 3.6)
- Add checkDeletionsManifest() in doctor.go (Check 18)
- Add HydrateDeletionsManifest() fix in doctor/fix/deletions.go
- Add looksLikeIssueID() validation to prevent false positives
- Add comprehensive tests for sanitization logic

🤖 Generated with Claude Code

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

2025-11-25 18:11:45 -08:00

..

doctor

feat(sync): prevent zombie resurrection from stale clones

2025-11-25 18:11:45 -08:00

setup

fix: skip file permission tests on Windows

2025-11-24 22:23:45 -08:00

templates

chore: Bump version to 0.25.0

2025-11-25 16:39:09 -08:00

testdata

…

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

feat: Complete command set standardization (bd-au0)

2025-11-23 20:33:31 -08:00

cleanup.go

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

2025-11-25 11:46:06 -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

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

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

2025-11-25 16:36:46 -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

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

Add tip system infrastructure (bd-d4i)

2025-11-24 10:56:14 -08:00

daemon_autoimport_test.go

…

daemon_autostart.go

refactor: remove deprecated global daemon support

2025-11-24 23:39:54 -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

…

daemon_debouncer.go

…

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

refactor: remove deprecated global daemon support

2025-11-24 23:39:54 -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

test: Tag 16 slow integration tests with build tags

2025-11-21 14:40:22 -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

feat: Respect BEADS_SYNC_BRANCH environment variable

2025-11-22 18:17:19 -08:00

daemon_sync_branch.go

feat: Respect BEADS_SYNC_BRANCH environment variable

2025-11-22 18:17:19 -08:00

daemon_sync_test.go

Fix bd-v0y: Remove mtime fast-path in hasJSONLChanged

2025-11-23 22:53:54 -08:00

daemon_sync.go

Fix bd-v0y: Remove mtime fast-path in hasJSONLChanged

2025-11-23 22:53:54 -08:00

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

…

daemon_watcher_platform_test.go

…

daemon_watcher_test.go

…

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

refactor: remove deprecated global daemon support

2025-11-24 23:39:54 -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_recording_test.go

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

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

delete_test.go

test: Tag 16 slow integration tests with build tags

2025-11-21 14:40:22 -05:00

delete.go

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

2025-11-25 11:46:06 -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 bd-pq5k: merge conflicts now prefer closed>open and deletion>modification

2025-11-23 21:42:43 -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

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

Context propagation with graceful cancellation (bd-rtp, bd-yb8, bd-2o2)

2025-11-20 21:57:23 -05:00

doctor_test.go

Add bd doctor check and fix for missing sync.branch config (bd-rsua)

2025-11-23 21:09:55 -08:00

doctor.go

feat(sync): prevent zombie resurrection from stale clones

2025-11-25 18:11:45 -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

…

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

…

export_test.go

Fix context propagation lifecycle bugs

2025-11-20 21:54:11 -05:00

export.go

feat: Complete command set standardization (bd-au0)

2025-11-23 20:33:31 -08:00

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

…

helpers_test.go

bd sync: 2025-11-09 14:53:59

2025-11-09 14:53:59 -08:00

hooks_test.go

Add tests and documentation for --shared hooks feature

2025-11-23 12:39:11 -08:00

hooks.go

Add --shared flag to bd hooks install for versioned hooks

2025-11-23 12:36:38 -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

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

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

2025-11-25 11:46:06 -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 bd-77gm: bd import silently ignores positional arguments

2025-11-24 01:25:09 -08:00

info_test.go

…

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

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

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

init_test.go

fix: Support both canonical and legacy JSONL filenames in merge driver check

2025-11-23 20:07:26 -08:00

init.go

feat(init): add --stealth flag for invisible beads usage (#381)

2025-11-25 14:46:01 -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

Fix bd-v0y: Remove mtime fast-path in hasJSONLChanged

2025-11-23 22:53:54 -08:00

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

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

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

main_test.go

fix: CI test failures and lint errors

2025-11-24 00:21:01 -08:00

main.go

feat: Complete command set standardization (bd-au0)

2025-11-23 20:33:31 -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

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

feat: Complete command set standardization (bd-au0)

2025-11-23 20:33:31 -08:00

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

Implement BD_GUIDE.md generation for version-stamped documentation (bd-woro)

2025-11-23 21:16:09 -08:00

onboard.go

fix: CI test failures and lint errors

2025-11-24 00:21:01 -08:00

output_test.go

…

prime.go

bd prime: Auto-detect ephemeral branches and adjust workflow

2025-11-25 17:12:42 -08:00

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

Add tip system infrastructure (bd-d4i)

2025-11-24 10:56:14 -08:00

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

feat: Complete command set standardization (bd-au0)

2025-11-23 20:33:31 -08:00

reopen_test.go

…

reopen.go

Support --reason flag in daemon mode for reopen command (bd-r46)

2025-11-24 01:12:33 -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

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

…

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

Add Aider integration for beads issue tracking

2025-11-23 15:13:54 -08:00

show.go

bd sync: 2025-11-24 15:46:47

2025-11-24 15:46:47 -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

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

Fix: Improve staleness check error handling (bd-2q6d, bd-o4qy, bd-n4td)

2025-11-23 20:54:18 -08:00

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

feat(sync): prevent zombie resurrection from stale clones

2025-11-25 18:11:45 -08:00

sync.go

feat(sync): prevent zombie resurrection from stale clones

2025-11-25 18:11:45 -08:00

template_security_test.go

…

template_test.go

…

template.go

…

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

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 errors

2025-11-24 22:21:55 -08:00

upgrade.go

fix: Code review fixes for bd-loka

2025-11-23 17:16:27 -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

…

version_tracking_test.go

fix: Code review fixes for auto-migration (bd-jgxi)

2025-11-23 18:28:01 -08:00

version_tracking.go

fix: CI test failures and lint errors

2025-11-24 00:21:01 -08:00

version.go

chore: Bump version to 0.25.0

2025-11-25 16:39:09 -08:00

worktree_test.go

…

worktree.go

…