Peter Chanthamynavong 12858f5146 fix(doctor): recognize lowercase 's' skip-worktree flag (#931) ...

* fix(doctor): handle 's' status in combined git flags

Problem:
- Git status detection failed when 's' was combined with other flags
- Branch synchronization checks produced incorrect results due to missing flag parsing

Solution:
- Update detection logic to correctly identify the 's' status within combined flag strings

Impact:
- Ensures branch synchronization state is accurately reported during doctor checks

* test(doctor): add unit tests for git flag parsing

- Extract git flag parsing logic into parseGitLsFilesFlag helper
- Add unit tests for git flag parsing logic

Coverage: Git flag parsing in sync_branch.go

2026-01-06 19:22:51 -08:00

..

doctor

fix(doctor): recognize lowercase 's' skip-worktree flag (#931)

2026-01-06 19:22:51 -08:00

setup

test: add unit tests for bd setup gemini

2026-01-02 00:19:14 -08:00

templates/hooks

chore: Bump version to 0.44.0

2026-01-04 23:08:58 -08:00

testdata

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.gitattributes

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@AGENTS.md

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activity_test.go

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activity.go

feat: add FreeBSD release builds (#832)

2026-01-01 10:51:51 -08:00

admin_aliases.go

…

admin.go

…

agent_routing_test.go

fix(agent): add routing support for cross-repo agent resolution (#864)

2026-01-03 11:53:14 -08:00

agent_test.go

fix(agent): support hyphenated rig names in parseAgentIDFields (GH#868)

2026-01-03 13:25:15 -08:00

agent.go

fix(agent): support hyphenated rig names in parseAgentIDFields (GH#868)

2026-01-03 13:25:15 -08:00

AGENTS.md

…

audit.go

feat(completion): optimize ID prefix filtering and add completions to more commands

2026-01-06 19:05:34 -08:00

autoflush.go

…

autoimport_test.go

feat(daemon): unify auto-sync config for simpler agent workflows (#904)

2026-01-06 12:52:19 -08:00

autoimport.go

fix(init): prevent parent hub contamination during bd init (GH#896)

2026-01-04 15:43:57 -08:00

autostart_test.go

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cleanup.go

…

cli_coverage_show_test.go

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cli_fast_test.go

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close.go

feat(completion): add dynamic shell completions for issue IDs (#935)

2026-01-06 18:59:25 -08:00

comments_test.go

…

comments.go

feat(completion): optimize ID prefix filtering and add completions to more commands

2026-01-06 19:05:34 -08:00

compact_rpc.go

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compact_test.go

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compact_tombstone.go

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compact.go

…

completions_test.go

feat(completion): add dynamic shell completions for issue IDs (#935)

2026-01-06 18:59:25 -08:00

completions.go

feat(completion): optimize ID prefix filtering and add completions to more commands

2026-01-06 19:05:34 -08:00

config_test.go

fix: allow yaml-only config operations without database (GH#536)

2026-01-02 00:02:20 -08:00

config.go

…

context_test.go

fix: prevent nil context panic in multi-repo hydration (#840)

2026-01-01 10:46:56 -08:00

context.go

fix: prevent nil context panic in multi-repo hydration (#840)

2026-01-01 10:46:56 -08:00

cook_test.go

test(cook): add gate bead creation tests (bd-4k3c)

2026-01-02 14:01:56 -08:00

cook.go

fix(mol): substitute title/desc vars in root molecule bead

2026-01-02 16:00:54 -08:00

count.go

…

create_form_test.go

…

create_form.go

…

create_notes_test.go

feat: add --notes flag to bd create command (GH#830)

2026-01-01 10:53:59 -08:00

create_test.go

feat(dates): add --due and --defer timestamp options with natural language parsing (#847)

2026-01-01 20:06:13 -08:00

create.go

feat(types): add rig identity bead type (gt-zmznh)

2026-01-06 18:55:45 -08:00

daemon_autoimport_test.go

feat: add session_id field to issue close/update mutations (bd-tksk)

2025-12-31 13:14:15 -08:00

daemon_autopull_yaml_test.go

fix(daemon): Use syncbranch.IsConfigured() for autoPull (#837)

2026-01-01 10:48:14 -08:00

daemon_autostart_unit_test.go

fix(doctor): detect missing git repo and improve daemon startup message (#890)

2026-01-04 11:13:48 -08:00

daemon_autostart.go

feat(daemon): add BD_SOCKET env var for test isolation (#914)

2026-01-06 19:13:49 -08:00

daemon_basics_test.go

…

daemon_config.go

feat(daemon): add BD_SOCKET env var for test isolation (#914)

2026-01-06 19:13:49 -08:00

daemon_crash_test.go

…

daemon_debouncer_test.go

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daemon_debouncer.go

…

daemon_event_loop.go

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daemon_health_freebsd.go

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daemon_health_solaris.go

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daemon_health_unix.go

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daemon_health_wasm.go

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daemon_health_windows.go

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daemon_integration_test.go

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daemon_lifecycle.go

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daemon_local_test.go

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daemon_lock_test.go

…

daemon_lock_unix.go

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daemon_lock_wasm.go

…

daemon_lock_windows.go

…

daemon_lock.go

…

daemon_logger.go

fix(rename-prefix): sync JSONL before and after prefix rename (#893)

2026-01-04 10:53:31 -08:00

daemon_parent_test.go

…

daemon_rotation_test.go

…

daemon_server.go

…

daemon_socket_test.go

feat(daemon): add BD_SOCKET env var for test isolation (#914)

2026-01-06 19:13:49 -08:00

daemon_sync_branch_test.go

feat: add session_id field to issue close/update mutations (bd-tksk)

2025-12-31 13:14:15 -08:00

daemon_sync_branch.go

fix: bd sync fails to copy local changes TO beads-sync worktree (#810)

2025-12-30 16:49:50 -08:00

daemon_sync_state.go

…

daemon_sync_test.go

…

daemon_sync.go

fix: finalize metadata after commit, not after push (GH#885)

2026-01-04 16:16:53 -08:00

daemon_test.go

…

daemon_unix_test.go

…

daemon_unix.go

…

daemon_wasm.go

…

daemon_watcher_platform_test.go

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daemon_watcher_test.go

…

daemon_watcher.go

fix: prevent event storm when gitRefsPath is empty (#883)

2026-01-04 11:14:36 -08:00

daemon_windows.go

…

daemon.go

feat(daemon): unify auto-sync config for simpler agent workflows (#904)

2026-01-06 12:52:19 -08:00

daemons_test.go

…

daemons.go

fix(daemon): normalize paths for case-insensitive filesystem comparison (GH#869)

2026-01-03 13:22:52 -08:00

defer.go

feat(completion): add dynamic shell completions for issue IDs (#935)

2026-01-06 18:59:25 -08:00

delete_rpc_test.go

…

delete_test.go

…

delete.go

feat(completion): optimize ID prefix filtering and add completions to more commands

2026-01-06 19:05:34 -08:00

deletion_tracking_test.go

…

deletion_tracking.go

…

dep_test.go

feat(dep): add --blocks shorthand flag for natural dependency syntax

2026-01-04 16:20:04 -08:00

dep.go

feat(completion): optimize ID prefix filtering and add completions to more commands

2026-01-06 19:05:34 -08:00

detect_pollution.go

…

direct_mode_test.go

…

direct_mode.go

…

docs.md

…

doctor_fix.go

fix: hide issues.jsonl from git status when sync.branch configured (GH#870)

2026-01-03 21:07:32 -08:00

doctor_health.go

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doctor_pollution.go

…

doctor_repair_chaos_test.go

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doctor_repair_test.go

…

doctor_test.go

…

doctor.go

feat(daemon): unify auto-sync config for simpler agent workflows (#904)

2026-01-06 12:52:19 -08:00

dual_mode_test.go

feat(daemon): unify auto-sync config for simpler agent workflows (#904)

2026-01-06 12:52:19 -08:00

duplicate.go

feat(completion): optimize ID prefix filtering and add completions to more commands

2026-01-06 19:05:34 -08:00

duplicates_test.go

…

duplicates.go

feat: add session_id field to issue close/update mutations (bd-tksk)

2025-12-31 13:14:15 -08:00

edit.go

feat(completion): add dynamic shell completions for issue IDs (#935)

2026-01-06 18:59:25 -08:00

epic_test.go

…

epic.go

feat: add session_id field to issue close/update mutations (bd-tksk)

2025-12-31 13:14:15 -08:00

errors.go

…

export_import_test.go

feat: add session_id field to issue close/update mutations (bd-tksk)

2025-12-31 13:14:15 -08:00

export_integrity_integration_test.go

…

export_mtime_test.go

…

export_obsidian_test.go

feat: add Obsidian Tasks markdown export format (GH#819)

2025-12-31 11:39:17 -08:00

export_obsidian.go

feat(types): add rig identity bead type (gt-zmznh)

2026-01-06 18:55:45 -08:00

export_staleness_test.go

…

export_test.go

…

export.go

feat(list): Add type aliases for --type flag (gt-pvhsv)

2026-01-01 18:17:12 -08:00

external_ref_test.go

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flags.go

feat: add --notes flag to bd create command (GH#830)

2026-01-01 10:53:59 -08:00

flush_manager_test.go

…

flush_manager.go

…

fork_protection_test.go

fix(fork-protection): only apply protection to actual beads forks (#823) (#828)

2026-01-01 10:51:22 -08:00

fork_protection.go

fix: bd sync fails with exit 128 in bare repo worktrees (GH#827)

2026-01-01 11:05:05 -08:00

formula.go

…

gate_discover.go

feat(gate): add bd gate discover for gh:run await_id auto-discovery (bd-z6kw)

2026-01-02 16:14:35 -08:00

gate_test.go

feat(gate): add cross-rig bead gate support (Phase 4)

2026-01-02 13:11:36 -08:00

gate.go

feat(completion): optimize ID prefix filtering and add completions to more commands

2026-01-06 19:05:34 -08:00

git_sync_test.go

feat: add session_id field to issue close/update mutations (bd-tksk)

2025-12-31 13:14:15 -08:00

git_test_helpers.go

…

graph_test.go

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graph.go

feat(completion): optimize ID prefix filtering and add completions to more commands

2026-01-06 19:05:34 -08:00

helpers_test.go

…

hooks_test.go

fix: prevent infinite loop in bd hooks run when .old is a bd shim (#843)

2026-01-01 19:46:34 -08:00

hooks.go

fix: prevent infinite loop in bd hooks run when .old is a bd shim (#843)

2026-01-01 19:46:34 -08:00

human.go

…

import_bug_test.go

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import_cancellation_test.go

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import_helpers_test.go

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import_idempotent_test.go

…

import_mtime_test.go

…

import_multipart_id_test.go

…

import_profile_test.go

…

import_shared.go

fix(sync): make snapshot protection timestamp-aware (GH#865)

2026-01-03 13:27:36 -08:00

import_uncommitted_test.go

…

import.go

fix(sync): make snapshot protection timestamp-aware (GH#865)

2026-01-03 13:27:36 -08:00

info_test.go

…

info.go

chore: Bump version to 0.44.0

2026-01-04 23:08:58 -08:00

init_agent.go

…

init_contributor.go

…

init_git_hooks.go

fix: git hook chaining now works correctly (GH#816)

2025-12-30 20:40:09 -08:00

init_hooks_test.go

…

init_stealth.go

…

init_team.go

feat(daemon): unify auto-sync config for simpler agent workflows (#904)

2026-01-06 12:52:19 -08:00

init_templates.go

…

init_test.go

fix(init): ensure sync branch persistence on init

2026-01-06 15:22:15 -08:00

init.go

fix(init): ensure sync branch persistence on init

2026-01-06 15:22:15 -08:00

integrity_content_test.go

…

integrity_test.go

…

integrity.go

…

jira_test.go

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jira.go

feat: add FreeBSD release builds (#832)

2026-01-01 10:51:51 -08:00

jsonl_integrity_test.go

…

label_test.go

…

label.go

feat(completion): optimize ID prefix filtering and add completions to more commands

2026-01-06 19:05:34 -08:00

last_touched_test.go

Add 'last touched' issue tracking for update/close without ID

2025-12-30 16:58:10 -08:00

last_touched.go

Add 'last touched' issue tracking for update/close without ID

2025-12-30 16:58:10 -08:00

linear_conflict.go

…

linear_sync.go

…

linear_test.go

…

linear.go

…

lint.go

feat(cli): add bd lint command for template validation (bd-gn5r)

2026-01-01 14:18:49 -08:00

list_helpers_test.go

…

list_test.go

feat(dates): add --due and --defer timestamp options with natural language parsing (#847)

2026-01-01 20:06:13 -08:00

list.go

feat: add --filter-parent as alias for --parent in bd list (bd-3p4u)

2026-01-04 23:51:02 -08:00

mail.go

…

main_daemon.go

…

main_errors.go

fix: rename wisp prefix from 'eph' to 'wisp' (bd-ucj8)

2026-01-01 23:55:40 -08:00

main_help.go

…

main_test.go

…

main.go

fix: allow yaml-only config operations without database (GH#536)

2026-01-02 00:02:20 -08:00

markdown_test.go

…

markdown.go

…

merge_security_test.go

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merge_slot.go

feat(slot): Add merge-slot gate for serialized conflict resolution

2026-01-02 18:03:27 -08:00

merge.go

…

migrate_hash_ids_test.go

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migrate_hash_ids.go

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migrate_issues.go

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migrate_sync_test.go

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migrate_sync.go

…

migrate_test.go

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migrate_tombstones.go

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migrate.go

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mol_bond.go

feat: implement Step.Condition evaluation in bd cook (bd-7zka.1)

2025-12-31 00:33:11 -08:00

mol_burn.go

…

mol_current.go

feat: add display guards for large molecules in bd mol current (bd-vln0)

2025-12-31 13:08:41 -08:00

mol_distill.go

…

mol_progress.go

fix: use lightweight molecule discovery in bd mol progress

2025-12-31 13:04:19 -08:00

mol_show.go

refactor(mol): remove redundant guard in showCompoundBondingInfo

2026-01-02 14:08:22 -08:00

mol_squash.go

…

mol_stale.go

…

mol_test.go

fix(mol): substitute title/desc vars in root molecule bead

2026-01-02 16:00:54 -08:00

mol.go

…

move_test.go

feat: add bd move command for cross-rig issue relocation (bd-v43g)

2026-01-02 01:31:19 -08:00

move.go

feat(completion): optimize ID prefix filtering and add completions to more commands

2026-01-06 19:05:34 -08:00

nodb_test.go

fix(nodb): set cmdCtx.StoreActive in initializeNoDbMode (GH#897)

2026-01-04 16:24:18 -08:00

nodb.go

fix(nodb): set cmdCtx.StoreActive in initializeNoDbMode (GH#897)

2026-01-04 16:24:18 -08:00

onboard_test.go

…

onboard.go

…

orphans_test.go

…

orphans.go

…

output_test.go

…

periodic_remote_sync_test.go

…

pour.go

feat: implement Step.Condition evaluation in bd cook (bd-7zka.1)

2025-12-31 00:33:11 -08:00

preflight_test.go

feat: add nix-hash staleness detection to bd preflight --check (bd-lfak.4)

2025-12-31 00:05:53 -08:00

preflight.go

feat: add FreeBSD release builds (#832)

2026-01-01 10:51:51 -08:00

prime_test.go

feat(daemon): unify auto-sync config for simpler agent workflows (#904)

2026-01-06 12:52:19 -08:00

prime.go

feat(daemon): unify auto-sync config for simpler agent workflows (#904)

2026-01-06 12:52:19 -08:00

quick.go

…

quickstart.go

…

readonly_test.go

…

ready_test.go

feat(dates): add --due and --defer timestamp options with natural language parsing (#847)

2026-01-01 20:06:13 -08:00

ready.go

feat(dates): add --due and --defer timestamp options with natural language parsing (#847)

2026-01-01 20:06:13 -08:00

refile.go

feat(completion): optimize ID prefix filtering and add completions to more commands

2026-01-06 19:05:34 -08:00

reinit_test.go

…

relate_test.go

…

relate.go

feat(completion): optimize ID prefix filtering and add completions to more commands

2026-01-06 19:05:34 -08:00

rename_prefix_jsonl_update_test.go

fix(rename-prefix): sync JSONL before and after prefix rename (#893)

2026-01-04 10:53:31 -08:00

rename_prefix_repair_test.go

fix(rename-prefix): sync JSONL before and after prefix rename (#893)

2026-01-04 10:53:31 -08:00

rename_prefix_test.go

…

rename_prefix.go

fix(rename-prefix): sync JSONL before and after prefix rename (#893)

2026-01-04 10:53:31 -08:00

reopen_test.go

feat: add session_id field to issue close/update mutations (bd-tksk)

2025-12-31 13:14:15 -08:00

reopen.go

feat(completion): add dynamic shell completions for issue IDs (#935)

2026-01-06 18:59:25 -08:00

repair_deps_test.go

…

repair_orphans_test.go

…

repair.go

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repo.go

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reset_test.go

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reset.go

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restore_test.go

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restore.go

…

routed.go

…

sandbox_test.go

…

sandbox_unix.go

…

sandbox_windows.go

…

scripttest_test.go

…

search_test.go

feat: add session_id field to issue close/update mutations (bd-tksk)

2025-12-31 13:14:15 -08:00

search.go

…

setup.go

fix(lint): address gosec, misspell, and unparam warnings

2026-01-05 22:06:52 -08:00

ship.go

…

show_test.go

fix(show): display external_ref field in text output (#899)

2026-01-04 17:30:04 -08:00

show_thread.go

…

show_unit_helpers_test.go

…

show_unit_helpers.go

…

show.go

feat(completion): add dynamic shell completions for issue IDs (#935)

2026-01-06 18:59:25 -08:00

simple_helpers_test.go

…

slot.go

fix(slot): add cross-beads prefix routing to bd slot set (bd-hmeb)

2026-01-04 15:21:36 -08:00

snapshot_manager.go

fix(sync): make snapshot protection timestamp-aware (GH#865)

2026-01-03 13:27:36 -08:00

stale_test.go

…

stale.go

…

staleness.go

…

state_test.go

…

state.go

…

status_test.go

…

status.go

…

swarm.go

…

sync_branch_priority_test.go

fix: bypass gitHasBeadsChanges when using sync-branch (#812)

2025-12-30 18:04:26 -08:00

sync_branch.go

Fix bd sync failing to copy local changes to beads-sync worktree (GH#810)

2025-12-30 18:11:08 -08:00

sync_check.go

…

sync_export.go

fix: defer SQLite metadata updates until after git commit (GH#885)

2026-01-04 15:16:07 -08:00

sync_git_test.go

test(sync): add unit tests for gitHasUncommittedBeadsChanges (bd-p7i2)

2026-01-04 16:22:20 -08:00

sync_git.go

fix(sync): handle .beads/redirect in git status checks (bd-arjb)

2026-01-05 19:57:19 -08:00

sync_helpers_more_test.go

…

sync_import.go

fix(sync): use inline import for --import-only with redirect (bd-ysal)

2026-01-06 18:51:38 -08:00

sync_local_only_test.go

feat(daemon): unify auto-sync config for simpler agent workflows (#904)

2026-01-06 12:52:19 -08:00

sync_merge_test.go

…

sync_test.go

Fix bd sync failing to copy local changes to beads-sync worktree (GH#810)

2025-12-30 18:11:08 -08:00

sync_validation_test.go

test(sync): add tests for pre-sync validation hook (bd-nv4g)

2026-01-02 00:05:12 -08:00

sync.go

fix(sync): use inline import for --import-only with redirect (bd-ysal)

2026-01-06 18:51:38 -08:00

template_test.go

…

template.go

feat(template): propagate gate fields through template cloning

2026-01-03 12:44:16 -08:00

test_guard_helpers.go

…

test_helpers_test.go

…

test_repo_beads_guard_test.go

feat(daemon): unify auto-sync config for simpler agent workflows (#904)

2026-01-06 12:52:19 -08:00

test_wait_helper.go

…

thanks.go

…

thread_test.go

…

tips_example_test.go

…

tips_test.go

…

tips.go

…

undefer.go

feat(completion): add dynamic shell completions for issue IDs (#935)

2026-01-06 18:59:25 -08:00

update.go

feat(completion): add dynamic shell completions for issue IDs (#935)

2026-01-06 18:59:25 -08:00

upgrade.go

…

utils_unit_test.go

Add unit tests to improve cmd/bd CLI coverage (bd-llfl)

2025-12-30 17:14:55 -08:00

version_test.go

…

version_tracking_test.go

chore: bump version to 0.43.0 (bd-lejq)

2026-01-02 01:07:34 -08:00

version_tracking.go

…

version.go

chore: Bump version to 0.44.0

2026-01-04 23:08:58 -08:00

where.go

…

wisp.go

fix: rename wisp prefix from 'eph' to 'wisp' (bd-ucj8)

2026-01-01 23:55:40 -08:00

worktree_cmd.go

fix(worktree): resolve worktrees by name from git registry (#921)

2026-01-06 18:45:27 -08:00

worktree_daemon_test.go

…

worktree_test.go

fix(worktree): resolve worktrees by name from git registry (#921)

2026-01-06 18:45:27 -08:00

worktree.go

…