Steve Yegge 466c606eb9 feat(mol): rename bond→spawn, add BondRef data model ...

Molecule evolution:
- Rename `bd mol bond` to `bd mol spawn` for instantiation
- Add BondRef type for tracking compound lineage
- Add `bonded_from` field to Issue for compound molecules
- Add BondType constants (sequential, parallel, conditional, root)
- Add IsCompound() and GetConstituents() helpers
- Add 'protomolecule' easter egg alias

Closes: bd-mh4w, bd-rnnr
Part of: bd-o5xe (Molecule bonding epic)

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

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

2025-12-21 01:20:25 -08:00

..

doctor

fix(doctor): check .local_version instead of deprecated LastBdVersion (fixes #662)

2025-12-20 14:41:13 -08:00

setup

fix(setup): preserve symlinks in atomicWriteFile

2025-12-20 20:15:55 -05:00

templates/hooks

chore: bump version to 0.32.1

2025-12-20 21:56:28 -08:00

testdata

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.gitattributes

Fix tests (bd-6ss and sub-issues) (#626)

2025-12-18 18:23:30 -08:00

@AGENTS.md

Fix tests (bd-6ss and sub-issues) (#626)

2025-12-18 18:23:30 -08:00

AGENTS.md

Fix tests (bd-6ss and sub-issues) (#626)

2025-12-18 18:23:30 -08:00

audit.go

feat(audit): add append-only agent audit trail (.beads/interactions.jsonl)

2025-12-20 03:24:51 -08:00

autoflush.go

refactor(ui): standardize on lipgloss semantic color system

2025-12-20 17:09:50 -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

feat(jsonl): add omitempty to reduce JSONL bloat (beads-399)

2025-12-19 23:18:11 -08:00

autostart_test.go

Fix tests (bd-6ss and sub-issues) (#626)

2025-12-18 18:23:30 -08:00

clean_security_test.go

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clean.go

refactor(ui): standardize on lipgloss semantic color system

2025-12-20 17:09:50 -08:00

cleanup.go

refactor(ui): standardize on lipgloss semantic color system

2025-12-20 17:09:50 -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

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comments.go

fix: misc improvements and dependency updates

2025-12-20 17:09:50 -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

fix: misc improvements and dependency updates

2025-12-20 17:09:50 -08:00

config_test.go

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config.go

Merge upstream/main into subtle-ux-improvements

2025-12-20 17:22:43 -08:00

count.go

Merge upstream/main into subtle-ux-improvements

2025-12-20 17:22:43 -08:00

create_form_test.go

cleanup

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

create_form.go

refactor(ui): standardize on lipgloss semantic color system

2025-12-20 17:09:50 -08:00

create_test.go

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create.go

refactor(ui): standardize on lipgloss semantic color system

2025-12-20 17:09:50 -08:00

daemon_autoimport_test.go

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daemon_autostart.go

Auto-disable daemon in git worktrees for safety (#567)

2025-12-16 00:06:19 -08:00

daemon_basics_test.go

Fix tests (bd-6ss and sub-issues) (#626)

2025-12-18 18:23:30 -08:00

daemon_config.go

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daemon_crash_test.go

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daemon_debouncer_test.go

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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_freebsd.go

fix(unix): handle Statfs field types for disk space check (#646)

2025-12-19 17:50:14 -08:00

daemon_health_unix.go

fix(unix): handle Statfs field types for disk space check (#646)

2025-12-19 17:50:14 -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_integration_test.go

Fix tests (bd-6ss and sub-issues) (#626)

2025-12-18 18:23:30 -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

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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

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daemon_parent_test.go

Fix integration test compilation errors in cmd/bd

2025-12-11 07:11:15 -05:00

daemon_rotation_test.go

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daemon_server.go

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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

feat(jsonl): add omitempty to reduce JSONL bloat (beads-399)

2025-12-19 23:18:11 -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

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daemon_unix.go

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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

feat: add Git worktree compatibility (PR #478)

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

daemon_windows.go

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daemon.go

fix: misc improvements and dependency updates

2025-12-20 17:09:50 -08:00

daemons_test.go

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daemons.go

fix: misc improvements and dependency updates

2025-12-20 17:09:50 -08:00

defer.go

Merge upstream/main into subtle-ux-improvements

2025-12-20 17:22:43 -08:00

delete_test.go

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delete.go

refactor(ui): standardize on lipgloss semantic color system

2025-12-20 17:09:50 -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

Fix tests (bd-6ss and sub-issues) (#626)

2025-12-18 18:23:30 -08:00

dep.go

Merge upstream/main into subtle-ux-improvements

2025-12-20 17:22:43 -08:00

detect_pollution.go

refactor(ui): standardize on lipgloss semantic color system

2025-12-20 17:09:50 -08:00

direct_mode_test.go

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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): check .local_version instead of deprecated LastBdVersion (fixes #662)

2025-12-20 14:41:13 -08:00

doctor.go

refactor(ui): standardize on lipgloss semantic color system

2025-12-20 17:09:50 -08:00

duplicate.go

refactor(ui): standardize on lipgloss semantic color system

2025-12-20 17:09:50 -08:00

duplicates_test.go

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duplicates.go

refactor(ui): standardize on lipgloss semantic color system

2025-12-20 17:09:50 -08:00

epic_test.go

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epic.go

refactor(ui): standardize on lipgloss semantic color system

2025-12-20 17:09:50 -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

fix: misc improvements and dependency updates

2025-12-20 17:09:50 -08:00

flags.go

bd create: support --description=- for stdin input

2025-12-19 01:47:03 -08:00

flush_manager_test.go

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flush_manager.go

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fork_protection_test.go

feat: auto-protect forks from committing upstream issue database

2025-12-18 18:56:59 -08:00

fork_protection.go

feat: auto-protect forks from committing upstream issue database

2025-12-18 18:56:59 -08:00

git_sync_test.go

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graph_test.go

fix(graph): pass subgraph to renderGraph to fix nil pointer crash

2025-12-20 01:59:31 -08:00

graph.go

Merge upstream/main into subtle-ux-improvements

2025-12-20 17:22:43 -08:00

helpers_test.go

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hooks_test.go

feat(hooks): implement thin shim pattern (GH#615)

2025-12-20 02:38:56 -08:00

hooks.go

Merge upstream/main into subtle-ux-improvements

2025-12-20 17:22:43 -08:00

import_bug_test.go

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import_cancellation_test.go

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import_idempotent_test.go

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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

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

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

import_uncommitted_test.go

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import.go

fix: misc improvements and dependency updates

2025-12-20 17:09:50 -08:00

info_test.go

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info.go

Merge branch 'main' into subtle-ux-improvements

2025-12-20 23:26:35 -08:00

init_contributor.go

refactor(ui): standardize on lipgloss semantic color system

2025-12-20 17:09:50 -08:00

init_hooks_test.go

feat: add Git worktree compatibility (PR #478)

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

init_team.go

refactor(ui): standardize on lipgloss semantic color system

2025-12-20 17:09:50 -08:00

init_test.go

fix(init): handle read-only gitignore gracefully in stealth mode (#663)

2025-12-20 16:43:43 -08:00

init.go

Merge upstream/main into subtle-ux-improvements

2025-12-20 17:22:43 -08:00

integrity_content_test.go

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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: misc improvements and dependency updates

2025-12-20 17:09:50 -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

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label.go

refactor(ui): standardize on lipgloss semantic color system

2025-12-20 17:09:50 -08:00

linear_test.go

feat: Linear Integration (#655)

2025-12-19 17:58:24 -08:00

linear.go

fix: misc improvements and dependency updates

2025-12-20 17:09:50 -08:00

list_test.go

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list.go

Merge branch 'main' into subtle-ux-improvements

2025-12-20 23:26:35 -08:00

mail.go

feat(mail): add bd mail delegate command for agent UX

2025-12-21 00:34:49 -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(ux): reorganize command groups and add Tufte-inspired help styling

2025-12-20 12:57:16 -08:00

markdown_test.go

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markdown.go

refactor(ui): standardize on lipgloss semantic color system

2025-12-20 17:09:50 -08:00

merge_security_test.go

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merge.go

fix: misc improvements and dependency updates

2025-12-20 17:09:50 -08:00

migrate_hash_ids_test.go

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migrate_hash_ids.go

refactor(ui): standardize on lipgloss semantic color system

2025-12-20 17:09:50 -08:00

migrate_issues.go

fix: misc improvements and dependency updates

2025-12-20 17:09:50 -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

fix: misc improvements and dependency updates

2025-12-20 17:09:50 -08:00

migrate_test.go

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migrate_tombstones.go

refactor(ui): standardize on lipgloss semantic color system

2025-12-20 17:09:50 -08:00

migrate.go

refactor(ui): standardize on lipgloss semantic color system

2025-12-20 17:09:50 -08:00

mol.go

feat(mol): rename bond→spawn, add BondRef data model

2025-12-21 01:20:25 -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

feat(jsonl): add omitempty to reduce JSONL bloat (beads-399)

2025-12-19 23:18:11 -08:00

onboard_test.go

refactor(onboard): simplify to minimal snippet pointing to bd prime

2025-12-18 11:48:02 -08:00

onboard.go

refactor(ui): standardize on lipgloss semantic color system

2025-12-20 17:09:50 -08:00

output_test.go

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pin.go

refactor(ui): standardize on lipgloss semantic color system

2025-12-20 17:09:50 -08:00

prime_test.go

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

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

prime.go

fix: misc improvements and dependency updates

2025-12-20 17:09:50 -08:00

quick.go

fix: misc improvements and dependency updates

2025-12-20 17:09:50 -08:00

quickstart.go

refactor(ui): standardize on lipgloss semantic color system

2025-12-20 17:09:50 -08:00

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

Merge upstream/main into subtle-ux-improvements

2025-12-20 17:22:43 -08:00

reinit_test.go

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

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

relate_test.go

Add tests for Decision 004 Phase 4 edge schema consolidation

2025-12-18 11:25:17 -08:00

relate.go

refactor(ui): standardize on lipgloss semantic color system

2025-12-20 17:09:50 -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

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rename_prefix.go

refactor(ui): standardize on lipgloss semantic color system

2025-12-20 17:09:50 -08:00

reopen_test.go

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reopen.go

refactor(ui): standardize on lipgloss semantic color system

2025-12-20 17:09:50 -08:00

repair_deps_test.go

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repair_deps.go

refactor(ui): standardize on lipgloss semantic color system

2025-12-20 17:09:50 -08:00

repo.go

fix: misc improvements and dependency updates

2025-12-20 17:09:50 -08:00

reset_test.go

feat(schema): add messaging fields for bd-kwro epic

2025-12-16 13:06:47 -08:00

reset.go

refactor(ui): standardize on lipgloss semantic color system

2025-12-20 17:09:50 -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

refactor(ui): standardize on lipgloss semantic color system

2025-12-20 17:09:50 -08:00

sandbox_test.go

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sandbox_unix.go

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sandbox_windows.go

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scripttest_test.go

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search_test.go

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search.go

Merge upstream/main into subtle-ux-improvements

2025-12-20 17:22:43 -08:00

setup.go

fix: misc improvements and dependency updates

2025-12-20 17:09:50 -08:00

show.go

refactor(ui): standardize on lipgloss semantic color system

2025-12-20 17:09:50 -08:00

simple_helpers_test.go

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snapshot_manager.go

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stale_test.go

fix: replace string(rune()) with strconv.Itoa in tests (bd-fmc)

2025-12-02 22:41:07 -08:00

stale.go

Merge upstream/main into subtle-ux-improvements

2025-12-20 17:22:43 -08:00

staleness.go

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status_test.go

refactor(status): merge stats command into status (GH#644)

2025-12-20 13:14:39 -08:00

status.go

Merge upstream/main into subtle-ux-improvements

2025-12-20 17:22:43 -08:00

sync_branch_priority_test.go

fix(sync): respect sync.branch config when no upstream tracking (#640)

2025-12-19 17:52:27 -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

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sync_test.go

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

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

sync.go

fix: misc improvements and dependency updates

2025-12-20 17:09:50 -08:00

template_test.go

refactor: Remove YAML template system entirely

2025-12-18 00:18:37 -08:00

template.go

feat(mol): add bd mol commands, deprecate bd template

2025-12-21 00:01:53 -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

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thanks.go

DOCTOR IMPROVEMENTS: visual improvements/grouping + add comprehensive tests + fix gosec warnings (#656)

2025-12-20 03:10:06 -08:00

thread_test.go

Add tests for Decision 004 Phase 4 thread traversal functions

2025-12-18 11:30:26 -08:00

tips_example_test.go

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tips_test.go

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tips.go

feat: add Git worktree compatibility (PR #478)

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

undefer.go

Merge upstream/main into subtle-ux-improvements

2025-12-20 17:22:43 -08:00

unpin.go

refactor(ui): standardize on lipgloss semantic color system

2025-12-20 17:09:50 -08:00

upgrade.go

fix: misc improvements and dependency updates

2025-12-20 17:09:50 -08:00

validate_test.go

fix: add test parallelism and increase Windows CI timeout

2025-12-03 18:30:53 -08:00

validate.go

refactor(ui): standardize on lipgloss semantic color system

2025-12-20 17:09:50 -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

chore: remove obsolete BD_GUIDE.md references

2025-12-20 20:50:33 -08:00

version.go

chore: bump version to 0.32.1

2025-12-20 21:56:28 -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

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worktree.go

Auto-disable daemon in git worktrees for safety (#567)

2025-12-16 00:06:19 -08:00