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d6ab9ab62c2575a9c17cdca15e4e7be5ef82ed16
beads/cmd/bd
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Steve Yegge d6ab9ab62c feat(mol): spawn molecules as ephemeral by default (bd-2vh3.2) 
Molecule spawning now creates ephemeral issues that can be bulk-deleted
when closed using `bd cleanup --ephemeral`. This supports the ephemeral
molecule workflow pattern where execution traces are cleaned up while
outcomes persist.

Changes:
- Add `ephemeral` parameter to cloneSubgraph() and spawnMolecule()
- mol spawn: ephemeral=true by default, add --persistent flag to opt out
- mol run: ephemeral=true (molecule execution)
- mol bond: ephemeral=true (bonded protos)
- template instantiate: ephemeral=false (deprecated, backwards compat)

This is Tier 1 of the ephemeral molecule workflow epic (bd-2vh3).

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

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
2025-12-21 13:44:25 -08:00
..
doctor
docs: update docs.md for bidirectional DBJSONLSync fix (bd-68e4)
2025-12-21 11:25:57 -07:00
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
…
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
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comments_test.go
…
comments.go
fix: misc improvements and dependency updates
2025-12-20 17:09:50 -08:00
compact_test.go
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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
…
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
…
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
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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
…
daemon_health_windows.go
…
daemon_integration_test.go
Fix tests (bd-6ss and sub-issues) (#626)
2025-12-18 18:23:30 -08:00
daemon_lifecycle.go
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daemon_local_test.go
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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
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daemon_rotation_test.go
…
daemon_server.go
…
daemon_sync_branch_test.go
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daemon_sync_branch.go
…
daemon_sync_test.go
…
daemon_sync.go
feat(jsonl): add omitempty to reduce JSONL bloat (beads-399)
2025-12-19 23:18:11 -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
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daemon_windows.go
…
daemon.go
fix: misc improvements and dependency updates
2025-12-20 17:09:50 -08:00
daemons_test.go
…
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
…
delete.go
refactor(ui): standardize on lipgloss semantic color system
2025-12-20 17:09:50 -08:00
deletion_tracking_test.go
…
deletion_tracking.go
…
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
…
direct_mode.go
…
docs.md
…
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
…
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
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export_import_test.go
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export_integrity_integration_test.go
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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
…
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
…
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
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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
…
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
…
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
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integrity.go
fix: Include tombstones in DB count for stale check (bd-53c)
2025-12-18 00:41:49 -08:00
jira_test.go
…
jira.go
fix: misc improvements and dependency updates
2025-12-20 17:09:50 -08:00
jsonl_integrity_test.go
…
label_test.go
…
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
…
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
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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
…
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
…
migrate_sync.go
fix: misc improvements and dependency updates
2025-12-20 17:09:50 -08:00
migrate_test.go
…
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_bond.go
feat(mol): spawn molecules as ephemeral by default (bd-2vh3.2)
2025-12-21 13:44:25 -08:00
mol_catalog.go
refactor(mol): split 1218-line mol.go into subcommand files
2025-12-21 11:43:43 -08:00
mol_distill.go
refactor(mol): split 1218-line mol.go into subcommand files
2025-12-21 11:43:43 -08:00
mol_run.go
feat(mol): spawn molecules as ephemeral by default (bd-2vh3.2)
2025-12-21 13:44:25 -08:00
mol_show.go
refactor(mol): split 1218-line mol.go into subcommand files
2025-12-21 11:43:43 -08:00
mol_spawn.go
feat(mol): spawn molecules as ephemeral by default (bd-2vh3.2)
2025-12-21 13:44:25 -08:00
mol_test.go
fix(mol): persist template label in bondProtoProto + add comprehensive tests
2025-12-21 11:18:27 -08:00
mol.go
feat(mol): spawn molecules as ephemeral by default (bd-2vh3.2)
2025-12-21 13:44:25 -08:00
nodb_test.go
…
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
…
pin.go
refactor(ui): standardize on lipgloss semantic color system
2025-12-20 17:09:50 -08:00
prime_test.go
…
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
…
ready_test.go
…
ready.go
Merge upstream/main into subtle-ux-improvements
2025-12-20 17:22:43 -08:00
reinit_test.go
…
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
…
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
…
reopen.go
refactor(ui): standardize on lipgloss semantic color system
2025-12-20 17:09:50 -08:00
repair_deps_test.go
…
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
…
reset.go
refactor(ui): standardize on lipgloss semantic color system
2025-12-20 17:09:50 -08:00
restore_test.go
…
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
…
snapshot_manager.go
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stale_test.go
…
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
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sync_merge_test.go
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sync_test.go
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sync.go
fix: clean goroutine exit in timeout message helpers
2025-12-21 12:43:18 -08:00
template_test.go
feat(mol): spawn molecules as ephemeral by default (bd-2vh3.2)
2025-12-21 13:44:25 -08:00
template.go
feat(mol): spawn molecules as ephemeral by default (bd-2vh3.2)
2025-12-21 13:44:25 -08:00
test_helpers_test.go
…
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
…
tips.go
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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
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validate.go
refactor(ui): standardize on lipgloss semantic color system
2025-12-20 17:09:50 -08:00
version_test.go
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version_tracking_test.go
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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
…
worktree_test.go
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worktree.go
…