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cadf798b23ec562f4d25781b7fdd037e7ccbeb60
beads/cmd/bd
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Steve Yegge cadf798b23 feat: implement molecular chemistry UX commands 
Add chemistry-inspired commands for the molecular work metaphor:

New commands:
- bd pour <proto>: Instantiate proto as persistent mol (liquid phase)
- bd wisp create <proto>: Instantiate proto as ephemeral wisp (vapor)
- bd hook: Inspect what's pinned to an agent's hook

Enhanced commands:
- bd mol spawn: Add --pour flag, deprecate --persistent
- bd mol bond: Add --pour flag (force liquid on wisp target)
- bd pin: Add --for <agent> and --start flags

Phase transitions:
  Proto (solid) --pour--> Mol (liquid) --squash--> Digest
  Proto (solid) --wisp--> Wisp (vapor) --burn--> (nothing)

Design docs: gastown/mayor/rig/docs/molecular-chemistry.md

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

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
2025-12-22 02:21:40 -08:00
..
doctor
fix(doctor): UX improvements for diagnostics and daemon (#687)
2025-12-22 01:25:23 -08:00
setup
fix(setup): preserve symlinks in atomicWriteFile
2025-12-20 20:15:55 -05:00
templates/hooks
chore: bump version to 0.33.2
2025-12-21 16:12:37 -08:00
testdata
…
.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: rename Ephemeral → Wisp (Steam Engine metaphor)
2025-12-21 15:22:45 -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
…
clean.go
refactor(ui): standardize on lipgloss semantic color system
2025-12-20 17:09:50 -08:00
cleanup.go
refactor: rename Ephemeral → Wisp (Steam Engine metaphor)
2025-12-21 15:22:45 -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
…
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
…
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
…
daemon_autostart.go
fix(doctor): UX improvements for diagnostics and daemon (#687)
2025-12-22 01:25:23 -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
…
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_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
…
daemon_lock_unix.go
…
daemon_lock_wasm.go
…
daemon_lock_windows.go
…
daemon_lock.go
…
daemon_logger.go
…
daemon_parent_test.go
Fix integration test compilation errors in cmd/bd
2025-12-11 07:11:15 -05:00
daemon_rotation_test.go
…
daemon_server.go
…
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
…
daemon_unix.go
…
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
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
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
chore: remove dead deprecated wrapper functions
2025-12-21 15:50:10 -08:00
dep_test.go
Fix tests (bd-6ss and sub-issues) (#626)
2025-12-18 18:23:30 -08:00
dep.go
feat: add cross-project dependency support - config and external: prefix (bd-66w1, bd-om4a)
2025-12-21 23:08:00 -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
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
fix(doctor): UX improvements for diagnostics and daemon (#687)
2025-12-22 01:25:23 -08:00
duplicate.go
refactor(ui): standardize on lipgloss semantic color system
2025-12-20 17:09:50 -08:00
duplicates_test.go
Implement auto-merge functionality for duplicates command
2025-11-27 22:39:13 -08:00
duplicates.go
refactor(ui): standardize on lipgloss semantic color system
2025-12-20 17:09:50 -08:00
epic_test.go
…
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
…
export_staleness_test.go
…
export_test.go
…
export.go
refactor: rename Ephemeral → Wisp (Steam Engine metaphor)
2025-12-21 15:22:45 -08:00
external_ref_test.go
feat: add cross-project dependency support - config and external: prefix (bd-66w1, bd-om4a)
2025-12-21 23:08:00 -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
…
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
…
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
…
hook.go
feat: implement molecular chemistry UX commands
2025-12-22 02:21:40 -08:00
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
…
import_idempotent_test.go
…
import_mtime_test.go
…
import_multipart_id_test.go
…
import_profile_test.go
…
import_shared.go
refactor: remove all deletions.jsonl code (bd-fom)
2025-12-16 14:20:49 -08:00
import_uncommitted_test.go
…
import.go
fix: misc improvements and dependency updates
2025-12-20 17:09:50 -08:00
info_test.go
…
info.go
fix: add third change to satisfy versionChanges test
2025-12-21 16:14:41 -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
…
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
…
label.go
feat: add bd ship command for cross-project capabilities (bd-eijl)
2025-12-21 23:11:48 -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
fix(lint): add nosec for mail delegate exec.Command
2025-12-21 15:29:58 -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
…
markdown.go
fix: priority:0 omitempty and markdown nil pointer (GH#671, GH#674)
2025-12-21 15:41:22 -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
…
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
…
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: implement molecular chemistry UX commands
2025-12-22 02:21:40 -08:00
mol_burn.go
feat: add wisp commands (bd-kwjh)
2025-12-22 01:13:50 -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
fix: remove slice bounds panic in mol run output (bd-987a)
2025-12-21 22:58:05 -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: implement molecular chemistry UX commands
2025-12-22 02:21:40 -08:00
mol_squash.go
feat: add cross-store wisp→digest squash (bd-kwjh.4)
2025-12-22 00:54:35 -08:00
mol_test.go
feat: add cross-store wisp→digest squash (bd-kwjh.4)
2025-12-22 00:54:35 -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
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
…
pin.go
feat: implement molecular chemistry UX commands
2025-12-22 02:21:40 -08:00
pour.go
feat: implement molecular chemistry UX commands
2025-12-22 02:21:40 -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
…
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_test.go
fix: handle empty config values in getRepoConfig() (GH#680)
2025-12-21 21:08:57 -08:00
repo.go
fix: bd repo commands write to YAML and cleanup on remove (#683)
2025-12-22 01:26:45 -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
…
sandbox_unix.go
…
sandbox_windows.go
…
scripttest_test.go
…
search_test.go
…
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
ship.go
feat: add bd ship command for cross-project capabilities (bd-eijl)
2025-12-21 23:11:48 -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
fix(doctor): UX improvements for diagnostics and daemon (#687)
2025-12-22 01:25:23 -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
Merge upstream/main into subtle-ux-improvements
2025-12-20 17:22:43 -08:00
staleness.go
bd-6xd: Standardize on issues.jsonl as canonical filename
2025-11-26 22:02:59 -08:00
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
…
sync_test.go
refactor: remove all deletions.jsonl code (bd-fom)
2025-12-16 14:20:49 -08:00
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
refactor: rename Ephemeral → Wisp (Steam Engine metaphor)
2025-12-21 15:22:45 -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
…
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
refactor: rename Ephemeral → Wisp (Steam Engine metaphor)
2025-12-21 15:22:45 -08:00
tips_example_test.go
…
tips_test.go
…
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 0.33.2
2025-12-21 16:12:37 -08:00
wisp.go
feat: implement molecular chemistry UX commands
2025-12-22 02:21:40 -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