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cb6f3cdb5e77809e3560730f48fe1b72dc1cbf91
beads/cmd/bd
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Steve Yegge cb6f3cdb5e feat: Add formula name support to bd mol bond (gt-8tmz.25) 
Bond command now accepts formula names (e.g., mol-polecat-arm) in addition
to issue IDs. When a formula name is given:

1. Looks up the formula using formula.Parser
2. Resolves inheritance and applies transformations (control flow, advice,
   expansions, aspects)
3. Cooks the formula inline to create an ephemeral proto
4. Uses the cooked proto for bonding

This eliminates the need for pre-cooked proto beads in the database,
enabling more dynamic workflow composition.

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

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
2025-12-25 16:39:27 -08:00
..
doctor
fix(doctor): handle installed_plugins.json v2 format (GH#741)
2025-12-25 16:20:02 -08:00
setup
Add tests for setup package (28.4% → 53.8% coverage)
2025-12-23 22:40:16 -08:00
templates/hooks
release: v0.36.0
2025-12-24 15:57:22 -08:00
testdata
bd sync: 2025-12-23 23:38:57
2025-12-24 00:06:41 -08:00
.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
activity_test.go
fix: emit rich mutation events for status changes (bd-313v)
2025-12-23 04:16:26 -08:00
activity.go
fix: emit rich mutation events for status changes (bd-313v)
2025-12-23 04:16:26 -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
fix(json): audit and standardize JSON output across commands (bd-au0.7)
2025-12-24 00:10:14 -08:00
autoimport_test.go
refactor: consolidate duplicate path-finding utilities (bd-74w1, bd-4nqq)
2025-12-22 21:15:41 -08:00
autoimport.go
Refactor duplicate JSONL-from-git parsing code (bd-y2v)
2025-12-23 22:41:05 -08:00
autostart_test.go
bd sync: 2025-12-23 23:38:57
2025-12-24 00:06:41 -08:00
cleanup.go
feat: consolidate maintenance commands into bd doctor --fix (bd-bqcc)
2025-12-23 01:31:18 -08:00
cli_fast_test.go
refactor: remove legacy autoflush code paths (bd-xsl9)
2025-12-23 01:56:19 -08:00
comments_test.go
…
comments.go
fix: Use FatalErrorRespectJSON across all commands (bd-28sq)
2025-12-25 13:56:19 -08:00
compact_test.go
feat(compact): Add --prune mode for standalone tombstone pruning (bd-c7y5)
2025-12-24 00:08:10 -08:00
compact.go
feat(compact): Add --prune mode for standalone tombstone pruning (bd-c7y5)
2025-12-24 00:08:10 -08:00
config_test.go
…
config.go
bd sync: 2025-12-23 23:38:57
2025-12-24 00:06:41 -08:00
cook.go
feat: Add source tracing metadata to cooked steps (gt-8tmz.18)
2025-12-25 16:27:48 -08:00
count.go
feat: add gate issue type and CLI commands for async coordination (bd-udsi)
2025-12-23 12:06:42 -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
wip: simplify wisp architecture - single db with Wisp flag (bd-bkul)
2025-12-24 20:31:27 -08:00
daemon_autoimport_test.go
…
daemon_autostart.go
chore: code health review - test fix and error comments (bd-9g1z, bd-ork0)
2025-12-22 21:30:57 -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
…
daemon_debouncer.go
…
daemon_event_loop.go
feat(daemon): add auto_pull config parameter for periodic remote sync
2025-12-22 18:47:18 -05:00
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
…
daemon_health_windows.go
…
daemon_integration_test.go
bd sync: 2025-12-23 23:38:57
2025-12-24 00:06:41 -08:00
daemon_lifecycle.go
bd sync: 2025-12-23 23:38:57
2025-12-24 00:06:41 -08:00
daemon_local_test.go
bd sync: 2025-12-23 23:38:57
2025-12-24 00:06:41 -08:00
daemon_lock_test.go
…
daemon_lock_unix.go
…
daemon_lock_wasm.go
…
daemon_lock_windows.go
…
daemon_lock.go
chore: code health review - test fix and error comments (bd-9g1z, bd-ork0)
2025-12-22 21:30:57 -08:00
daemon_logger.go
bd sync: 2025-12-23 23:38:57
2025-12-24 00:06:41 -08:00
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
bd sync: 2025-12-23 23:38:57
2025-12-24 00:06:41 -08:00
daemon_sync_branch_test.go
bd sync: 2025-12-23 23:38:57
2025-12-24 00:06:41 -08:00
daemon_sync_branch.go
fix(sync): respect sync.remote config in daemon sync operations (#736)
2025-12-24 12:43:18 -08:00
daemon_sync_test.go
bd sync: 2025-12-23 23:38:57
2025-12-24 00:06:41 -08:00
daemon_sync.go
refactor(cmd): migrate sort.Slice to slices.SortFunc (bd-u2sc.2)
2025-12-22 15:39:55 -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
bd sync: 2025-12-23 23:38:57
2025-12-24 00:06:41 -08:00
daemon_watcher.go
fix(daemon): deduplicate file and git ref change log messages
2025-12-22 19:02:42 -05:00
daemon_windows.go
…
daemon.go
bd sync: 2025-12-23 23:38:57
2025-12-24 00:06:41 -08:00
daemons_test.go
…
daemons.go
refactor(cmd): replace map[string]interface{} with typed JSON response structs (bd-u2sc.1)
2025-12-22 15:48:36 -08:00
defer.go
Merge upstream/main into subtle-ux-improvements
2025-12-20 17:22:43 -08:00
delete_rpc_test.go
test(delete): Add comprehensive tests for deleteViaDaemon RPC client (bd-dtl8)
2025-12-24 00:07:55 -08:00
delete_test.go
bd sync: 2025-12-23 23:38:57
2025-12-24 00:06:41 -08:00
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
chore: remove dead deprecated wrapper functions
2025-12-21 15:50:10 -08:00
dep_test.go
feat(deps): detect/prevent child→parent dependency anti-pattern (bd-nim5)
2025-12-24 13:03:27 -08:00
dep.go
fix: Use FatalErrorRespectJSON across all commands (bd-28sq)
2025-12-25 13:56:19 -08:00
detect_pollution.go
feat: consolidate maintenance commands into bd doctor --fix (bd-bqcc)
2025-12-23 01:31:18 -08:00
direct_mode_test.go
refactor: remove legacy autoflush code paths (bd-xsl9)
2025-12-23 01:56:19 -08:00
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): handle installed_plugins.json v2 format (GH#741)
2025-12-25 16:20:02 -08:00
doctor.go
fix: Make child→parent dep fix opt-in with --fix-child-parent (bd-cuek)
2025-12-25 14:05:55 -08:00
duplicate.go
chore: code health review - test fix and error comments (bd-9g1z, bd-ork0)
2025-12-22 21:30:57 -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
…
epic.go
fix: Use FatalErrorRespectJSON across all commands (bd-28sq)
2025-12-25 13:56:19 -08:00
errors.go
fix(json): standardize JSON output for errors and empty arrays (bd-au0.7)
2025-12-24 00:07:52 -08:00
export_import_test.go
…
export_integrity_integration_test.go
…
export_mtime_test.go
bd sync: 2025-12-23 23:38:57
2025-12-24 00:06:41 -08:00
export_staleness_test.go
…
export_test.go
…
export.go
feat(export): add --priority exact match filter (bd-au0.6)
2025-12-24 00:06:51 -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
refactor: remove legacy autoflush code paths (bd-xsl9)
2025-12-23 01:56:19 -08:00
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
refactor: consolidate duplicate path-finding utilities (bd-74w1, bd-4nqq)
2025-12-22 21:15:41 -08:00
formula.go
feat: Add bd formula list/show commands (gt-8tmz.14)
2025-12-25 12:38:00 -08:00
gate.go
Remove hardcoded deacon assignee from gate.go
2025-12-25 01:14:53 -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
…
import_cancellation_test.go
…
import_idempotent_test.go
…
import_mtime_test.go
…
import_multipart_id_test.go
bd sync: 2025-12-23 23:38:57
2025-12-24 00:06:41 -08:00
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
refactor: remove legacy autoflush code paths (bd-xsl9)
2025-12-23 01:56:19 -08:00
info_test.go
refactor: consolidate duplicate path-finding utilities (bd-74w1, bd-4nqq)
2025-12-22 21:15:41 -08:00
info.go
refactor: Simplify wisp architecture - badges not separate storage
2025-12-25 01:49:57 -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
fix(init): guard git.IsWorktree() with isGitRepo() check (GH#727)
2025-12-25 14:13:59 -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
refactor(cmd): migrate sort.Slice to slices.SortFunc (bd-u2sc.2)
2025-12-22 15:39:55 -08:00
jira_test.go
…
jira.go
refactor: consolidate duplicate path-finding utilities (bd-74w1, bd-4nqq)
2025-12-22 21:15:41 -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
fix: Use FatalErrorRespectJSON across all commands (bd-28sq)
2025-12-25 13:56:19 -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
feat(list): add --pretty and --watch flags for built-in viewer (#729)
2025-12-24 12:35:57 -08:00
mail.go
fix(lint): add nosec for mail delegate exec.Command
2025-12-21 15:29:58 -08:00
main_test.go
refactor: remove legacy autoflush code paths (bd-xsl9)
2025-12-23 01:56:19 -08:00
main.go
feat(config): add override notification for config parameters (#731)
2025-12-24 12:35:54 -08:00
markdown_test.go
…
markdown.go
fix: bd create -f now works with daemon mode (GH#719)
2025-12-22 23:30:08 -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(cmd): migrate sort.Slice to slices.SortFunc (bd-u2sc.2)
2025-12-22 15:39:55 -08:00
migrate_issues.go
chore: code health review - test fix and error comments (bd-9g1z, bd-ork0)
2025-12-22 21:30:57 -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: consolidate duplicate path-finding utilities (bd-74w1, bd-4nqq)
2025-12-22 21:15:41 -08:00
migrate.go
bd sync: 2025-12-23 23:38:57
2025-12-24 00:06:41 -08:00
mol_bond.go
feat: Add formula name support to bd mol bond (gt-8tmz.25)
2025-12-25 16:39:27 -08:00
mol_burn.go
refactor: simplify wisp architecture - single DB with Wisp flag (bd-bkul)
2025-12-24 20:42:54 -08:00
mol_catalog.go
refactor(mol): remove bd mol spawn - use pour/wisp only (bd-8y9t)
2025-12-24 12:52:47 -08:00
mol_current.go
Remove bd mol run - orchestration belongs in gt
2025-12-25 01:05:16 -08:00
mol_distill.go
feat: Add proto prefix for distilled molecules (bd-hobo)
2025-12-25 02:11:52 -08:00
mol_show.go
feat: add parallel step detection for molecules (bd-xo1o.4)
2025-12-23 03:57:08 -08:00
mol_squash.go
refactor: simplify wisp architecture - single DB with Wisp flag (bd-bkul)
2025-12-24 20:42:54 -08:00
mol_stale.go
feat: Add bd mol stale command to detect complete-but-unclosed molecules (bd-anv2)
2025-12-25 12:31:24 -08:00
mol_test.go
feat: Distinct prefixes for protos, molecules, wisps (bd-hobo)
2025-12-25 02:05:25 -08:00
mol.go
feat: Distinct prefixes for protos, molecules, wisps (bd-hobo)
2025-12-25 02:05:25 -08:00
nodb_test.go
…
nodb.go
fix: filter wisps from nodb writeIssuesToJSONL (bd-9avq)
2025-12-24 21:19:00 -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
…
periodic_remote_sync_test.go
feat(daemon): add auto_pull config parameter for periodic remote sync
2025-12-22 18:47:18 -05:00
pin.go
feat: implement molecular chemistry UX commands
2025-12-22 02:21:40 -08:00
pour.go
feat: Distinct prefixes for protos, molecules, wisps (bd-hobo)
2025-12-25 02:05:25 -08:00
prime_test.go
…
prime.go
feat(prime): add no-git-ops config to disable git ops in session close (GH#593)
2025-12-25 14:25:45 -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
fix: resolve golangci-lint errors
2025-12-23 05:10:38 -08:00
reinit_test.go
fix: make database_removal_scenario test more realistic
2025-12-23 00:04:55 -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(doctor): consolidate maintenance commands + improve daemon startup
2025-12-22 20:21:30 -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
…
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
chore: code health review - test fix and error comments (bd-9g1z, bd-ork0)
2025-12-22 21:30:57 -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
…
sandbox_unix.go
…
sandbox_windows.go
…
scripttest_test.go
…
search_test.go
…
search.go
bd sync: 2025-12-23 23:38:57
2025-12-24 00:06:41 -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
fix: Use FatalErrorRespectJSON for JSON-consistent error output (bd-28sq.1)
2025-12-25 13:41:06 -08:00
simple_helpers_test.go
…
snapshot_manager.go
chore: code health review - test fix and error comments (bd-9g1z, bd-ork0)
2025-12-22 21:30:57 -08:00
stale_test.go
fix(json): audit and standardize JSON output across commands (bd-au0.7)
2025-12-24 00:10:14 -08:00
stale.go
fix(json): audit and standardize JSON output across commands (bd-au0.7)
2025-12-24 00:10:14 -08:00
staleness.go
…
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_branch.go
fix: Prevent bd sync from committing non-.beads files (bd-trgb)
2025-12-25 12:05:46 -08:00
sync_check.go
fix: address CI lint errors (gosec, errcheck, unparam, duplicate tests) (#730)
2025-12-24 12:35:32 -08:00
sync_export.go
fix: filter wisps from sync_export.go (bd-687g)
2025-12-24 20:55:31 -08:00
sync_import.go
fix: address CI lint errors (gosec, errcheck, unparam, duplicate tests) (#730)
2025-12-24 12:35:32 -08:00
sync_local_only_test.go
…
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: Prevent bd sync from committing non-.beads files (bd-trgb)
2025-12-25 12:05:46 -08:00
template_test.go
fix: mol run loads all hierarchical children + supports title lookup (bd-c8d5, bd-drcx)
2025-12-24 23:33:34 -08:00
template.go
feat: Distinct prefixes for protos, molecules, wisps (bd-hobo)
2025-12-25 02:05:25 -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
refactor(cmd): migrate sort.Slice to slices.SortFunc (bd-u2sc.2)
2025-12-22 15:39:55 -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
chore: code health review - test fix and error comments (bd-9g1z, bd-ork0)
2025-12-22 21:30:57 -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
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
…
version_tracking.go
chore: remove obsolete BD_GUIDE.md references
2025-12-20 20:50:33 -08:00
version.go
release: v0.36.0
2025-12-24 15:57:22 -08:00
wisp.go
feat: Distinct prefixes for protos, molecules, wisps (bd-hobo)
2025-12-25 02:05:25 -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