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54a051aba3e1e4abe1f82303f5e23940cee0e6f8
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Steve Yegge 54a051aba3 gt-4v1eo: Implement ephemeral protos - cook formulas inline 
Major refactor of molecular chemistry to make protos ephemeral:
- Formulas are now cooked directly to in-memory TemplateSubgraph
- No more proto beads stored in the database

Changes:
- cook.go: Add cookFormulaToSubgraph() and resolveAndCookFormula()
  for in-memory formula cooking
- template.go: Add VarDefs field to TemplateSubgraph for default
  value handling, add extractRequiredVariables() and
  applyVariableDefaults() helpers
- pour.go: Try formula loading first for any name (not just mol-)
- wisp.go: Same pattern as pour
- mol_bond.go: Use resolveOrCookToSubgraph() for in-memory subgraphs
- mol_catalog.go: List formulas from disk instead of DB proto beads
- mol_distill.go: Output .formula.json files instead of proto beads

Flow: Formula (.formula.json) -> pour/wisp (cook inline) -> Mol/Wisp

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

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
2025-12-25 17:22:00 -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
gt-4v1eo: Implement ephemeral protos - cook formulas inline
2025-12-25 17:22:00 -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
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
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
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
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
docs: add info.go versionChanges entry for 0.37.0
2025-12-25 16:51:26 -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
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: 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
gt-4v1eo: Implement ephemeral protos - cook formulas inline
2025-12-25 17:22:00 -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
gt-4v1eo: Implement ephemeral protos - cook formulas inline
2025-12-25 17:22:00 -08:00
mol_current.go
Remove bd mol run - orchestration belongs in gt
2025-12-25 01:05:16 -08:00
mol_distill.go
gt-4v1eo: Implement ephemeral protos - cook formulas inline
2025-12-25 17:22:00 -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
test: replace manual os.Chdir with t.Chdir in tests (#457)
2025-12-04 11:21:43 -08:00
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
gt-4v1eo: Implement ephemeral protos - cook formulas inline
2025-12-25 17:22:00 -08:00
prime_test.go
feat(prime): add --stealth flag for flush-only workflow
2025-12-03 18:08:33 -08:00
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
feat: add --readonly flag for worker sandboxes (gt-ymo)
2025-12-02 23:44:22 -08:00
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
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
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
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: 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
gt-4v1eo: Implement ephemeral protos - cook formulas inline
2025-12-25 17:22:00 -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
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
release: v0.36.0
2025-12-24 15:57:22 -08:00
wisp.go
gt-4v1eo: Implement ephemeral protos - cook formulas inline
2025-12-25 17:22:00 -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