Julian Knutsen f276b9d28a fix(prime): show molecule instructions BEFORE bare bead instructions (#920) ...

When a hooked bead has attached_molecule (formula workflow), the polecat
was being told "run bd show <bead-id>" first, then seeing molecule context
later. The polecat would follow the first instruction and work directly
on the bead, ignoring the formula steps entirely.

Now checks for attached_molecule FIRST and gives different instructions:
- If molecule attached: "Work through molecule steps - see CURRENT STEP"
- If no molecule: "Run bd show <bead-id>"

Also adds explicit warning: "Skip molecule steps or work on base bead directly"
to the DO NOT list when a molecule is attached.

Co-authored-by: julianknutsen <julianknutsen@users.noreply.github>
Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com>

2026-01-24 21:45:09 -08:00

..

account_test.go

Fixing unit tests on windows (#813)

2026-01-20 14:17:35 -08:00

account.go

feat(account): add gt account switch command

2026-01-07 21:41:51 -08:00

activity.go

…

agent_state_test.go

…

agent_state.go

…

agents.go

…

audit_test.go

…

audit.go

…

bead.go

feat: add aliases and deacon status line display

2026-01-21 22:40:10 -08:00

beads_db_init_test.go

fix(beads): init db for tracked beads after clone (#376)

2026-01-11 23:03:47 -08:00

beads_routing_integration_test.go

fix(beads): prevent routes.jsonl corruption and add doctor check for rig-level routes.jsonl (#377)

2026-01-12 01:45:26 -08:00

beads_version_test.go

…

beads_version.go

chore: increase timeout for bd version check (#871)

2026-01-22 16:41:42 -08:00

boot_test.go

feat(refinery,boot): add --agent flag for model selection (#469)

2026-01-13 13:14:47 -08:00

boot.go

fix(tmux): use KillSessionWithProcesses to prevent zombie bash processes

2026-01-20 20:45:58 -08:00

broadcast.go

fix(broadcast): exclude sender from recipients

2026-01-17 03:19:08 -08:00

callbacks.go

…

cat.go

feat(cmd): add 'gt cat' command to display bead content

2026-01-15 17:44:40 -08:00

checkpoint_cmd.go

…

cleanup.go

fix(polecat): kill orphaned Claude processes when nuking polecats

2026-01-22 21:43:23 -08:00

close.go

feat(cmd): add --comment as alias for --reason in gt close

2026-01-21 18:04:58 -08:00

commit_test.go

feat(identity): add gt commit wrapper and gt trail command

2026-01-13 19:34:29 -08:00

commit.go

feat(identity): add gt commit wrapper and gt trail command

2026-01-13 19:34:29 -08:00

config_test.go

…

config.go

feat(identity): add gt commit wrapper and gt trail command

2026-01-13 19:34:29 -08:00

convoy.go

fix(convoy): ensure custom types registered before creating convoy

2026-01-22 21:41:25 -08:00

costs_test.go

fix(costs): derive session name for mayor/deacon without GT_TOWN

2026-01-07 19:17:28 -08:00

costs_workdir_test.go

fix(costs): skip test affected by bd CLI 0.47.2 commit bug

2026-01-20 20:46:43 -08:00

costs.go

refactor(costs): rename wisp references to entries

2026-01-24 21:29:57 -08:00

crew_add.go

feat(roles): switch daemon to config-based roles, remove role beads (Phase 2+3)

2026-01-20 12:58:01 -08:00

crew_at.go

fix(crew): don't kill pane processes when creating new session

2026-01-21 22:46:00 -08:00

crew_cycle.go

…

crew_helpers.go

fix(tmux): use switch-client when already inside tmux session

2026-01-16 15:27:59 -08:00

crew_lifecycle.go

fix(orphan): prevent Claude Code session leaks on macOS

2026-01-17 03:49:18 -08:00

crew_list_test.go

test: cover gt crew list --all

2026-01-09 02:22:36 +13:00

crew_list.go

feat: add --all to gt crew list

2026-01-09 02:22:20 +13:00

crew_maintenance.go

fix(tmux): use KillSessionWithProcesses to prevent zombie bash processes

2026-01-20 20:45:58 -08:00

crew_status.go

feat(crew): accept rig name as positional arg in crew status

2026-01-12 23:07:49 -08:00

crew.go

docs: improve help text and add nudge documentation

2026-01-17 02:55:39 -08:00

cycle.go

…

daemon.go

…

dashboard_test.go

…

dashboard.go

…

deacon.go

fix(tmux): use KillSessionWithProcesses to prevent zombie bash processes

2026-01-20 20:45:58 -08:00

disable.go

feat: Set and Forget - Seamless Gas Town Integration (#255)

2026-01-08 20:25:01 -08:00

dnd_test.go

…

dnd.go

…

doctor.go

feat(wisp): add misclassified wisp detection and defense-in-depth filtering (#833)

2026-01-20 20:20:49 -08:00

dog.go

docs: improve help text and add nudge documentation

2026-01-17 02:55:39 -08:00

done_test.go

fix(done): restrict gt done to polecats only

2026-01-20 19:51:37 -08:00

done.go

fix(sling): auto-apply mol-polecat-work (#288) and fix wisp orphan lifecycle bug (#842) (#859)

2026-01-21 20:52:26 -08:00

down_test.go

Feat/gt down tests (#15) (#18) (#330)

2026-01-10 22:56:33 -08:00

down.go

fix(shutdown): use KillSessionWithProcesses to prevent orphans

2026-01-20 23:20:50 +01:00

enable.go

feat: Set and Forget - Seamless Gas Town Integration (#255)

2026-01-08 20:25:01 -08:00

errors_test.go

fix(errors): use errors.As for wrapped error handling (#462)

2026-01-16 11:05:59 -08:00

errors.go

fix(errors): use errors.As for wrapped error handling (#462)

2026-01-16 11:05:59 -08:00

escalate_impl.go

fix(config): don't export empty GT_ROOT/BEADS_DIR in AgentEnv (#385)

2026-01-12 02:45:03 -08:00

escalate.go

feat(escalate): align config schema with design doc

2026-01-12 02:31:06 -08:00

feed.go

…

formula.go

fix(beads): align agent bead prefixes and force multi-hyphen IDs (#482)

2026-01-16 12:33:51 -08:00

gate.go

…

gitinit.go

Merge upstream/main into fix/fresh-install-fixes

2026-01-21 22:48:06 +07:00

handoff_test.go

fix(handoff): use env var fallback when town root detection fails

2026-01-21 18:05:00 -08:00

handoff.go

fix(tmux): kill pane processes before all RespawnPane calls to prevent orphans

2026-01-21 21:09:30 -08:00

help.go

feat(ui): import comprehensive UX system from beads

2026-01-09 22:46:06 -08:00

hook_slot_integration_test.go

…

hook.go

feat: add aliases and deacon status line display

2026-01-21 22:40:10 -08:00

hooks_install.go

fix: update test assertions and set BEADS_DIR in EnsureCustomTypes (#853)

2026-01-22 16:43:21 -08:00

hooks_registry.go

feat(hooks): add hook registry and install command (bd-qj9nc)

2026-01-21 17:40:05 -08:00

hooks_test.go

fix(hooks): discover crew-level and polecats-level settings

2026-01-22 21:39:31 -08:00

hooks.go

fix(hooks): discover crew-level and polecats-level settings

2026-01-22 21:39:31 -08:00

info.go

chore(release): v0.5.0

2026-01-21 23:05:00 -08:00

init.go

feat(doctor): add custom types check and centralize BeadsCustomTypes

2026-01-09 13:30:11 -08:00

install_integration_test.go

Fixing unit tests on windows (#813)

2026-01-20 14:17:35 -08:00

install.go

Merge upstream/main into fix/fresh-install-fixes

2026-01-21 22:48:06 +07:00

issue.go

…

log.go

…

mail_announce.go

refactor(beads,mail): split large files into focused modules

2026-01-09 23:01:55 -08:00

mail_channel.go

fix(mail): improve channel subscribe/unsubscribe feedback

2026-01-17 09:49:53 -08:00

mail_check.go

refactor(beads,mail): split large files into focused modules

2026-01-09 23:01:55 -08:00

mail_group_test.go

feat(mail): add group management commands

2026-01-14 21:18:20 -08:00

mail_group.go

feat(mail): add group management commands

2026-01-14 21:18:20 -08:00

mail_hook.go

feat(mail): add gt mail hook as alias for gt hook attach

2026-01-21 21:53:18 -08:00

mail_identity.go

refactor(beads,mail): split large files into focused modules

2026-01-09 23:01:55 -08:00

mail_inbox.go

feat(mail): add numeric index support to 'gt mail read'

2026-01-21 21:55:07 -08:00

mail_queue.go

feat(mail): add queue management commands

2026-01-14 21:29:37 -08:00

mail_search.go

refactor(beads,mail): split large files into focused modules

2026-01-09 23:01:55 -08:00

mail_send.go

feat(mail): update mail send to use address resolver

2026-01-14 21:19:54 -08:00

mail_test.go

feat(mail): implement beads-native gt mail claim command

2026-01-14 21:25:11 -08:00

mail_thread.go

feat(mail): accept multiple message IDs in delete command

2026-01-21 21:19:04 -08:00

mail.go

feat(mail): add numeric index support to 'gt mail read'

2026-01-21 21:55:07 -08:00

mayor.go

fix(tmux): kill pane processes before all RespawnPane calls to prevent orphans

2026-01-21 21:09:30 -08:00

molecule_attach_from_mail_test.go

…

molecule_attach_from_mail.go

…

molecule_attach.go

…

molecule_await_signal_test.go

…

molecule_await_signal.go

fix(await-signal): update agent last_activity on signal received (#774)

2026-01-20 14:10:26 -08:00

molecule_lifecycle_test.go

fix: update test assertions and set BEADS_DIR in EnsureCustomTypes (#853)

2026-01-22 16:43:21 -08:00

molecule_lifecycle.go

feat(patrol): add daily patrol digest aggregation

2026-01-17 02:11:12 -08:00

molecule_status.go

fix(hook): warn when hooked bead is already closed

2026-01-09 22:10:09 -08:00

molecule_step_test.go

…

molecule_step.go

Fix deacon patrol process leak by killing pane processes before respawn (#745)

2026-01-20 22:30:23 -08:00

molecule.go

…

mq_integration.go

feat(mq): add configurable integration branch naming (#104)

2026-01-09 00:41:35 -08:00

mq_list.go

fix(mq): use label instead of issue_type for merge-request filtering (#831)

2026-01-20 19:31:26 -08:00

mq_next.go

fix(mq): skip closed MRs in list, next, and ready views (#563)

2026-01-16 15:23:28 -08:00

mq_status.go

…

mq_submit.go

fix(resume): capture error in handoff message fallback (#583)

2026-01-16 15:27:38 -08:00

mq_test.go

fix(mq): use label instead of issue_type for merge-request filtering (#831)

2026-01-20 19:31:26 -08:00

mq_testutil_test.go

…

mq.go

feat(mq): add configurable integration branch naming (#104)

2026-01-09 00:41:35 -08:00

namepool.go

fix(namepool): only persist runtime state, not config in state file

2026-01-17 01:40:02 -08:00

notify.go

…

nudge_test.go

…

nudge.go

docs: improve help text and add nudge documentation

2026-01-17 02:55:39 -08:00

orphans.go

feat(orphans): add gt orphans kill command

2026-01-21 18:04:00 -08:00

park.go

…

patrol_helpers.go

fix(patrol): use gt formula list instead of bd mol catalog (#827)

2026-01-20 19:31:17 -08:00

patrol_test.go

test(patrol): add unit tests for patrol.go

2026-01-17 03:47:18 -08:00

patrol.go

fix(patrol): add idempotency check for digest command

2026-01-17 03:41:18 -08:00

peek.go

…

plugin.go

feat(plugin): add run and history commands for plugin management

2026-01-12 16:42:33 -08:00

polecat_cycle_test.go

…

polecat_cycle.go

…

polecat_dotdir_test.go

Skip dot dirs when scanning polecats

2026-01-08 22:10:40 +13:00

polecat_helpers.go

fix(beads): align agent bead prefixes and force multi-hyphen IDs (#482)

2026-01-16 12:33:51 -08:00

polecat_identity.go

fix(identity): copy all agent fields during polecat identity rename

2026-01-21 18:04:55 -08:00

polecat_spawn.go

fix(polecat): kill orphan sessions and clear stale hooks during allocation (#448)

2026-01-13 13:37:00 -08:00

polecat.go

fix(polecat): kill orphaned Claude processes when nuking polecats

2026-01-22 21:43:23 -08:00

prime_molecule.go

fix: handle bd --no-daemon exit code 0 bug on not-found (#339)

2026-01-11 18:37:01 -08:00

prime_output.go

feat(crew): accept rig name as positional arg in crew status

2026-01-12 23:07:49 -08:00

prime_session.go

refactor(prime): split 1833-line file into logical modules

2026-01-10 18:28:14 -08:00

prime_state.go

refactor(prime): split 1833-line file into logical modules

2026-01-10 18:28:14 -08:00

prime_test.go

fix(dog): exclude non-dog entries from kennel listing

2026-01-17 09:46:25 -08:00

prime.go

fix(prime): show molecule instructions BEFORE bare bead instructions (#920)

2026-01-24 21:45:09 -08:00

process_unix.go

fix: Windows build support with platform-specific process/signal handling

2026-01-13 20:59:15 -08:00

process_windows.go

fix: Windows build support with platform-specific process/signal handling

2026-01-13 20:59:15 -08:00

ready_test.go

fix(ready): filter formula scaffolds from gt ready output (gt-579)

2026-01-16 15:38:08 -08:00

ready.go

feat(wisp): add misclassified wisp detection and defense-in-depth filtering (#833)

2026-01-20 20:20:49 -08:00

refinery_test.go

feat(refinery,boot): add --agent flag for model selection (#469)

2026-01-13 13:14:47 -08:00

refinery.go

refactor(witness,refinery): ZFC-compliant state management

2026-01-20 20:00:56 -08:00

release.go

…

resume.go

fix(resume): capture error in handoff message fallback (#583)

2026-01-16 15:27:38 -08:00

rig_config.go

…

rig_detect.go

Fix GT_ROOT export for beads formula search compatibility (#718)

2026-01-21 19:50:38 -08:00

rig_dock.go

fix(rig): dock/undock require main branch to prevent silent failures

2026-01-22 21:27:38 -08:00

rig_helpers.go

…

rig_integration_test.go

test(rig): add tests for agent bead creation during rig add (#578)

2026-01-16 15:23:35 -08:00

rig_park.go

feat(rig): support parking multiple rigs in single call

2026-01-12 17:44:37 -08:00

rig_quick_add_test.go

fix: respect GT_TOWN_ROOT in quick-add command (#840)

2026-01-21 10:31:16 -08:00

rig_quick_add.go

fix: respect GT_TOWN_ROOT in quick-add command (#840)

2026-01-21 10:31:16 -08:00

rig.go

fix(witness,rig): code review cleanup

2026-01-20 20:19:05 -08:00

role_e2e_test.go

feat: add RoleEnvVars and improve gt role CLI

2026-01-09 21:52:09 -08:00

role.go

feat(roles): add config-based role definition system (Phase 1)

2026-01-20 12:57:46 -08:00

root.go

fix(stale): enable stale binary warning and fix source detection

2026-01-24 20:52:27 -08:00

routes_jsonl_corruption_test.go

fix(beads): prevent routes.jsonl corruption and add doctor check for rig-level routes.jsonl (#377)

2026-01-12 01:45:26 -08:00

seance_test.go

fix: update test assertions and set BEADS_DIR in EnsureCustomTypes (#853)

2026-01-22 16:43:21 -08:00

seance.go

fix(seance): add tests and fix race condition in session index (#864)

2026-01-21 19:30:49 -08:00

session.go

Skip dot dirs when scanning polecats

2026-01-08 22:10:40 +13:00

shell.go

feat: Set and Forget - Seamless Gas Town Integration (#255)

2026-01-08 20:25:01 -08:00

show.go

feat(cli): add 'gt show' command for inspecting beads

2026-01-15 19:19:13 -08:00

sling_288_test.go

fix: update test assertions and set BEADS_DIR in EnsureCustomTypes (#853)

2026-01-22 16:43:21 -08:00

sling_batch.go

fix(sling): auto-apply mol-polecat-work (#288) and fix wisp orphan lifecycle bug (#842) (#859)

2026-01-21 20:52:26 -08:00

sling_convoy.go

fix(sling): don't show closed convoy tracking

2026-01-21 18:04:11 -08:00

sling_dog.go

refactor(sling): split 1560-line file into 7 focused modules

2026-01-12 03:11:59 -08:00

sling_formula.go

Fixing unit tests on windows (#813)

2026-01-20 14:17:35 -08:00

sling_helpers.go

fix(sling): auto-apply mol-polecat-work (#288) and fix wisp orphan lifecycle bug (#842) (#859)

2026-01-21 20:52:26 -08:00

sling_target.go

refactor(sling): split 1560-line file into 7 focused modules

2026-01-12 03:11:59 -08:00

sling_test.go

Fixing unit tests on windows (#813)

2026-01-20 14:17:35 -08:00

sling.go

fix(sling): auto-apply mol-polecat-work (#288) and fix wisp orphan lifecycle bug (#842) (#859)

2026-01-21 20:52:26 -08:00

stale.go

feat(stale): add gt stale command for binary staleness check

2026-01-12 03:10:58 -08:00

start_orphan_unix.go

fix(cmd): extract orphan cleanup to platform-specific files (#835)

2026-01-20 22:34:37 -08:00

start_orphan_windows.go

fix(cmd): extract orphan cleanup to platform-specific files (#835)

2026-01-20 22:34:37 -08:00

start.go

fix: clean up orphaned tmux sessions at gt start time

2026-01-22 21:42:27 -08:00

status_test.go

…

status.go

Fix bd daemon command syntax and flags (#522)

2026-01-17 00:00:50 -08:00

statusline_test.go

…

statusline.go

feat: add aliases and deacon status line display

2026-01-21 22:40:10 -08:00

swarm.go

fix(polecat): kill orphan sessions and clear stale hooks during allocation (#448)

2026-01-13 13:37:00 -08:00

synthesis_test.go

Fixing unit tests on windows (#813)

2026-01-20 14:17:35 -08:00

synthesis.go

codex

2026-01-08 12:36:54 -05:00

tap_guard.go

refactor(hooks): rename to gt tap guard pr-workflow

2026-01-19 11:21:54 -08:00

tap.go

refactor(hooks): rename to gt tap guard pr-workflow

2026-01-19 11:21:54 -08:00

test_helpers_test.go

Fixing unit tests on windows (#813)

2026-01-20 14:17:35 -08:00

thanks.go

feat(ui): import comprehensive UX system from beads

2026-01-09 22:46:06 -08:00

theme.go

…

town_cycle.go

…

trail.go

feat(identity): add gt commit wrapper and gt trail command

2026-01-13 19:34:29 -08:00

uninstall.go

feat: Set and Forget - Seamless Gas Town Integration (#255)

2026-01-08 20:25:01 -08:00

unsling.go

fix(sling): remove obsolete --naked flag

2026-01-11 22:23:21 -08:00

up_test.go

perf(up): parallelize all agent startup with concurrency limit (#476)

2026-01-13 13:46:50 -08:00

up.go

fix(rig): respect parked/docked status in gt up and gt rig start

2026-01-17 00:50:46 -08:00

version.go

chore(release): v0.5.0

2026-01-21 23:05:00 -08:00

whoami.go

…

witness_test.go

feat: add witness start agent override

2026-01-09 21:56:53 -08:00

witness.go

fix(tmux): use KillSessionWithProcesses to prevent zombie bash processes

2026-01-20 20:45:58 -08:00

worktree.go

…