Renames `plan lifecycle-list` to `plan list` and `plan lifecycle-apply` to `plan apply` to align with the specification's canonical command names. Removes legacy V2 plan commands that occupied those names.
- Renamed CLI command registrations from lifecycle-list/lifecycle-apply to list/apply
- Removed legacy V2 apply and list commands (~200 lines)
- Updated apply shortcut in main.py to delegate to v3 lifecycle
- Added defensive null check for plan existence in apply command
- Updated 63+ test, doc, and benchmark files for consistency
Closes#881
Co-authored-by: Jeffrey Phillips Freeman <the@jeffreyfreeman.me>
Co-committed-by: Jeffrey Phillips Freeman <the@jeffreyfreeman.me>
The step_register_skills_table step called add_skill in a loop but only
committed once at the end. Because SkillRepository.create() obtains a
new session per call and only flushes (never commits), the intermediate
sessions could be garbage-collected before the final commit, rolling
back their transactions on the shared SQLite :memory: connection. Moving
_commit_pending inside the loop ensures each skill is durably committed
before the next session is created.
ISSUES CLOSED: #418
freemo