Replace flat shutil.copy2 apply with spec-aligned git worktree flow
(specification.md §13225-13276):
Execute phase: creates an isolated git worktree via GitWorktreeSandbox
for the plan's linked git-checkout resource. LLM file output is
written to the worktree and committed on branch
cleveragents/plan-<plan_id> — no merge yet.
Apply phase: merges the worktree branch into the project's current
branch via git merge. Prints spec-aligned panels:
- Apply Summary: Plan ID, artifacts count, insertions/deletions,
project name, applied-at timestamp
- Sandbox Cleanup: worktree removed, branch merged to main
- Footer: ✓ OK Changes applied
Non-git projects (fs-directory resources) fall back to the original
flat directory sandbox with shutil.copy2.
Also fixes:
- context_tier_hydrator metadata types (int/float → string) that
caused Pydantic validation errors during context assembly
- A2A facade duplicate execute dispatch (idempotent handler)
- Logs actual error from context assembly failures
ISSUES CLOSED: #4454
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>
hamza.khyari
freemo