fix .agent commits

convert-to-phased/SKILL.md

@@ -88,7 +88,7 @@ Create (or merge into what already exists) with file tools:
 - **`AGENTS.md`** — the five base rules below, plus the domain additions.
 - **`.agent/phases/todo/`** — the roadmap from Phase 5.
 - **`.agent/phases/complete/`** — create the directory, leave it empty (it mirrors `todo/` as phases complete).
-- **`.gitignore`** — add `.agent/` and `.agent/phase-sessions/` if missing.
+- **`.gitignore`** — add `.agent/phase-sessions/` and `.agent/pipeline.log` if missing (never `.agent/` itself — the planning tree is tracked and committed); if an existing `.gitignore` has a `.agent/` ignore line, remove it.
 
 **AGENTS.md base rules:**
 
@@ -189,9 +189,9 @@ final pass is where they are verified end-to-end):
 ## Phase 6 — Version Control & Hand-Off
 
 - Git is mandatory: `git init` if the project is not a repository.
-- Commit the conversion — `AGENTS.md`, `.gitignore`, and any other modified
-  non-`.agent/` files (the `.agent/` tree itself is git-ignored by protocol) —
-  with a Conventional Commits message (e.g. `chore(agent): adopt phased
+- Commit the conversion — `AGENTS.md`, `.gitignore`, the whole `.agent/`
+  tree (it is tracked, not git-ignored), and any other modified files — with
+  a Conventional Commits message (e.g. `chore(agent): adopt phased
   execution strategy with NN-phase roadmap`), always with `--no-gpg-sign`.
 - Record in `AGENTS.md`: atomic commit at the conclusion of every completed
   phase, Conventional Commits messages, and `--no-gpg-sign` on every