fix .agent commits

todo-to-phased/SKILL.md

@@ -138,7 +138,7 @@ tools:
   5. "Strictly adhere to the **LOCKED DECISIONS** listed in `.agent/PLAN.md`."
 - **`.agent/phases/todo/`** and **`.agent/phases/complete/`** (the latter
   created empty).
-- **`.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.
 
 Then write one phase directory per confirmed phase at
 `.agent/phases/todo/NN_name/`, numbered from the audit's "next phase
@@ -169,12 +169,14 @@ roadmap table does not list these appended phases.
 
 - Git is mandatory: `git init` if the project is not a repository.
 - **Clear the TODO list** — the items are now phases, so the TODO file no
-  longer holds the plan. Replace its entire item list with a one-line
-  pointer (e.g. `Phased on YYYY-MM-DD — items now live in
-  .agent/phases/todo/`); never delete the file itself.
-- Commit the conversion — `AGENTS.md`, the cleared TODO file, 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): phase
+  longer holds the plan. Overwrite the file with a clean, empty document:
+  just a single top-level title `# TODO` and nothing else (no pointer
+  line, no leftover items, no trailing notes). Never delete the file
+  itself — leave the empty `TODO.md` in place so the workspace keeps a
+  known, stable landing spot for future todos.
+- Commit the conversion — `AGENTS.md`, the cleared TODO file, the whole
+  `.agent/` tree (it is tracked, not git-ignored), and any other modified
+  files — with a Conventional Commits message (e.g. `chore(agent): phase
   roadmap from TODO.md, NN phases`), always with `--no-gpg-sign`.
 
 Finish by summarizing: the anchors (Protocol A), the phase list (number,