fix .agent commits

new-project/SKILL.md

@@ -60,7 +60,7 @@ applying **only your branch's** stack section.
 
 #### Common (all types)
 - `uv` project: `pyproject.toml`, `src/<name>/` package layout, `[project.scripts]` entry point where a CLI/library applies.
-- `.gitignore` that **includes `.agent/`** and `.agent/phase-sessions/`.
+- `.gitignore` that **includes `.agent/phase-sessions/` and `.agent/pipeline.log`** — but never `.agent/` itself (the phase roadmap is tracked and committed).
 - Multi-stage `Containerfile` (assumes `podman`/`docker`).
 - `README.md` with `uv` + configuration instructions.
 - **Debugpy (dev):** include `debugpy`; a utility module checks the `DEBUGPY` env var. Default (`DEBUGPY=0`/unset) → **not** imported, minimal overhead. `DEBUGPY=1` → import and listen (e.g. port 5678) without blocking.
@@ -125,6 +125,11 @@ Create with file tools:
 Do **not** create `.agent/validate.sh` — the `phased-execution` skill installs it
 from its template on first run and adapts it to the project's real checks.
 
+- **Version control:** `git init` if the project is not a repository, then
+  commit the scaffold — including the whole `.agent/` tree (tracked, never
+  git-ignored; only `.agent/phase-sessions/` and `.agent/pipeline.log` are
+  ignored) — with a Conventional Commits message, always `--no-gpg-sign`.
+
 Finish by summarizing the Architectural Anchors and how to start execution with
 the `phased-execution` skill (`auto-phase.sh`).