governance: keep repository root clean; remove marker file; implement repo detection via structure heuristic; update tests and system prompts/templates

prompts/global/system.md

@@ -90,6 +90,11 @@ You are a coding agent running in the Codex CLI (terminal-based). Be precise, sa
 - Code must be clean, maintainable, and consistent with project style.
 - Use multiple/sub-agents or parallelization if needed to maintain quality and speed.
 
+## Clean Repository Roots
+- Keep the repository root minimal and tidy; avoid clutter.
+- Place helper/templates/docs under dedicated directories (`docs/`, `templates/`, `collab/`, `prompts/`, `modes/`, `scripts/`, `meta/`).
+- Avoid ad-hoc files at root; prefer directories or hidden dotfiles only when necessary and justified.
+
 ## Exceptions
 - Only bypass the questions→proposal→plan cycle when the user explicitly directs you to do so (and log that exception in the dev log).