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

docs/wrapper.md

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+# CodexHelper Wrapper — Usage and Design (Phase 1)
+
+Overview
+- CodexHelper wraps `codex`/`codex-cli` to provide modes, project scaffolding, and prompt composition.
+- Governance: TDD, zero technical debt, plan-first via Questions → Proposal → Plan, production-ready always.
+
+Status (Phase 1 in progress)
+- Implemented: `new-mode` scaffolder (repo-only), CLI skeleton, guardrails.
+- Pending (per plan): `new-project`, `run`, config precedence (YAML+yq).
+
+CLI
+- Help: `./CodexHelper --help`
+- Repo-only: `./CodexHelper new-mode --name <ModeName> [--force]`
+- Outside-repo (pending): `CodexHelper new-project --mode <ModeName> --name <project-name> --path <dir> [--force]`
+- Outside-repo (pending): `CodexHelper run [--mode <ModeName>] [--prompt-file <file>] [--config <file>] [--sandbox <mode>] [--full-auto]`
+
+Development
+- Tests: run `scripts/test.sh` (uses bats if available, falls back to internal runner).
+- Follow TDD: write failing tests first, make them pass, refactor.
+- Keep `docs/architecture.md` and README up to date as features land.
+