diff --git a/CodexHelper b/CodexHelper
new file mode 100755
index 0000000..43f7aa5
--- /dev/null
+++ b/CodexHelper
@@ -0,0 +1,99 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+SCRIPT_DIR="$(cd "$(dirname "$0")" && pwd)"
+
+die() { echo "error: $*" >&2; exit 1; }
+note() { echo "$*" >&2; }
+
+find_helper_repo_root() {
+  # Walk upwards to find a dir that looks like the helper repo
+  local d="$(pwd)"
+  while [ "$d" != "/" ]; do
+    if [ -d "$d/collab" ] && [ -f "$d/prompts/global/system.md" ]; then
+      printf '%s' "$d"
+      return 0
+    fi
+    d="$(dirname "$d")"
+  done
+  return 1
+}
+
+print_help() {
+  cat <<EOF
+CodexHelper — wrapper for codex-cli with modes and scaffolding
+
+Usage:
+  CodexHelper new-mode --name <ModeName>
+  CodexHelper new-project --mode <ModeName> --name <project-name> --path <dir> [--force]
+  CodexHelper run [--mode <ModeName>] [--prompt-file <file>] [--config <file>] [--sandbox <mode>] [--full-auto]
+  CodexHelper --help
+
+Notes:
+  - Inside the CodexHelper repo, only 'new-mode' is allowed.
+  - Outside the repo, 'new-project' and 'run' are allowed.
+EOF
+}
+
+require_outside_repo_for() {
+  local subcmd="$1"
+  if find_helper_repo_root >/dev/null 2>&1; then
+    if [ "$subcmd" != "new-mode" ]; then
+      die "Only 'new-mode' is allowed when running inside the CodexHelper repository"
+    fi
+  fi
+}
+
+detect_codex() {
+  if [ -n "${CODEX_BIN:-}" ]; then echo "$CODEX_BIN"; return 0; fi
+  if command -v codex >/dev/null 2>&1; then echo codex; return 0; fi
+  if command -v codex-cli >/dev/null 2>&1; then echo codex-cli; return 0; fi
+  die "No codex binary found. Set CODEX_BIN or install 'codex'/'codex-cli' in PATH."
+}
+
+cmd_new_mode() {
+  local name=""
+  while [ $# -gt 0 ]; do
+    case "$1" in
+      --name) name="$2"; shift 2;;
+      --force) FORCE=1; shift;;
+      --help|-h) print_help; exit 0;;
+      *) die "Unknown option for new-mode: $1";;
+    esac
+  done
+  [ -n "$name" ] || die "--name is required"
+  local dir="modes/$name"
+  if [ -e "$dir" ] && [ -z "${FORCE:-}" ]; then
+    die "Mode '$name' already exists. Use --force to overwrite."
+  fi
+  mkdir -p "$dir"
+  : >"$dir/mode.md"
+  : >"$dir/defaults.yaml"
+  note "Created $dir/mode.md and $dir/defaults.yaml"
+}
+
+cmd_new_project() {
+  require_outside_repo_for new-project
+  # Implementation follows in later milestones
+  die "Not yet implemented: new-project (per plan)."
+}
+
+cmd_run() {
+  require_outside_repo_for run
+  # Implementation follows in later milestones
+  die "Not yet implemented: run (per plan)."
+}
+
+main() {
+  local subcmd="${1:-}"; if [ -z "$subcmd" ] || [ "$subcmd" = "--help" ] || [ "$subcmd" = "-h" ]; then
+    print_help; exit 0
+  fi
+  case "$subcmd" in
+    new-mode) shift; cmd_new_mode "$@";;
+    new-project) shift; cmd_new_project "$@";;
+    run) shift; cmd_run "$@";;
+    *) die "Unknown subcommand: $subcmd";;
+  esac
+}
+
+main "$@"
diff --git a/README.md b/README.md
index 1fa6b28..806a0e3 100644
--- a/README.md
+++ b/README.md
@@ -1,3 +1,18 @@
-# ChatGPTScaffolding
+# ChatGPTScaffolding / CodexHelper
 
-Scaffolding (prompts/personas/modes/rules etc) around codex-cli. Tuned for @ReachableCEO needs as a solo entrepreneur. Developed from scratch in an afternoon after three weeks of intense AI usage across multiple providers/systems.
\ No newline at end of file
+Scaffolding (prompts/personas/modes/rules etc) around codex-cli. Tuned for @ReachableCEO needs as a solo entrepreneur.
+
+CodexHelper adds:
+- Modes (global/mode/project prompts)
+- Project scaffolding
+- Prompt composition and safe defaults
+- Governance: TDD, zero technical debt, plan-first via Questions → Proposal → Plan
+
+Status: Phase 1 in progress — `new-mode` implemented; `new-project` and `run` coming next.
+
+Quickstart (dev)
+- Run tests: `scripts/test.sh` (uses bats if available)
+- Show help: `./CodexHelper --help`
+- Create a demo mode (in this repo): `./CodexHelper new-mode --name Demo`
+
+See `docs/wrapper.md` and `prompts/global/` for details and governance rules.
diff --git a/collab/proposals/01-codexhelper.llm.md b/collab/proposals/01-codexhelper.llm.md
index 77737c5..3d42e98 100644
--- a/collab/proposals/01-codexhelper.llm.md
+++ b/collab/proposals/01-codexhelper.llm.md
@@ -15,8 +15,9 @@
 - Layout (project): `AGENTS.md`, `prompts/{project.md,style.md?}`, `prompts/_mode/`, `codex.yaml`, `codex.sh`, `runs/`.
 - Governance/Propagation: non-project-specific workflow changes get recorded in `prompts/global/` and seed AGENTS templates; proposal/plan updated so scaffolding includes them.
 - TDD Governance: adopt test-driven development with full unit/integration tests for all features in this repo and generated projects; tests written first and required for acceptance.
-- Zero Technical Debt: safety first; no technical debt; production-ready at all times; no deferring tests/docs/refactors; use sub-agents as needed.
+ - Zero Technical Debt: safety first; no technical debt; production-ready at all times; no deferring tests/docs/refactors; use sub-agents as needed.
  - Planning/Architecture Governance: plan ahead via Questions→Proposal→Plan; maintain a global architecture/module map; implement module-by-module; avoid refactors except when assumptions change and plans/docs are updated.
+  - Clean Root Governance: keep repo root minimal; organize assets under `docs/`, `templates/`, `collab/`, `prompts/`, `modes/`, `scripts/`, `meta/`.
 - Phase 1 acceptance:
   - new-mode creates mode skeleton
   - new-project scaffolds without overwrites
@@ -28,6 +29,7 @@
   - tests: unit/integration tests (bats) cover CLI flows and guardrails; TDD observed
   - zero debt: docs/tests included with every feature; no pending TODOs/deferrals; production-ready criteria met
   - planning: architecture/module map documented; module implementations follow approved plan with no unplanned refactors
+  - clean root: root remains minimal; scaffolding organizes assets under subdirectories
 \n+## Approval — Tick All That Apply
 
 - Subcommands approved: `new-project`, `run`, `new-mode` [ ]
diff --git a/collab/proposals/01-codexhelper.md b/collab/proposals/01-codexhelper.md
index b00ff45..1ef2726 100644
--- a/collab/proposals/01-codexhelper.md
+++ b/collab/proposals/01-codexhelper.md
@@ -41,7 +41,8 @@ Purpose: Implement a bash wrapper (CodexHelper) around codex-cli with “modes
 - Governance/Propagation: maintain global norms in `prompts/global/` and seed AGENTS templates; reflect such changes in proposal/plan for scaffolding.
 - TDD Governance: enforce test-driven development; require unit/integration tests for all features here and in generated projects.
 - Zero Technical Debt: safety first; always production-ready; no deferring tests/docs/refactors; leverage sub-agents when needed.
- - Planning/Architecture Governance: plan ahead via Questions→Proposal→Plan; keep a global architecture/module map; implement module-by-module; avoid refactors except when assumptions change and plans/docs are updated.
+- Planning/Architecture Governance: plan ahead via Questions→Proposal→Plan; keep a global architecture/module map; implement module-by-module; avoid refactors except when assumptions change and plans/docs are updated.
+ - Clean Root Governance: keep repo root minimal; organize assets under `docs/`, `templates/`, `collab/`, `prompts/`, `modes/`, `scripts/`, `meta/`.
 
 ## Project Layout (generated)
 - `AGENTS.md` (from `templates/project/_shared/AGENTS.md`)
@@ -100,10 +101,11 @@ Purpose: Implement a bash wrapper (CodexHelper) around codex-cli with “modes
 - Precedence works: CLI options override env, which override project config, which override mode defaults.
 - Running `CodexHelper run` in this repo prints an error guiding usage.
  - Project scaffold includes `AGENTS.md` copied from `templates/project/_shared/AGENTS.md`.
-  - `prompts/global/{system.md, system.llm.md}` exist and are included in composition.
-  - Governance/Propagation honored: when norms change, update `prompts/global/` and AGENTS templates; log in DevLog.
-  - TDD honored: a test suite (bats) covers CLI flows and guardrails; tests pass.
-  - Zero Debt honored: code, tests, and docs complete; no debt items remain.
+- `prompts/global/{system.md, system.llm.md}` exist and are included in composition.
+- Governance/Propagation honored: when norms change, update `prompts/global/` and AGENTS templates; log in DevLog.
+- TDD honored: a test suite (bats) covers CLI flows and guardrails; tests pass.
+- Zero Debt honored: code, tests, and docs complete; no debt items remain.
+ - Clean Root honored: only essential files at root; scaffolding places assets under subdirectories.
 
 ## Open Items for Confirmation
 - Template coverage: include `prompts/style.md` by default? (we’ll include as optional, empty file)
diff --git a/docs/devlog/DEVLOG_LLM.md b/docs/devlog/DEVLOG_LLM.md
index 0c0f4de..9ade76b 100644
--- a/docs/devlog/DEVLOG_LLM.md
+++ b/docs/devlog/DEVLOG_LLM.md
@@ -162,3 +162,12 @@ This log is concise and structured for quick machine parsing and summarization.
   - Updated proposal/plan to add architecture/module map deliverable and acceptance
 - next:
   - Add `docs/architecture.md` early in implementation per plan
+
+## 2025-09-17T16:38Z
+- context: Root cleanliness governance and marker removal
+- actions:
+  - Added clean-root rule to system prompts and AGENTS templates
+  - Removed `.codexhelper-repo`; replaced guard detection with repo-structure heuristic
+  - Updated CLI guardrail tests accordingly
+- next:
+  - Keep root minimal going forward; store assets under subdirectories
diff --git a/docs/wrapper.md b/docs/wrapper.md
new file mode 100644
index 0000000..d353813
--- /dev/null
+++ b/docs/wrapper.md
@@ -0,0 +1,21 @@
+# 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.
+
diff --git a/meta/AGENTS.seed.llm.md b/meta/AGENTS.seed.llm.md
index a12b864..122e266 100644
--- a/meta/AGENTS.seed.llm.md
+++ b/meta/AGENTS.seed.llm.md
@@ -13,3 +13,5 @@
 - Zero Technical Debt: Safety first; no technical debt; always production-ready; no deferring tests/docs/refactors; TDD by default; keep docs current.
  
 - Planning/Architecture: Plan via Questions→Proposal→Plan; maintain global architecture/module map; implement module-by-module; avoid refactors unless assumptions change and plans/docs are updated.
+ 
+- Clean Roots: Keep project root minimal; use `docs/`, `templates/`, `prompts/`, `scripts/`, etc.; avoid ad-hoc root files.
diff --git a/meta/AGENTS.seed.md b/meta/AGENTS.seed.md
index 168049b..02f504a 100644
--- a/meta/AGENTS.seed.md
+++ b/meta/AGENTS.seed.md
@@ -71,3 +71,7 @@ Customize this AGENTS.md to fit your project specifics while preserving the one-
 - Plan ahead: use Questions → Proposal → Plan to align before coding.
 - Maintain a project architecture/module map and document boundaries.
 - Implement module-by-module per plan; avoid refactors, except when new info requires plan/doc updates.
+
+## Clean Repository Roots
+- Keep the project root minimal and tidy. Prefer directories over many files at root.
+- Place docs, templates, prompts, and scripts under dedicated subdirectories.
diff --git a/modes/DemoMode/defaults.yaml b/modes/DemoMode/defaults.yaml
new file mode 100644
index 0000000..e69de29
diff --git a/modes/DemoMode/mode.md b/modes/DemoMode/mode.md
new file mode 100644
index 0000000..e69de29
diff --git a/nm.err b/nm.err
new file mode 100644
index 0000000..1076622
--- /dev/null
+++ b/nm.err
@@ -0,0 +1 @@
+Created modes/DemoMode/mode.md and modes/DemoMode/defaults.yaml
diff --git a/nm.out b/nm.out
new file mode 100644
index 0000000..e69de29
diff --git a/nm2.err b/nm2.err
new file mode 100644
index 0000000..89fa250
--- /dev/null
+++ b/nm2.err
@@ -0,0 +1 @@
+error: Mode 'DemoMode' already exists. Use --force to overwrite.
diff --git a/nm2.out b/nm2.out
new file mode 100644
index 0000000..e69de29
diff --git a/nm3.err b/nm3.err
new file mode 100644
index 0000000..1076622
--- /dev/null
+++ b/nm3.err
@@ -0,0 +1 @@
+Created modes/DemoMode/mode.md and modes/DemoMode/defaults.yaml
diff --git a/nm3.out b/nm3.out
new file mode 100644
index 0000000..e69de29
diff --git a/np.err b/np.err
new file mode 100644
index 0000000..3856018
--- /dev/null
+++ b/np.err
@@ -0,0 +1 @@
+error: Only 'new-mode' is allowed when running inside the CodexHelper repository
diff --git a/np.out b/np.out
new file mode 100644
index 0000000..e69de29
diff --git a/prompts/global/system.llm.md b/prompts/global/system.llm.md
index 3dc6146..ef10378 100644
--- a/prompts/global/system.llm.md
+++ b/prompts/global/system.llm.md
@@ -26,3 +26,6 @@
 - Plan before coding via Questions → Proposal → Plan.
 - Maintain a global architecture/module map; document boundaries.
 - Implement module-by-module; avoid refactors except when assumptions change and plans/docs are updated.
+
+-- Clean Roots --
+- Keep repo root minimal; store assets under `docs/`, `templates/`, `collab/`, `prompts/`, `modes/`, `scripts/`, `meta/`. Avoid ad-hoc root files.
diff --git a/prompts/global/system.md b/prompts/global/system.md
index 1833b7b..ded27e6 100644
--- a/prompts/global/system.md
+++ b/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).
 
diff --git a/run.err b/run.err
new file mode 100644
index 0000000..3856018
--- /dev/null
+++ b/run.err
@@ -0,0 +1 @@
+error: Only 'new-mode' is allowed when running inside the CodexHelper repository
diff --git a/run.out b/run.out
new file mode 100644
index 0000000..e69de29
diff --git a/scripts/test.sh b/scripts/test.sh
new file mode 100755
index 0000000..e3647f7
--- /dev/null
+++ b/scripts/test.sh
@@ -0,0 +1,33 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+ROOT_DIR="$(cd "$(dirname "$0")/.." && pwd)"
+
+if command -v bats >/dev/null 2>&1; then
+  exec bats "$ROOT_DIR/tests"
+fi
+
+# Minimal internal test runner (fallback when bats is not installed)
+echo "[info] bats not found; using internal test runner" >&2
+
+failures=0
+total=0
+
+for t in "$ROOT_DIR"/tests/*.sh; do
+  [ -f "$t" ] || continue
+  total=$((total+1))
+  echo "[run] $t"
+  if bash "$t"; then
+    echo "[ok]  $t"
+  else
+    echo "[fail] $t" >&2
+    failures=$((failures+1))
+  fi
+done
+
+echo "[summary] total=$total failures=$failures"
+if [ "$failures" -ne 0 ]; then
+  exit 1
+fi
+exit 0
+
diff --git a/templates/project/_shared/AGENTS.md b/templates/project/_shared/AGENTS.md
index 70e545e..62dfc95 100644
--- a/templates/project/_shared/AGENTS.md
+++ b/templates/project/_shared/AGENTS.md
@@ -46,3 +46,6 @@ This file is copied by scaffolding into new projects. Edit to suit the project w
 - Plan ahead via Questions → Proposal → Plan to align before coding.
 - Maintain an architecture/module map and clear module boundaries.
 - Implement module-by-module; refactor only when new information requires plan/doc updates.
+
+## Clean Repository Roots
+- Keep the project root minimal and tidy; prefer organizing assets under subdirectories (docs, templates, prompts, scripts, etc.).
diff --git a/tests/00_cli_guardrails.sh b/tests/00_cli_guardrails.sh
new file mode 100644
index 0000000..83a4ab8
--- /dev/null
+++ b/tests/00_cli_guardrails.sh
@@ -0,0 +1,23 @@
+#!/usr/bin/env bash
+set -euo pipefail
+ROOT_DIR="$(cd "$(dirname "$0")/.." && pwd)"
+. "$ROOT_DIR/tests/helpers/assert.sh"
+
+cd "$ROOT_DIR"
+
+# 1) Help prints usage and exits 0
+out="$(bash ./CodexHelper --help 2>&1 || true)"
+echo "$out" | grep -q "CodexHelper" || { echo "help text missing" >&2; exit 1; }
+
+# 2) Guardrails: inside helper repo, run/new-project should be blocked
+if bash ./CodexHelper run 2>run.err 1>run.out; then
+  echo "run should fail in helper repo" >&2; exit 1
+fi
+grep -q "Only 'new-mode'" run.err || { echo "missing guardrail message for run" >&2; exit 1; }
+
+if bash ./CodexHelper new-project --mode Demo --name demo --path /tmp 2>np.err 1>np.out; then
+  echo "new-project should fail in helper repo" >&2; exit 1
+fi
+grep -q "Only 'new-mode'" np.err || { echo "missing guardrail message for new-project" >&2; exit 1; }
+
+exit 0
diff --git a/tests/01_new_mode.sh b/tests/01_new_mode.sh
new file mode 100644
index 0000000..13b17de
--- /dev/null
+++ b/tests/01_new_mode.sh
@@ -0,0 +1,33 @@
+#!/usr/bin/env bash
+set -euo pipefail
+ROOT_DIR="$(cd "$(dirname "$0")/.." && pwd)"
+
+cd "$ROOT_DIR"
+
+mode="DemoMode"
+dir="modes/$mode"
+
+# Clean up from prior runs
+rm -rf "$dir"
+
+# Create new mode
+if ! bash ./CodexHelper new-mode --name "$mode" >nm.out 2>nm.err; then
+  echo "new-mode failed unexpectedly" >&2; exit 1
+fi
+
+[ -f "$dir/mode.md" ] || { echo "missing $dir/mode.md" >&2; exit 1; }
+[ -f "$dir/defaults.yaml" ] || { echo "missing $dir/defaults.yaml" >&2; exit 1; }
+
+# Running again without --force should fail
+if bash ./CodexHelper new-mode --name "$mode" >nm2.out 2>nm2.err; then
+  echo "new-mode should have failed on overwrite without --force" >&2; exit 1
+fi
+grep -qi "already exists" nm2.err || { echo "missing overwrite message" >&2; exit 1; }
+
+# With --force should succeed
+if ! bash ./CodexHelper new-mode --name "$mode" --force >nm3.out 2>nm3.err; then
+  echo "new-mode --force failed unexpectedly" >&2; exit 1
+fi
+
+exit 0
+
diff --git a/tests/helpers/assert.sh b/tests/helpers/assert.sh
new file mode 100644
index 0000000..15fa790
--- /dev/null
+++ b/tests/helpers/assert.sh
@@ -0,0 +1,24 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+fail() { echo "ASSERTION FAILED: $*" >&2; return 1; }
+
+assert_eq() {
+  local expected="$1" actual="$2"; shift 2
+  if [ "$expected" != "$actual" ]; then
+    fail "expected='$expected' actual='$actual' $*"
+  fi
+}
+
+assert_contains() {
+  local haystack="$1" needle="$2"; shift 2
+  if ! grep -Fq -- "$needle" <<<"$haystack"; then
+    fail "did not find '$needle' in output"
+  fi
+}
+
+run_cmd() {
+  local out err rc
+  out="$({ err=$( { "$@"; } 2>&1 1>&3 ); rc=$?; echo "$err" >&2; echo $rc >&4; } 3>&1 4>&1)"
+}
+