fix(install): make install.sh idempotent + add onboard-project.sh

- install.sh: no longer exits early when ~/.automaton exists.
  Skips the clone but runs all setup (VRAM detection, guards,
  self-improvement loop, virtualenv). Both curl|bash and
  git-clone + ./install.sh now work correctly.
- onboard-project.sh: new script that bootstraps automaton in a
  project — creates .automaton/ skeleton, detects models, writes
  config.md, inits git, installs hooks, adds .gitignore entries.
- README.md: fix install flow docs (curl|bash + clone-then-run),
  add onboard-project.sh as Option A for project setup

README.md

@@ -6,22 +6,28 @@ A contract-based operating system for LLM agents, designed to enforce discipline
 
 Before you can use the framework in any project, you must install the core logic into your local environment.
 
-**Run these commands in your terminal:**
+Choose one of the following methods:
+
+### Option A: One-liner (curl pipe, recommended)
 
 ```bash
-# Clone the framework into the global config directory
+curl -fsSL https://raw.githubusercontent.com/<your-org>/automaton/main/scripts/install.sh | bash -s -- <your-git-url>
-git clone <your-git-url> ~/.automaton
-
-# Enter the directory
-cd ~/.automaton
-
-# Make the installation script executable and run it
-# You must provide the git URL as the first argument
-chmod +x install.sh
-./install.sh <your-git-url>
 ```
 
-The git URL is required because the framework uses it for self-updates and the self-improvement loop. Choose carefully -- it cannot be changed later without reinstalling.
+This clones the framework to `~/.automaton/`, runs VRAM detection, installs pre-edit guards, creates the self-improvement loop, and sets up the Python virtualenv.
+
+### Option B: Clone first
+
+```bash
+git clone <your-git-url> ~/.automaton
+bash ~/.automaton/scripts/install.sh
+```
+
+The script detects that `~/.automaton` already exists, skips the clone, and runs all setup steps (VRAM detection, guards, loop, virtualenv).
+
+### Both methods do the same thing
+
+The git URL is required on fresh install because the framework uses it for self-updates and the self-improvement loop. Choose carefully -- it cannot be changed later without reinstalling.
 
 *Note: This creates the "brain" of the framework (prompts, state machines, and rules) in your home directory. A self-improvement loop is created and scheduled by default (see Loop Engineering below).*
 
@@ -49,7 +55,24 @@ If a project was set up under the old model (with copies of framework files), it
 
 Once the framework is installed globally, you must "onboard" every individual project you work on.
 
-### Option A: The Agent-Driven Way (Recommended)
+### Option A: The Onboarding Script (Recommended)
+
+```bash
+bash ~/.automaton/scripts/onboard-project.sh /path/to/project
+```
+
+This will:
+1. Create `.automaton/` skeleton if missing.
+2. Run `detect_models.py --write` to probe local models (falls back to a minimal `models.json`).
+3. Generate `config.md` with VRAM recommendations.
+4. Write `project-name.md` from the directory name.
+5. Initialize git if not already a repo.
+6. Install git hooks (pre-commit + pre-push).
+7. Add automaton entries to `.gitignore`.
+8. Run `status.py --audit` to verify the setup.
+
+### Option B: The Agent-Driven Way
+
 If you want the agent to handle the configuration for you, navigate to your project root and run:
 
 > *"Onboard this project into automaton."
@@ -60,17 +83,21 @@ The agent will automatically:
 3. Generate your `.agent.md` and `.rules.md` files.
 4. Initiate the "Exploration Ritual" to understand your codebase.
 
-### Option B: The Manual Way
+### Option C: The Manual Way
-If you prefer to set it up manually, create a `.automaton/` directory in your project root and add:
+If you prefer to set it up manually:
-- `.agent.md`: Project-specific configuration (Mode, rules, etc.).
-- `.rules.md`: Project-specific constraints and past failure modes.
 
-Then install the git pre-commit hook:
 ```bash
-ln -sf ~/.automaton/scripts/git-hooks/pre-commit .git/hooks/pre-commit
+# Create the automaton directory
+mkdir -p .automaton/tasks .automaton/loops .automaton/design
+
+# Install git hooks
+bash ~/.automaton/scripts/install-hooks.sh .
+
+# Configure your model(s)
+python3 ~/.automaton/scripts/detect_models.py --write --project .
 ```
 
-This hook blocks commits when no task is in `implement` or `doc_review` phase, preventing accidental code changes without a tracked task.
+Then add `.agent.md` and `.rules.md` for the agent.
 
 ### The Self-Improvement Loop is framework-scoped
 

scripts/automaton-cleanup.sh

@@ -1,2 +1,2 @@
 #!/usr/bin/env bash
-python3 "/Users/laptran/.automaton/scripts/status.py" --cleanup-done --days 7 --project "/private/var/folders/f5/yv0dzbnx47x3yp8sc_2519gh0000gn/T/pytest-of-laptran/pytest-127/test_uninstall_via_disabled_re0"
+python3 "/Users/laptran/.automaton/scripts/status.py" --cleanup-done --days 7 --project "/private/var/folders/f5/yv0dzbnx47x3yp8sc_2519gh0000gn/T/pytest-of-laptran/pytest-128/test_uninstall_via_disabled_re0"

scripts/install.sh

@@ -3,27 +3,39 @@ set -e
 
 FRAMEWORK_DIR="$HOME/.automaton"
 
-if [ -d "$FRAMEWORK_DIR" ]; then
-  echo "automaton already installed at $FRAMEWORK_DIR"
-  echo "Run './update.sh' to update."
-  exit 0
-fi
-
 GIT_URL="${1:-}"
-if [ -z "$GIT_URL" ]; then
+
-  echo "ERROR: Git URL required."
+if [ ! -d "$FRAMEWORK_DIR" ]; then
-  echo "Usage: ./install.sh <git-url>"
+  # Fresh install — need a Git URL to clone
-  echo "Example: ./install.sh https://github.com/user/automaton.git"
+  if [ -z "$GIT_URL" ]; then
+    echo "ERROR: Git URL required for fresh install."
+    echo ""
+    echo "Usage:"
+    echo "  curl -fsSL https://raw.githubusercontent.com/<user>/automaton/main/scripts/install.sh | bash -s -- <git-url>"
+    echo ""
+    echo "  --- or ---"
+    echo ""
+    echo "  git clone <git-url> ~/.automaton"
+    echo "  bash ~/.automaton/scripts/install.sh"
+    echo ""
+    echo "The framework is cloned to ~/.automaton. Choose your URL carefully"
+    echo "as it cannot be changed later without reinstalling."
+    exit 1
+  fi
+  echo "Cloning automaton from $GIT_URL to $FRAMEWORK_DIR..."
+  git clone "$GIT_URL" "$FRAMEWORK_DIR"
+  echo ""
+else
+  echo "automaton already installed at $FRAMEWORK_DIR — running setup steps..."
+  if [ -n "$GIT_URL" ]; then
+    echo "Note: Git URL argument ignored because ~/.automaton already exists."
+    echo "To update, run: cd ~/.automaton && ./update.sh"
+  fi
   echo ""
-  echo "The framework is cloned to ~/.automaton. Choose your URL carefully"
-  echo "as it cannot be changed later without reinstalling."
-  exit 1
 fi
 
-echo "Cloning automaton from $GIT_URL to $FRAMEWORK_DIR..."
+# --- Everything below is idempotent and runs on both fresh and existing installs ---
-git clone "$GIT_URL" "$FRAMEWORK_DIR"
 
-echo ""
 echo "=== VRAM / Context Detection ==="
 echo "Detecting your system's VRAM to recommend task decomposition settings..."
 echo ""
@@ -31,7 +43,7 @@ echo ""
 # Run VRAM detection script if it exists
 if [ -f "$FRAMEWORK_DIR/scripts/vram_detect.py" ]; then
   # Run in project-dir context so it can read framework overhead
-  detection_output=$(cd "$FRAMEWORK_DIR" && python3 "$FRAMEWORK_DIR/scripts/vram_detect.py" 2>&1)
+  detection_output=$(cd "$FRAMEWORK_DIR" && python3 "$FRAMEWORK_DIR/scripts/vram_detect.py" 2>&1 || true)
 
   # Extract JSON output (the block after "=== JSON Output ===")
   json_output=$(echo "$detection_output" | sed -n '/=== JSON Output ===/,$p' | tail -n +2)
@@ -40,12 +52,9 @@ if [ -f "$FRAMEWORK_DIR/scripts/vram_detect.py" ]; then
     echo "$detection_output"
 
     # Extract key values from JSON using Python
-    recommended_k=$(echo "$json_output" | python3 -c 'import json,sys; print(json.load(sys.stdin)["recommended_k"])')
+    recommended_k=$(echo "$json_output" | python3 -c 'import json,sys; print(json.load(sys.stdin)["recommended_k"])' 2>/dev/null || echo "?")
-    max_peak_kb=$(echo "$json_output" | python3 -c 'import json,sys; print(json.load(sys.stdin)["max_peak_context_kb"])')
+    max_peak_kb=$(echo "$json_output" | python3 -c 'import json,sys; print(json.load(sys.stdin)["max_peak_context_kb"])' 2>/dev/null || echo "?")
-    headroom=$(echo "$json_output" | python3 -c 'import json,sys; print(json.load(sys.stdin)["headroom"])')
+    headroom=$(echo "$json_output" | python3 -c 'import json,sys; print(json.load(sys.stdin)["headroom"])' 2>/dev/null || echo "?")
-    gpu_vram=$(echo "$json_output" | python3 -c 'import json,sys; print(json.load(sys.stdin)["gpu_vram_gb"])')
-    ram_gb=$(echo "$json_output" | python3 -c 'import json,sys; print(json.load(sys.stdin)["ram_gb"])')
-    model_context=$(echo "$json_output" | python3 -c 'import json,sys; print(json.load(sys.stdin)["model_context_kb"])')
     
     echo ""
     echo "=== Recommended VRAM Configuration ==="
@@ -72,11 +81,8 @@ echo ""
 echo "Installation complete."
 echo ""
 echo "Next steps:"
-echo "  1. cd into a project and run the onboarding prompt"
+echo "  1. Onboard a project: bash ~/.automaton/scripts/onboard-project.sh /path/to/project"
-echo "  2. In each project that uses git, install the automaton hooks:"
+echo "  2. Or tell your agent: 'Onboard this project into automaton'"
-echo "     bash ~/.automaton/scripts/install-hooks.sh /path/to/project"
-echo ""
-echo "These hooks block commits and pushes when no task is in an edit-allowed phase."
 echo ""
 
 # Register pre-edit guards for detected harnesses

scripts/onboard-project.sh

@@ -0,0 +1,184 @@
+#!/usr/bin/env bash
+# onboard-project.sh — Bootstrap automaton in a new or existing project.
+#
+# Usage:
+#   bash ~/.automaton/scripts/onboard-project.sh /path/to/project
+#
+# Creates .automaton/ skeleton, detects models, creates config, inits git,
+# installs hooks, and verifies everything works.
+
+set -euo pipefail
+
+FRAMEWORK_DIR="$HOME/.automaton"
+PROJECT_DIR="${1:-}"
+
+# Colors
+RED='\033[0;31m'
+GREEN='\033[0;32m'
+YELLOW='\033[1;33m'
+BLUE='\033[0;34m'
+NC='\033[0m' # No Color
+
+info()  { echo -e "${BLUE}INFO:${NC} $1"; }
+ok()    { echo -e "${GREEN}OK:${NC}   $1"; }
+warn()  { echo -e "${YELLOW}WARN:${NC} $1"; }
+error() { echo -e "${RED}ERROR:${NC} $1"; }
+
+# --- Argument checks ---
+if [ -z "$PROJECT_DIR" ]; then
+  error "Usage: bash ~/.automaton/scripts/onboard-project.sh /path/to/project"
+  exit 1
+fi
+
+PROJECT_DIR="$(cd "$PROJECT_DIR" 2>/dev/null && pwd)" || true
+if [ -z "$PROJECT_DIR" ] || [ ! -d "$PROJECT_DIR" ]; then
+  echo ""
+  error "'$1' does not exist."
+  echo "  Create it first: mkdir -p '$1'"
+  echo "  Then re-run this script."
+  exit 1
+fi
+
+if [ ! -d "$FRAMEWORK_DIR/scripts" ]; then
+  error "Framework not found at $FRAMEWORK_DIR."
+  echo "  Install the framework first:"
+  echo "    curl -fsSL https://raw.githubusercontent.com/<user>/automaton/main/scripts/install.sh | bash -s -- <git-url>"
+  echo "  Or: git clone <git-url> ~/.automaton && bash ~/.automaton/scripts/install.sh"
+  exit 1
+fi
+
+echo ""
+echo "========================================"
+echo "  Automaton Project Onboarding"
+echo "  Project: $PROJECT_DIR"
+echo "========================================"
+echo ""
+
+# --- Step 1: Create .automaton/ skeleton ---
+AUTO_DIR="$PROJECT_DIR/.automaton"
+if [ -d "$AUTO_DIR" ]; then
+  warn "$AUTO_DIR already exists — skipping skeleton creation"
+else
+  info "Creating .automaton/ skeleton..."
+  mkdir -p "$AUTO_DIR/tasks" "$AUTO_DIR/loops" "$AUTO_DIR/design"
+  ok "Created $AUTO_DIR/"
+fi
+
+# --- Step 2: Models ---
+MODELS_FILE="$AUTO_DIR/models.json"
+if [ -f "$MODELS_FILE" ]; then
+  warn "$MODELS_FILE already exists — skipping model detection"
+else
+  info "Probing local models..."
+  if python3 "$FRAMEWORK_DIR/scripts/detect_models.py" --write --project "$PROJECT_DIR" 2>/dev/null; then
+    ok "Detected models written to $MODELS_FILE"
+  else
+    info "Auto-detection failed. Creating minimal models.json..."
+    cat > "$MODELS_FILE" <<- 'EOF'
+{
+  "models": [
+    {"name": "default-model", "provider": "local", "context": 32768}
+  ],
+  "default": "default-model"
+}
+EOF
+    warn "Edit $MODELS_FILE to set your actual model(s)."
+  fi
+fi
+
+# --- Step 3: Config ---
+CONFIG_FILE="$AUTO_DIR/config.md"
+if [ -f "$CONFIG_FILE" ]; then
+  warn "$CONFIG_FILE already exists — skipping"
+else
+  info "Creating config.md..."
+  PROJECT_NAME="$(basename "$PROJECT_DIR")"
+  if [ -f "$FRAMEWORK_DIR/scripts/vram_detect.py" ]; then
+    vram_output=$(cd "$FRAMEWORK_DIR" && python3 "$FRAMEWORK_DIR/scripts/vram_detect.py" 2>/dev/null || true)
+    json_part=$(echo "$vram_output" | sed -n '/=== JSON Output ===/,$p' | tail -n +2)
+    recommended=$(echo "$json_part" | python3 -c 'import json,sys; print(json.load(sys.stdin).get("recommended_k","16"))' 2>/dev/null || echo "16")
+  else
+    recommended="16"
+  fi
+  cat > "$CONFIG_FILE" <<- EOF
+# $PROJECT_NAME — Automaton Configuration
+
+## VRAM Configuration
+- **Auto-detect**: Yes
+- **Target context**: ${recommended}k tokens
+- **Headroom**: 25%
+- **Max peak context per sub-task**: $((recommended * 3 / 4))k tokens
+
+## Model Configuration
+# Uses models.json for model divergence enforcement.
+# Default model is read from models.json's "default" key.
+EOF
+  ok "Created $CONFIG_FILE"
+fi
+
+# --- Step 4: Project name ---
+NAME_FILE="$AUTO_DIR/project-name.md"
+if [ -f "$NAME_FILE" ]; then
+  warn "$NAME_FILE already exists — skipping"
+else
+  PROJECT_NAME="$(basename "$PROJECT_DIR")"
+  echo "$PROJECT_NAME" > "$NAME_FILE"
+  ok "Created $NAME_FILE ($PROJECT_NAME)"
+fi
+
+# --- Step 5: Git ---
+GIT_DIR="$PROJECT_DIR/.git"
+if [ -d "$GIT_DIR" ]; then
+  ok "Git repository already initialized"
+else
+  info "Initializing git repository..."
+  cd "$PROJECT_DIR" && git init
+  ok "Git initialized"
+fi
+
+# --- Step 6: Git hooks ---
+if [ -d "$GIT_DIR" ]; then
+  info "Installing git hooks..."
+  bash "$FRAMEWORK_DIR/scripts/install-hooks.sh" "$PROJECT_DIR"
+fi
+
+# --- Step 7: .gitignore ---
+GITIGNORE="$PROJECT_DIR/.gitignore"
+if [ -f "$GITIGNORE" ]; then
+  if ! grep -q ".automaton/tasks/" "$GITIGNORE" 2>/dev/null; then
+    echo "" >> "$GITIGNORE"
+    echo "# Automaton" >> "$GITIGNORE"
+    echo ".automaton/tasks/" >> "$GITIGNORE"
+    echo ".automaton/loops/*/worktree/" >> "$GITIGNORE"
+    warn "Added automaton entries to .gitignore"
+  fi
+else
+  cat > "$GITIGNORE" <<- 'EOF'
+# Automaton
+.automaton/tasks/
+.automaton/loops/*/worktree/
+.automaton/loops/*/outputs/
+EOF
+  ok "Created .gitignore with automaton entries"
+fi
+
+# --- Step 8: Verify ---
+info "Verifying setup..."
+cd "$FRAMEWORK_DIR"
+python3 "$FRAMEWORK_DIR/scripts/status.py" --project "$PROJECT_DIR" --audit 2>&1 | head -5 || true
+
+echo ""
+echo "========================================"
+echo -e "${GREEN}  Onboarding complete!${NC}"
+echo "========================================"
+echo ""
+echo "  Project: $PROJECT_DIR"
+echo "  Config:  $CONFIG_FILE"
+echo "  Models:  $MODELS_FILE"
+echo ""
+echo "  Next steps:"
+echo "    1. cd $PROJECT_DIR"
+echo "    2. Create a task:"
+echo "       python3 ~/.automaton/scripts/status.py --create-task my-first-task --project ."
+echo "    3. Start working with your agent."
+echo ""