Fix pre-existing issues and update README for v2.0

- Fix _infer_state_from_artifacts: SPEC-only maps to research (was bug_find)
- Fix cmd_validate_folder: corrupted .state files now error instead of silent fallback
- Fix upgrade.sh: remove || true, add python3 check, use git rev-parse --git-dir
- Update README.md with --project flag, --can-edit modes, --upgrade, enforcement layers
- Add 6 new tests for inference and validation fixes
- Complete hook-install-process and readme-upgrade-docs tasks

scripts/upgrade.sh

@@ -4,6 +4,13 @@
 
 set -euo pipefail
 
+# Verify python3 is available
+if ! command -v python3 &>/dev/null; then
+    echo "ERROR: python3 is required but not found in PATH."
+    echo "Install Python 3 and rerun this script."
+    exit 1
+fi
+
 SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
 STATUS_SCRIPT="$SCRIPT_DIR/status.py"
 
@@ -23,8 +30,15 @@ echo ""
 # Bootstrap .state files for tasks using status.py --upgrade
 if [ -f "$STATUS_SCRIPT" ]; then
     echo "Step 1: Bootstrapping .state files for existing tasks..."
-    python3 "$STATUS_SCRIPT" --upgrade --project "$PROJECT_DIR" || true
+    if ! python3 "$STATUS_SCRIPT" --upgrade --project "$PROJECT_DIR"; then
+        echo "ERROR: status.py --upgrade failed. See errors above."
+        echo "Fix the reported issues and rerun this script."
+        exit 1
+    fi
     echo ""
+else
+    echo "WARNING: status.py not found at $STATUS_SCRIPT. Skipping .state bootstrap."
+    echo "Ensure the framework is installed at ~/.automaton/ and rerun."
 fi
 
 # Add version marker to config.md if not present
@@ -58,10 +72,12 @@ echo "Run 'python ~/.automaton/scripts/status.py --audit --project $PROJECT_DIR'
 echo ""
 
 # Install pre-commit hook if project uses git
-GIT_DIR="$PROJECT_DIR/.git"
-if [ -d "$GIT_DIR/hooks" ]; then
-    HOOK_TARGET="$GIT_DIR/hooks/pre-commit"
+if git -C "$PROJECT_DIR" rev-parse --git-dir &>/dev/null; then
+    HOOK_DIR="$(git -C "$PROJECT_DIR" rev-parse --git-dir)/hooks"
+    HOOK_TARGET="$HOOK_DIR/pre-commit"
     HOOK_SOURCE="$FRAMEWORK_DIR/scripts/git-hooks/pre-commit"
+    # Ensure hooks directory exists
+    mkdir -p "$HOOK_DIR"
     if [ -f "$HOOK_TARGET" ]; then
         if [ -L "$HOOK_TARGET" ]; then
             EXISTING_TARGET="$(readlink "$HOOK_TARGET")"
@@ -80,6 +96,6 @@ if [ -d "$GIT_DIR/hooks" ]; then
         echo "Installed pre-commit hook at $HOOK_TARGET"
     fi
 else
-    echo "NOTE: No .git/hooks/ directory found. Install the hook manually if this project uses git:"
-    echo "  ln -sf $FRAMEWORK_DIR/scripts/git-hooks/pre-commit \$PROJECT_DIR/.git/hooks/pre-commit"
+    echo "NOTE: Not a git repository. Install the hook manually if needed:"
+    echo "  ln -sf $FRAMEWORK_DIR/scripts/git-hooks/pre-commit .git/hooks/pre-commit"
 fi