Complete tasks 3-7: harden verdict parsing, outputs retention, base branch, linux schedule parity, claim loop task

scripts/upgrade.sh

@@ -1,5 +1,5 @@
 #!/usr/bin/env bash
-# upgrade.sh — Upgrade existing Automaton projects to support .state files and status.py
+# upgrade.sh -- Upgrade existing Automaton projects to support .state files and status.py
 # Usage: ./upgrade.sh [project-path]
 
 set -euo pipefail
@@ -79,24 +79,15 @@ if git -C "$PROJECT_DIR" rev-parse --git-dir &>/dev/null; then
         HOOK_TARGET="$HOOK_DIR/$HOOK"
         HOOK_SOURCE="$FRAMEWORK_DIR/scripts/git-hooks/$HOOK"
         if [ -f "$HOOK_TARGET" ]; then
-            if [ -L "$HOOK_TARGET" ]; then
-                EXISTING_TARGET="$(readlink "$HOOK_TARGET")"
-                if [ "$EXISTING_TARGET" = "$HOOK_SOURCE" ]; then
-                    echo "$HOOK hook already linked to automaton."
-                else
-                    echo "WARNING: $HOOK hook already exists (symlink to: $EXISTING_TARGET)"
-                    echo "  To use automaton's hook, run: ln -sf $HOOK_SOURCE $HOOK_TARGET"
-                fi
-            else
-                echo "WARNING: $HOOK hook already exists at $HOOK_TARGET"
-                echo "  To replace it with automaton's hook, run: ln -sf $HOOK_SOURCE $HOOK_TARGET"
-            fi
+            echo "WARNING: $HOOK hook already exists at $HOOK_TARGET"
+            echo "  To replace it with automaton's hook, run: bash $FRAMEWORK_DIR/scripts/install-hooks.sh"
         else
-            ln -sf "$HOOK_SOURCE" "$HOOK_TARGET"
+            cp "$HOOK_SOURCE" "$HOOK_TARGET"
+            chmod +x "$HOOK_TARGET"
             echo "Installed $HOOK hook at $HOOK_TARGET"
         fi
     done
 else
     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
+    echo "  bash $FRAMEWORK_DIR/scripts/install-hooks.sh"
+fi