Add incremental manifest-time code quality checks and JS duplicate method detection

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Co-Authored-By: Claude <noreply@anthropic.com>

app/RSpade/CodeQuality/Rules/Manifest/InstanceMethods_CodeQualityRule.php

@@ -57,6 +57,14 @@ class InstanceMethods_CodeQualityRule extends CodeQualityRule_Abstract
         return true;
     }
 
+    /**
+     * This is a cross-file rule - needs full manifest context
+     */
+    public function is_incremental(): bool
+    {
+        return false;
+    }
+
     /**
      * Check the manifest for instance method violations
      */