Add class override system for framework customization

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

bin/framework-pull-upstream.sh

@@ -181,6 +181,44 @@ if [ "$SHOW_DIFF" = true ]; then
     exit 0
 fi
 
+# =============================================================================
+# STEP: Clean up class override artifacts before checking for uncommitted changes
+# =============================================================================
+# The manifest's class override system renames framework files to .upstream when
+# an rsx/ override exists. Before updating, we need to:
+# 1. Restore any deleted files (git checkout)
+# 2. Delete any .upstream files (the originals will be restored by git)
+# This ensures git sees a clean state, and the next manifest build will
+# re-apply any overrides with the updated framework files.
+# =============================================================================
+
+echo "→ Cleaning up class override artifacts..."
+
+# Step 1: Restore deleted files
+DELETED_FILES=$(git status --porcelain 2>&1 | grep "^ D " | sed 's/^ D //' || true)
+if [ -n "$DELETED_FILES" ]; then
+    echo "  Restoring deleted files..."
+    echo "$DELETED_FILES" | while read -r file; do
+        if [ -n "$file" ]; then
+            git checkout HEAD -- "$file" 2>/dev/null && echo "    ✓ Restored: $file" || true
+        fi
+    done
+fi
+
+# Step 2: Delete .upstream files (framework files renamed by class override system)
+UPSTREAM_FILES=$(find . -name "*.upstream" -type f 2>/dev/null | grep -v "./rsx/" || true)
+if [ -n "$UPSTREAM_FILES" ]; then
+    echo "  Removing .upstream override markers..."
+    echo "$UPSTREAM_FILES" | while read -r upstream_file; do
+        if [ -n "$upstream_file" ] && [ -f "$upstream_file" ]; then
+            rm -f "$upstream_file" && echo "    ✓ Removed: $upstream_file" || true
+        fi
+    done
+fi
+
+echo "  ✓ Override cleanup complete"
+echo ""
+
 # In project mode, check for uncommitted changes outside ./rsx
 if [ "$IS_PROJECT_MODE" = true ]; then
     # Get uncommitted changes (modified, staged, deleted) excluding ./rsx