feat: add protection against capacitor.build.gradle overwrites

- Create fix-capacitor-build.sh script to restore fixes after Capacitor operations
- Update build-native.sh to automatically apply fix when needed
- Add warnings to BUILDING.md about auto-generated file risks
- Document which Capacitor commands will overwrite manual fixes

This protects against losing the capacitor.build.gradle fix when running
npx cap sync, npx cap update, or other Capacitor CLI commands.

scripts/fix-capacitor-build.sh

@@ -0,0 +1,22 @@
+#!/bin/bash
+
+# Fix for capacitor.build.gradle in plugin development projects
+# This script should be run after any 'npx cap sync' or 'npx cap update'
+
+set -e
+
+CAPACITOR_BUILD_GRADLE="android/app/capacitor.build.gradle"
+
+if [ -f "$CAPACITOR_BUILD_GRADLE" ]; then
+    echo "🔧 Fixing capacitor.build.gradle for plugin development project..."
+    
+    # Comment out the problematic line if it exists and isn't already commented
+    if grep -q "^apply from: \"../capacitor-cordova-android-plugins/cordova.variables.gradle\"" "$CAPACITOR_BUILD_GRADLE"; then
+        sed -i 's/^apply from: "\.\.\/capacitor-cordova-android-plugins\/cordova\.variables\.gradle"/\/\/ Plugin development project - no Capacitor integration files needed\n\/\/ &/' "$CAPACITOR_BUILD_GRADLE"
+        echo "✅ Fixed capacitor.build.gradle"
+    else
+        echo "ℹ️  capacitor.build.gradle already fixed or doesn't need fixing"
+    fi
+else
+    echo "⚠️  capacitor.build.gradle not found at $CAPACITOR_BUILD_GRADLE"
+fi