Apply continuous self-improvement to skills (#3072)

- pr-polisher: Relaxed the package-lock.json strictness. If package.json or dependencies.gradle are modified, changes to package-lock.json now correctly trigger a WARNING rather than a fatal ERROR, streamlining intentional dependency updates.
- java-ast-refactoring: Replaced the reliance on a local google-java-format binary with the project's native ./gradlew javaIncrementalFormatApply task for post-AST format fixes.
- Updated GEMINI.md and skill instructions to explicitly authorize and mandate the agent to proactively propose systemic infrastructure fixes to the user when it encounters recurring friction, false positives, or brittle workarounds.
- Overhauled the PR polisher "When to Use" instructions in GEMINI.md and SKILL.md into a critical mandate explicitly tying the execution of the polisher to the action of making or amending a commit to prevent agent forgetfulness.

.gemini/skills/java-ast-refactoring/scripts/run_rewrite.sh

@@ -73,14 +73,7 @@ echo "Executing OpenRewrite recipe: $RECIPE_NAME"
 ./gradlew --init-script "$INIT_SCRIPT" rewriteRun --no-parallel --no-configuration-cache
 
 echo "Running code formatters to fix Checkstyle line-length and import ordering..."
-./gradlew spotlessApply
-
-# Automatically handle line-wrapping and formatting for all files modified by OpenRewrite
-MODIFIED_JAVA_FILES=$(git diff --name-only --diff-filter=d | grep "\.java$" || true)
-if [ -n "$MODIFIED_JAVA_FILES" ]; then
-  echo "Applying google-java-format to all modified Java files to enforce LineLength..."
-  echo "$MODIFIED_JAVA_FILES" | xargs -r google-java-format --replace
-fi
+./gradlew spotlessApply javaIncrementalFormatApply
 
 # Clean up temporary files
 rm "$INIT_SCRIPT"