refactor: Cleanup git state - commit all staged changes

Major refactoring cleanup:
- Add new controller architecture (class-controller-*.php)
- Add new settings-v2 UI (views/settings-v2/)
- Add new CSS architecture (agentic-sidebar.css, tokens)
- Add esbuild build pipeline (scripts/build.js, package.json)
- Add composer dependencies (vendor/)
- Add frontend src directory (assets/js/src/index.jsx)
- Add documentation files
- Remove old/obsolete files (class-settings.php, old CSS)

This commits all pending changes from previous refactoring efforts.

vendor/phpdocumentor/reflection/.phpdoc/template/base.html.twig

@@ -0,0 +1,15 @@
+{% extends 'layout.html.twig' %}
+
+{% set topMenu = {
+    "menu": [
+        { "name": "About", "url": "https://phpdoc.org/"},
+        { "name": "Components", "url": "https://phpdoc.org/components.html"},
+        { "name": "Documentation", "url": "https://docs.phpdoc.org/"},
+    ],
+    "social": [
+        { "iconClass": "fab fa-mastodon", "url": "https://phpc.social/@phpdoc"},
+        { "iconClass": "fab fa-github", "url": "https://github.com/phpdocumentor/typeresolver"},
+        { "iconClass": "fas fa-envelope-open-text", "url": "https://github.com/orgs/phpDocumentor/discussions"}
+    ]
+}
+%}