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/filesystem/README.rst

@@ -0,0 +1,34 @@
+
+..  image:: https://poser.pugx.org/phpdocumentor/filesystem/require/php
+    :alt: PHP Version Require
+    :target: https://packagist.org/packages/phpdocumentor/filesystem
+
+..  image:: https://poser.pugx.org/phpdocumentor/filesystem/v/stable
+    :alt: Latest Stable Version
+    :target: https://packagist.org/packages/phpdocumentor/filesystem
+
+..  image:: https://poser.pugx.org/phpdocumentor/filesystem/v/unstable
+    :alt: Latest Unstable Version
+    :target: https://packagist.org/packages/phpdocumentor/filesystem
+
+..  image:: https://poser.pugx.org/phpdocumentor/filesystem/d/total
+    :alt: Total Downloads
+    :target: https://packagist.org/packages/phpdocumentor/filesystem
+
+..  image:: https://poser.pugx.org/phpdocumentor/filesystem/d/monthly
+    :alt: Monthly Downloads
+    :target: https://packagist.org/packages/phpdocumentor/filesystem
+
+========================
+phpDocumentor FileSystem
+========================
+
+This repository is part of `phpDocumentor's Guides library <https://github.com/phpDocumentor/guides>`__.
+
+The package `phpdocumentor/filesystem <https://packagist.org/packages/phpdocumentor/filesystem>`__ provides
+filesystem abstractions for phpDocumentor libraries.
+
+:Mono-Repository:   https://github.com/phpDocumentor/guides
+:Documentation:     https://docs.phpdoc.org/components/guides/guides/index.html
+:Packagist:         https://packagist.org/packages/phpdocumentor/filesystem
+:Contribution:      https://github.com/phpDocumentor/guides/tree/main/CONTRIBUTING.rst