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/guides-graphs/CONTRIBUTING.rst

@@ -0,0 +1,23 @@
+======================================
+Contribute to the phpDocumentor Guides
+======================================
+
+Go to the mono-repository
+=========================
+
+This project is developed in the mono-repository `phpDocumentor Guides <https://github.com/phpDocumentor/guides>`__.
+The repository you are currently in gets auto-created by splitting the mono-repository. You **must not** contribute
+to this repository directly but always to the mono-repository linked above.
+
+Create Issues
+=============
+
+*   If you find something missing or something is wrong in this library, you are welcome to write an issue
+    describing the problem: `Issues on GitHub <https://github.com/phpDocumentor/guides/issues>`__.
+*   If you can, please try to fix the problem yourself.
+
+Make changes (create pull requests)
+===================================
+
+See the `Contribution chapter <https://docs.phpdoc.org/components/guides/guides/contributions/index.html>`__ in the
+`Documentation` <https://docs.phpdoc.org/components/guides/guides/index.html>`__.