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/flyfinder/examples/04-sample-phpdoc-layout-using-glob.php

@@ -0,0 +1,35 @@
+<?php
+require_once(__DIR__ . '/../vendor/autoload.php');
+
+use Flyfinder\Specification\Glob;
+use League\Flysystem\Filesystem;
+use League\Flysystem\Adapter\Local;
+use Flyfinder\Finder;
+use Flyfinder\Path;
+use Flyfinder\Specification\IsHidden;
+use Flyfinder\Specification\HasExtension;
+use Flyfinder\Specification\InPath;
+use Flyfinder\Specification\AndSpecification;
+
+// (03-sample-files based on some phpDocumentor2 src files)
+$filesystem = new Filesystem(new Local(__DIR__ . '/03-sample-files'));
+$filesystem->addPlugin(new Finder());
+
+/*
+ * "phpdoc -d src -i src/phpDocumentor/DomainModel"
+ * should result in src/Cilex and src/phpDocumentor/. files being found,
+ * but src/phpDocumentor/DomainModel files being left out
+ */
+$dashDirectoryPath = new Glob('/src/**/*');
+$dashIgnorePath = new InPath(new Path('src/phpDocumentor/DomainModel'));
+$isHidden = new IsHidden();
+$isPhpFile = new HasExtension(['php']);
+$spec = new AndSpecification($dashDirectoryPath, $dashIgnorePath->notSpecification());
+$spec->andSpecification($isHidden->notSpecification());
+$spec->andSpecification($isPhpFile);
+
+$generator = $filesystem->find($spec);
+$result = [];
+foreach($generator as $value) {
+    $result[] = $value;
+}