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/tests/integration/FileDocblockTest.php

@@ -0,0 +1,96 @@
+<?php
+
+declare(strict_types=1);
+
+namespace integration;
+
+use phpDocumentor\Reflection\File\LocalFile;
+use phpDocumentor\Reflection\Php\ProjectFactory;
+use PHPUnit\Framework\Attributes\CoversNothing;
+use PHPUnit\Framework\TestCase;
+
+/**
+ * Integration tests to check the correct working of processing a namespace into a project.
+ *
+ * @coversNothing
+ */
+#[CoversNothing]
+final class FileDocblockTest extends TestCase
+{
+    /** @var ProjectFactory */
+    private $fixture;
+
+    protected function setUp() : void
+    {
+        $this->fixture = ProjectFactory::createInstance();
+    }
+
+    /**
+     * @dataProvider fileProvider
+     */
+    public function testFileDocblock(string  $fileName) : void
+    {
+        $project = $this->fixture->create(
+            'MyProject',
+            [new LocalFile($fileName)]
+        );
+
+        $this->assertEquals(
+            'This file is part of phpDocumentor.',
+            $project->getFiles()[$fileName]->getDocBlock()->getSummary()
+        );
+    }
+
+    public static function fileProvider() : array
+    {
+        return [
+            [ __DIR__ . '/data/GlobalFiles/empty.php' ],
+            [ __DIR__ . '/data/GlobalFiles/empty_with_declare.php' ],
+            [ __DIR__ . '/data/GlobalFiles/empty_shebang.php' ],
+            [ __DIR__ . '/data/GlobalFiles/psr12.php' ],
+            [ __DIR__ . '/data/GlobalFiles/docblock_followed_by_html.php' ],
+        ];
+    }
+
+    public function testConditionalFunctionDefine() : void
+    {
+        $fileName =  __DIR__ . '/data/GlobalFiles/conditional_function.php';
+        $project = $this->fixture->create(
+            'MyProject',
+            [new LocalFile($fileName)]
+        );
+
+        $this->assertCount(
+            4,
+            $project->getFiles()[$fileName]->getFunctions()
+        );
+    }
+
+    public function testGlobalNamespacedFunctionDefine() : void
+    {
+        $fileName =  __DIR__ . '/data/GlobalFiles/global_namspaced_function.php';
+        $project = $this->fixture->create(
+            'MyProject',
+            [new LocalFile($fileName)]
+        );
+
+        $this->assertCount(
+            1,
+            $project->getFiles()[$fileName]->getFunctions()
+        );
+    }
+
+    public function testFileWithInlineFunction() : void
+    {
+        $fileName =  __DIR__ . '/data/GlobalFiles/inline_function.php';
+        $project = $this->fixture->create(
+            'MyProject',
+            [new LocalFile($fileName)]
+        );
+
+        $this->assertCount(
+            1,
+            $project->getFiles()[$fileName]->getClasses()
+        );
+    }
+}