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/src/Handlers/ParseFileCommand.php

@@ -0,0 +1,67 @@
+<?php
+
+declare(strict_types=1);
+
+/**
+ * This file is part of phpDocumentor.
+ *
+ * For the full copyright and license information, please view the LICENSE
+ * file that was distributed with this source code.
+ *
+ * @link https://phpdoc.org
+ */
+
+namespace phpDocumentor\Guides\Handlers;
+
+use League\Flysystem\FilesystemInterface;
+use phpDocumentor\FileSystem\FileSystem;
+use phpDocumentor\Guides\Nodes\ProjectNode;
+
+final class ParseFileCommand
+{
+    public function __construct(
+        private readonly FilesystemInterface|FileSystem $origin,
+        private readonly string $directory,
+        private readonly string $file,
+        private readonly string $extension,
+        private readonly int $initialHeaderLevel,
+        private readonly ProjectNode $projectNode,
+        private readonly bool $isRoot,
+    ) {
+    }
+
+    public function getOrigin(): FilesystemInterface|FileSystem
+    {
+        return $this->origin;
+    }
+
+    public function getDirectory(): string
+    {
+        return $this->directory;
+    }
+
+    public function getFile(): string
+    {
+        return $this->file;
+    }
+
+    public function getExtension(): string
+    {
+        return $this->extension;
+    }
+
+    public function getInitialHeaderLevel(): int
+    {
+        return $this->initialHeaderLevel;
+    }
+
+    public function getProjectNode(): ProjectNode
+    {
+        return $this->projectNode;
+    }
+
+    public function isRoot(): bool
+    {
+        return $this->isRoot;
+    }
+}