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/01-find-hidden-files.php

@@ -0,0 +1,31 @@
+<?php
+require_once(__DIR__ . '/../vendor/autoload.php');
+
+use League\Flysystem\Filesystem;
+use League\Flysystem\Memory\MemoryAdapter as Adapter;
+use Flyfinder\Finder;
+use Flyfinder\Specification\IsHidden;
+
+/*
+ * First create a new Filesystem and add the FlySystem plugin
+ * In this example we are using a filesystem with the memory adapter
+ */
+$filesystem = new Filesystem(new Adapter());
+$filesystem->addPlugin(new Finder());
+
+// Create some demo files
+$filesystem->write('test.txt', 'test');
+$filesystem->write('.hiddendir/.test.txt', 'test');
+
+//In order to tell FlyFinder what to find, you need to give it a specification
+//In this example the specification will be satisfied by files and directories that are hidden
+$specification = new IsHidden();
+
+//FlyFinder will yield a generator object with the files that are found
+$generator = $filesystem->find($specification);
+
+$result = [];
+
+foreach ($generator as $value) {
+    $result[] = $value;
+}

vendor/phpdocumentor/flyfinder/examples/02-find-on-multiple-criteria.php

@@ -0,0 +1,42 @@
+<?php
+require_once(__DIR__ . '/../vendor/autoload.php');
+
+use League\Flysystem\Filesystem;
+use League\Flysystem\Memory\MemoryAdapter as Adapter;
+use Flyfinder\Finder;
+use Flyfinder\Path;
+use Flyfinder\Specification\IsHidden;
+use Flyfinder\Specification\HasExtension;
+use Flyfinder\Specification\InPath;
+
+/*
+ * First create a new Filesystem and add the FlySystem plugin
+ * In this example we are using a filesystem with the memory adapter
+ */
+$filesystem = new Filesystem(new Adapter());
+$filesystem->addPlugin(new Finder());
+
+// Create some demo files
+$filesystem->write('test.txt', 'test');
+$filesystem->write('.hiddendir/.test.txt', 'test');
+$filesystem->write('.hiddendir/found.txt', 'test');
+$filesystem->write('.hiddendir/normaldir/example.txt', 'test');
+
+/*
+ * In order to tell FlyFinder what to find, you need to give it a specification
+ * In this example the specification will be satisfied by *.txt files
+ * within the .hidden directory and its subdirectories that are not hidden
+ */
+$isHidden = new IsHidden();
+$hasExtension = new HasExtension(['txt']);
+$inPath = new InPath(new Path('.hiddendir'));
+$specification = $inPath->andSpecification($hasExtension)->andSpecification($isHidden->notSpecification());
+
+//FlyFinder will yield a generator object with the files that are found
+$generator = $filesystem->find($specification);
+
+$result = [];
+
+foreach ($generator as $value) {
+    $result[] = $value;
+}

vendor/phpdocumentor/flyfinder/examples/03-sample-files/src/Cilex/Provider/JmsSerializerServiceProvider.php

@@ -0,0 +1,2 @@
+<?php
+// dummy file

vendor/phpdocumentor/flyfinder/examples/03-sample-files/src/Cilex/Provider/MonologServiceProvider.php

@@ -0,0 +1,2 @@
+<?php
+// dummy file

vendor/phpdocumentor/flyfinder/examples/03-sample-files/src/phpDocumentor/Application.php

@@ -0,0 +1,2 @@
+<?php
+// dummy file

vendor/phpdocumentor/flyfinder/examples/03-sample-files/src/phpDocumentor/Bootstrap.php

@@ -0,0 +1,2 @@
+<?php
+// dummy file

vendor/phpdocumentor/flyfinder/examples/03-sample-files/src/phpDocumentor/DomainModel/Dsn.php

@@ -0,0 +1,2 @@
+<?php
+// dummy file

vendor/phpdocumentor/flyfinder/examples/03-sample-files/src/phpDocumentor/DomainModel/Parser/FileCollector.php

@@ -0,0 +1,2 @@
+<?php
+// dummy file

vendor/phpdocumentor/flyfinder/examples/03-sample-files/src/phpDocumentor/DomainModel/Path.php

@@ -0,0 +1,2 @@
+<?php
+// dummy file

vendor/phpdocumentor/flyfinder/examples/03-sample-phpdoc-layout.php

@@ -0,0 +1,34 @@
+<?php
+require_once(__DIR__ . '/../vendor/autoload.php');
+
+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
+ */
+$dashDirectoryPath = new InPath(new Path('src'));
+$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;
+}

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;
+}