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/bin/php-parse

@@ -0,0 +1,119 @@
+#!/usr/bin/env php
+<?php
+
+/**
+ * Proxy PHP file generated by Composer
+ *
+ * This file includes the referenced bin path (../nikic/php-parser/bin/php-parse)
+ * using a stream wrapper to prevent the shebang from being output on PHP<8
+ *
+ * @generated
+ */
+
+namespace Composer;
+
+$GLOBALS['_composer_bin_dir'] = __DIR__;
+$GLOBALS['_composer_autoload_path'] = __DIR__ . '/..'.'/autoload.php';
+
+if (PHP_VERSION_ID < 80000) {
+    if (!class_exists('Composer\BinProxyWrapper')) {
+        /**
+         * @internal
+         */
+        final class BinProxyWrapper
+        {
+            private $handle;
+            private $position;
+            private $realpath;
+
+            public function stream_open($path, $mode, $options, &$opened_path)
+            {
+                // get rid of phpvfscomposer:// prefix for __FILE__ & __DIR__ resolution
+                $opened_path = substr($path, 17);
+                $this->realpath = realpath($opened_path) ?: $opened_path;
+                $opened_path = $this->realpath;
+                $this->handle = fopen($this->realpath, $mode);
+                $this->position = 0;
+
+                return (bool) $this->handle;
+            }
+
+            public function stream_read($count)
+            {
+                $data = fread($this->handle, $count);
+
+                if ($this->position === 0) {
+                    $data = preg_replace('{^#!.*\r?\n}', '', $data);
+                }
+
+                $this->position += strlen($data);
+
+                return $data;
+            }
+
+            public function stream_cast($castAs)
+            {
+                return $this->handle;
+            }
+
+            public function stream_close()
+            {
+                fclose($this->handle);
+            }
+
+            public function stream_lock($operation)
+            {
+                return $operation ? flock($this->handle, $operation) : true;
+            }
+
+            public function stream_seek($offset, $whence)
+            {
+                if (0 === fseek($this->handle, $offset, $whence)) {
+                    $this->position = ftell($this->handle);
+                    return true;
+                }
+
+                return false;
+            }
+
+            public function stream_tell()
+            {
+                return $this->position;
+            }
+
+            public function stream_eof()
+            {
+                return feof($this->handle);
+            }
+
+            public function stream_stat()
+            {
+                return array();
+            }
+
+            public function stream_set_option($option, $arg1, $arg2)
+            {
+                return true;
+            }
+
+            public function url_stat($path, $flags)
+            {
+                $path = substr($path, 17);
+                if (file_exists($path)) {
+                    return stat($path);
+                }
+
+                return false;
+            }
+        }
+    }
+
+    if (
+        (function_exists('stream_get_wrappers') && in_array('phpvfscomposer', stream_get_wrappers(), true))
+        || (function_exists('stream_wrapper_register') && stream_wrapper_register('phpvfscomposer', 'Composer\BinProxyWrapper'))
+    ) {
+        return include("phpvfscomposer://" . __DIR__ . '/..'.'/nikic/php-parser/bin/php-parse');
+    }
+}
+
+return include __DIR__ . '/..'.'/nikic/php-parser/bin/php-parse';

vendor/bin/phpcbf

@@ -0,0 +1,119 @@
+#!/usr/bin/env php
+<?php
+
+/**
+ * Proxy PHP file generated by Composer
+ *
+ * This file includes the referenced bin path (../squizlabs/php_codesniffer/bin/phpcbf)
+ * using a stream wrapper to prevent the shebang from being output on PHP<8
+ *
+ * @generated
+ */
+
+namespace Composer;
+
+$GLOBALS['_composer_bin_dir'] = __DIR__;
+$GLOBALS['_composer_autoload_path'] = __DIR__ . '/..'.'/autoload.php';
+
+if (PHP_VERSION_ID < 80000) {
+    if (!class_exists('Composer\BinProxyWrapper')) {
+        /**
+         * @internal
+         */
+        final class BinProxyWrapper
+        {
+            private $handle;
+            private $position;
+            private $realpath;
+
+            public function stream_open($path, $mode, $options, &$opened_path)
+            {
+                // get rid of phpvfscomposer:// prefix for __FILE__ & __DIR__ resolution
+                $opened_path = substr($path, 17);
+                $this->realpath = realpath($opened_path) ?: $opened_path;
+                $opened_path = $this->realpath;
+                $this->handle = fopen($this->realpath, $mode);
+                $this->position = 0;
+
+                return (bool) $this->handle;
+            }
+
+            public function stream_read($count)
+            {
+                $data = fread($this->handle, $count);
+
+                if ($this->position === 0) {
+                    $data = preg_replace('{^#!.*\r?\n}', '', $data);
+                }
+
+                $this->position += strlen($data);
+
+                return $data;
+            }
+
+            public function stream_cast($castAs)
+            {
+                return $this->handle;
+            }
+
+            public function stream_close()
+            {
+                fclose($this->handle);
+            }
+
+            public function stream_lock($operation)
+            {
+                return $operation ? flock($this->handle, $operation) : true;
+            }
+
+            public function stream_seek($offset, $whence)
+            {
+                if (0 === fseek($this->handle, $offset, $whence)) {
+                    $this->position = ftell($this->handle);
+                    return true;
+                }
+
+                return false;
+            }
+
+            public function stream_tell()
+            {
+                return $this->position;
+            }
+
+            public function stream_eof()
+            {
+                return feof($this->handle);
+            }
+
+            public function stream_stat()
+            {
+                return array();
+            }
+
+            public function stream_set_option($option, $arg1, $arg2)
+            {
+                return true;
+            }
+
+            public function url_stat($path, $flags)
+            {
+                $path = substr($path, 17);
+                if (file_exists($path)) {
+                    return stat($path);
+                }
+
+                return false;
+            }
+        }
+    }
+
+    if (
+        (function_exists('stream_get_wrappers') && in_array('phpvfscomposer', stream_get_wrappers(), true))
+        || (function_exists('stream_wrapper_register') && stream_wrapper_register('phpvfscomposer', 'Composer\BinProxyWrapper'))
+    ) {
+        return include("phpvfscomposer://" . __DIR__ . '/..'.'/squizlabs/php_codesniffer/bin/phpcbf');
+    }
+}
+
+return include __DIR__ . '/..'.'/squizlabs/php_codesniffer/bin/phpcbf';

vendor/bin/phpcs

@@ -0,0 +1,119 @@
+#!/usr/bin/env php
+<?php
+
+/**
+ * Proxy PHP file generated by Composer
+ *
+ * This file includes the referenced bin path (../squizlabs/php_codesniffer/bin/phpcs)
+ * using a stream wrapper to prevent the shebang from being output on PHP<8
+ *
+ * @generated
+ */
+
+namespace Composer;
+
+$GLOBALS['_composer_bin_dir'] = __DIR__;
+$GLOBALS['_composer_autoload_path'] = __DIR__ . '/..'.'/autoload.php';
+
+if (PHP_VERSION_ID < 80000) {
+    if (!class_exists('Composer\BinProxyWrapper')) {
+        /**
+         * @internal
+         */
+        final class BinProxyWrapper
+        {
+            private $handle;
+            private $position;
+            private $realpath;
+
+            public function stream_open($path, $mode, $options, &$opened_path)
+            {
+                // get rid of phpvfscomposer:// prefix for __FILE__ & __DIR__ resolution
+                $opened_path = substr($path, 17);
+                $this->realpath = realpath($opened_path) ?: $opened_path;
+                $opened_path = $this->realpath;
+                $this->handle = fopen($this->realpath, $mode);
+                $this->position = 0;
+
+                return (bool) $this->handle;
+            }
+
+            public function stream_read($count)
+            {
+                $data = fread($this->handle, $count);
+
+                if ($this->position === 0) {
+                    $data = preg_replace('{^#!.*\r?\n}', '', $data);
+                }
+
+                $this->position += strlen($data);
+
+                return $data;
+            }
+
+            public function stream_cast($castAs)
+            {
+                return $this->handle;
+            }
+
+            public function stream_close()
+            {
+                fclose($this->handle);
+            }
+
+            public function stream_lock($operation)
+            {
+                return $operation ? flock($this->handle, $operation) : true;
+            }
+
+            public function stream_seek($offset, $whence)
+            {
+                if (0 === fseek($this->handle, $offset, $whence)) {
+                    $this->position = ftell($this->handle);
+                    return true;
+                }
+
+                return false;
+            }
+
+            public function stream_tell()
+            {
+                return $this->position;
+            }
+
+            public function stream_eof()
+            {
+                return feof($this->handle);
+            }
+
+            public function stream_stat()
+            {
+                return array();
+            }
+
+            public function stream_set_option($option, $arg1, $arg2)
+            {
+                return true;
+            }
+
+            public function url_stat($path, $flags)
+            {
+                $path = substr($path, 17);
+                if (file_exists($path)) {
+                    return stat($path);
+                }
+
+                return false;
+            }
+        }
+    }
+
+    if (
+        (function_exists('stream_get_wrappers') && in_array('phpvfscomposer', stream_get_wrappers(), true))
+        || (function_exists('stream_wrapper_register') && stream_wrapper_register('phpvfscomposer', 'Composer\BinProxyWrapper'))
+    ) {
+        return include("phpvfscomposer://" . __DIR__ . '/..'.'/squizlabs/php_codesniffer/bin/phpcs');
+    }
+}
+
+return include __DIR__ . '/..'.'/squizlabs/php_codesniffer/bin/phpcs';

vendor/bin/phpdoc

@@ -0,0 +1,119 @@
+#!/usr/bin/env php
+<?php
+
+/**
+ * Proxy PHP file generated by Composer
+ *
+ * This file includes the referenced bin path (../phpdocumentor/phpdocumentor/bin/phpdoc)
+ * using a stream wrapper to prevent the shebang from being output on PHP<8
+ *
+ * @generated
+ */
+
+namespace Composer;
+
+$GLOBALS['_composer_bin_dir'] = __DIR__;
+$GLOBALS['_composer_autoload_path'] = __DIR__ . '/..'.'/autoload.php';
+
+if (PHP_VERSION_ID < 80000) {
+    if (!class_exists('Composer\BinProxyWrapper')) {
+        /**
+         * @internal
+         */
+        final class BinProxyWrapper
+        {
+            private $handle;
+            private $position;
+            private $realpath;
+
+            public function stream_open($path, $mode, $options, &$opened_path)
+            {
+                // get rid of phpvfscomposer:// prefix for __FILE__ & __DIR__ resolution
+                $opened_path = substr($path, 17);
+                $this->realpath = realpath($opened_path) ?: $opened_path;
+                $opened_path = $this->realpath;
+                $this->handle = fopen($this->realpath, $mode);
+                $this->position = 0;
+
+                return (bool) $this->handle;
+            }
+
+            public function stream_read($count)
+            {
+                $data = fread($this->handle, $count);
+
+                if ($this->position === 0) {
+                    $data = preg_replace('{^#!.*\r?\n}', '', $data);
+                }
+
+                $this->position += strlen($data);
+
+                return $data;
+            }
+
+            public function stream_cast($castAs)
+            {
+                return $this->handle;
+            }
+
+            public function stream_close()
+            {
+                fclose($this->handle);
+            }
+
+            public function stream_lock($operation)
+            {
+                return $operation ? flock($this->handle, $operation) : true;
+            }
+
+            public function stream_seek($offset, $whence)
+            {
+                if (0 === fseek($this->handle, $offset, $whence)) {
+                    $this->position = ftell($this->handle);
+                    return true;
+                }
+
+                return false;
+            }
+
+            public function stream_tell()
+            {
+                return $this->position;
+            }
+
+            public function stream_eof()
+            {
+                return feof($this->handle);
+            }
+
+            public function stream_stat()
+            {
+                return array();
+            }
+
+            public function stream_set_option($option, $arg1, $arg2)
+            {
+                return true;
+            }
+
+            public function url_stat($path, $flags)
+            {
+                $path = substr($path, 17);
+                if (file_exists($path)) {
+                    return stat($path);
+                }
+
+                return false;
+            }
+        }
+    }
+
+    if (
+        (function_exists('stream_get_wrappers') && in_array('phpvfscomposer', stream_get_wrappers(), true))
+        || (function_exists('stream_wrapper_register') && stream_wrapper_register('phpvfscomposer', 'Composer\BinProxyWrapper'))
+    ) {
+        return include("phpvfscomposer://" . __DIR__ . '/..'.'/phpdocumentor/phpdocumentor/bin/phpdoc');
+    }
+}
+
+return include __DIR__ . '/..'.'/phpdocumentor/phpdocumentor/bin/phpdoc';

vendor/bin/phpdoc.php

@@ -0,0 +1,119 @@
+#!/usr/bin/env php
+<?php
+
+/**
+ * Proxy PHP file generated by Composer
+ *
+ * This file includes the referenced bin path (../phpdocumentor/phpdocumentor/bin/phpdoc.php)
+ * using a stream wrapper to prevent the shebang from being output on PHP<8
+ *
+ * @generated
+ */
+
+namespace Composer;
+
+$GLOBALS['_composer_bin_dir'] = __DIR__;
+$GLOBALS['_composer_autoload_path'] = __DIR__ . '/..'.'/autoload.php';
+
+if (PHP_VERSION_ID < 80000) {
+    if (!class_exists('Composer\BinProxyWrapper')) {
+        /**
+         * @internal
+         */
+        final class BinProxyWrapper
+        {
+            private $handle;
+            private $position;
+            private $realpath;
+
+            public function stream_open($path, $mode, $options, &$opened_path)
+            {
+                // get rid of phpvfscomposer:// prefix for __FILE__ & __DIR__ resolution
+                $opened_path = substr($path, 17);
+                $this->realpath = realpath($opened_path) ?: $opened_path;
+                $opened_path = $this->realpath;
+                $this->handle = fopen($this->realpath, $mode);
+                $this->position = 0;
+
+                return (bool) $this->handle;
+            }
+
+            public function stream_read($count)
+            {
+                $data = fread($this->handle, $count);
+
+                if ($this->position === 0) {
+                    $data = preg_replace('{^#!.*\r?\n}', '', $data);
+                }
+
+                $this->position += strlen($data);
+
+                return $data;
+            }
+
+            public function stream_cast($castAs)
+            {
+                return $this->handle;
+            }
+
+            public function stream_close()
+            {
+                fclose($this->handle);
+            }
+
+            public function stream_lock($operation)
+            {
+                return $operation ? flock($this->handle, $operation) : true;
+            }
+
+            public function stream_seek($offset, $whence)
+            {
+                if (0 === fseek($this->handle, $offset, $whence)) {
+                    $this->position = ftell($this->handle);
+                    return true;
+                }
+
+                return false;
+            }
+
+            public function stream_tell()
+            {
+                return $this->position;
+            }
+
+            public function stream_eof()
+            {
+                return feof($this->handle);
+            }
+
+            public function stream_stat()
+            {
+                return array();
+            }
+
+            public function stream_set_option($option, $arg1, $arg2)
+            {
+                return true;
+            }
+
+            public function url_stat($path, $flags)
+            {
+                $path = substr($path, 17);
+                if (file_exists($path)) {
+                    return stat($path);
+                }
+
+                return false;
+            }
+        }
+    }
+
+    if (
+        (function_exists('stream_get_wrappers') && in_array('phpvfscomposer', stream_get_wrappers(), true))
+        || (function_exists('stream_wrapper_register') && stream_wrapper_register('phpvfscomposer', 'Composer\BinProxyWrapper'))
+    ) {
+        return include("phpvfscomposer://" . __DIR__ . '/..'.'/phpdocumentor/phpdocumentor/bin/phpdoc.php');
+    }
+}
+
+return include __DIR__ . '/..'.'/phpdocumentor/phpdocumentor/bin/phpdoc.php';

vendor/bin/phpunit

@@ -0,0 +1,122 @@
+#!/usr/bin/env php
+<?php
+
+/**
+ * Proxy PHP file generated by Composer
+ *
+ * This file includes the referenced bin path (../phpunit/phpunit/phpunit)
+ * using a stream wrapper to prevent the shebang from being output on PHP<8
+ *
+ * @generated
+ */
+
+namespace Composer;
+
+$GLOBALS['_composer_bin_dir'] = __DIR__;
+$GLOBALS['_composer_autoload_path'] = __DIR__ . '/..'.'/autoload.php';
+$GLOBALS['__PHPUNIT_ISOLATION_EXCLUDE_LIST'] = $GLOBALS['__PHPUNIT_ISOLATION_BLACKLIST'] = array(realpath(__DIR__ . '/..'.'/phpunit/phpunit/phpunit'));
+
+if (PHP_VERSION_ID < 80000) {
+    if (!class_exists('Composer\BinProxyWrapper')) {
+        /**
+         * @internal
+         */
+        final class BinProxyWrapper
+        {
+            private $handle;
+            private $position;
+            private $realpath;
+
+            public function stream_open($path, $mode, $options, &$opened_path)
+            {
+                // get rid of phpvfscomposer:// prefix for __FILE__ & __DIR__ resolution
+                $opened_path = substr($path, 17);
+                $this->realpath = realpath($opened_path) ?: $opened_path;
+                $opened_path = 'phpvfscomposer://'.$this->realpath;
+                $this->handle = fopen($this->realpath, $mode);
+                $this->position = 0;
+
+                return (bool) $this->handle;
+            }
+
+            public function stream_read($count)
+            {
+                $data = fread($this->handle, $count);
+
+                if ($this->position === 0) {
+                    $data = preg_replace('{^#!.*\r?\n}', '', $data);
+                }
+                $data = str_replace('__DIR__', var_export(dirname($this->realpath), true), $data);
+                $data = str_replace('__FILE__', var_export($this->realpath, true), $data);
+
+                $this->position += strlen($data);
+
+                return $data;
+            }
+
+            public function stream_cast($castAs)
+            {
+                return $this->handle;
+            }
+
+            public function stream_close()
+            {
+                fclose($this->handle);
+            }
+
+            public function stream_lock($operation)
+            {
+                return $operation ? flock($this->handle, $operation) : true;
+            }
+
+            public function stream_seek($offset, $whence)
+            {
+                if (0 === fseek($this->handle, $offset, $whence)) {
+                    $this->position = ftell($this->handle);
+                    return true;
+                }
+
+                return false;
+            }
+
+            public function stream_tell()
+            {
+                return $this->position;
+            }
+
+            public function stream_eof()
+            {
+                return feof($this->handle);
+            }
+
+            public function stream_stat()
+            {
+                return array();
+            }
+
+            public function stream_set_option($option, $arg1, $arg2)
+            {
+                return true;
+            }
+
+            public function url_stat($path, $flags)
+            {
+                $path = substr($path, 17);
+                if (file_exists($path)) {
+                    return stat($path);
+                }
+
+                return false;
+            }
+        }
+    }
+
+    if (
+        (function_exists('stream_get_wrappers') && in_array('phpvfscomposer', stream_get_wrappers(), true))
+        || (function_exists('stream_wrapper_register') && stream_wrapper_register('phpvfscomposer', 'Composer\BinProxyWrapper'))
+    ) {
+        return include("phpvfscomposer://" . __DIR__ . '/..'.'/phpunit/phpunit/phpunit');
+    }
+}
+
+return include __DIR__ . '/..'.'/phpunit/phpunit/phpunit';

vendor/bin/plantuml

@@ -0,0 +1,37 @@
+#!/usr/bin/env sh
+
+# Support bash to support `source` with fallback on $0 if this does not run with bash
+# https://stackoverflow.com/a/35006505/6512
+selfArg="$BASH_SOURCE"
+if [ -z "$selfArg" ]; then
+    selfArg="$0"
+fi
+
+self=$(realpath "$selfArg" 2> /dev/null)
+if [ -z "$self" ]; then
+    self="$selfArg"
+fi
+
+dir=$(cd "${self%[/\\]*}" > /dev/null; cd '../jawira/plantuml/bin' && pwd)
+
+if [ -d /proc/cygdrive ]; then
+    case $(which php) in
+        $(readlink -n /proc/cygdrive)/*)
+            # We are in Cygwin using Windows php, so the path must be translated
+            dir=$(cygpath -m "$dir");
+            ;;
+    esac
+fi
+
+export COMPOSER_RUNTIME_BIN_DIR="$(cd "${self%[/\\]*}" > /dev/null; pwd)"
+
+# If bash is sourcing this file, we have to source the target as well
+bashSource="$BASH_SOURCE"
+if [ -n "$bashSource" ]; then
+    if [ "$bashSource" != "$0" ]; then
+        source "${dir}/plantuml" "$@"
+        return
+    fi
+fi
+
+exec "${dir}/plantuml" "$@"

vendor/bin/yaml-lint

@@ -0,0 +1,119 @@
+#!/usr/bin/env php
+<?php
+
+/**
+ * Proxy PHP file generated by Composer
+ *
+ * This file includes the referenced bin path (../symfony/yaml/Resources/bin/yaml-lint)
+ * using a stream wrapper to prevent the shebang from being output on PHP<8
+ *
+ * @generated
+ */
+
+namespace Composer;
+
+$GLOBALS['_composer_bin_dir'] = __DIR__;
+$GLOBALS['_composer_autoload_path'] = __DIR__ . '/..'.'/autoload.php';
+
+if (PHP_VERSION_ID < 80000) {
+    if (!class_exists('Composer\BinProxyWrapper')) {
+        /**
+         * @internal
+         */
+        final class BinProxyWrapper
+        {
+            private $handle;
+            private $position;
+            private $realpath;
+
+            public function stream_open($path, $mode, $options, &$opened_path)
+            {
+                // get rid of phpvfscomposer:// prefix for __FILE__ & __DIR__ resolution
+                $opened_path = substr($path, 17);
+                $this->realpath = realpath($opened_path) ?: $opened_path;
+                $opened_path = $this->realpath;
+                $this->handle = fopen($this->realpath, $mode);
+                $this->position = 0;
+
+                return (bool) $this->handle;
+            }
+
+            public function stream_read($count)
+            {
+                $data = fread($this->handle, $count);
+
+                if ($this->position === 0) {
+                    $data = preg_replace('{^#!.*\r?\n}', '', $data);
+                }
+
+                $this->position += strlen($data);
+
+                return $data;
+            }
+
+            public function stream_cast($castAs)
+            {
+                return $this->handle;
+            }
+
+            public function stream_close()
+            {
+                fclose($this->handle);
+            }
+
+            public function stream_lock($operation)
+            {
+                return $operation ? flock($this->handle, $operation) : true;
+            }
+
+            public function stream_seek($offset, $whence)
+            {
+                if (0 === fseek($this->handle, $offset, $whence)) {
+                    $this->position = ftell($this->handle);
+                    return true;
+                }
+
+                return false;
+            }
+
+            public function stream_tell()
+            {
+                return $this->position;
+            }
+
+            public function stream_eof()
+            {
+                return feof($this->handle);
+            }
+
+            public function stream_stat()
+            {
+                return array();
+            }
+
+            public function stream_set_option($option, $arg1, $arg2)
+            {
+                return true;
+            }
+
+            public function url_stat($path, $flags)
+            {
+                $path = substr($path, 17);
+                if (file_exists($path)) {
+                    return stat($path);
+                }
+
+                return false;
+            }
+        }
+    }
+
+    if (
+        (function_exists('stream_get_wrappers') && in_array('phpvfscomposer', stream_get_wrappers(), true))
+        || (function_exists('stream_wrapper_register') && stream_wrapper_register('phpvfscomposer', 'Composer\BinProxyWrapper'))
+    ) {
+        return include("phpvfscomposer://" . __DIR__ . '/..'.'/symfony/yaml/Resources/bin/yaml-lint');
+    }
+}
+
+return include __DIR__ . '/..'.'/symfony/yaml/Resources/bin/yaml-lint';