updating phpDocumentor, part 2: add new version

1 files changed, 978 insertions, 0 deletions

diff --git a/buildscripts/PhpDocumentor/phpDocumentor/Setup.inc.php b/buildscripts/PhpDocumentor/phpDocumentor/Setup.inc.php
new file mode 100755
index 00000000..db5b722f
--- /dev/null
+++ b/buildscripts/PhpDocumentor/phpDocumentor/Setup.inc.php
@@ -0,0 +1,978 @@
+<?php
+/**
+ * This was all in {@link phpdoc.inc}, and now encapsulates the complexity
+ * 
+ * phpDocumentor :: automatic documentation generator
+ * 
+ * PHP versions 4 and 5
+ *
+ * Copyright (c) 2002-2006 Gregory Beaver
+ * 
+ * LICENSE:
+ * 
+ * This library is free software; you can redistribute it
+ * and/or modify it under the terms of the GNU Lesser General
+ * Public License as published by the Free Software Foundation;
+ * either version 2.1 of the License, or (at your option) any
+ * later version.
+ * 
+ * This library is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this library; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+ *
+ * @package    phpDocumentor
+ * @author     Gregory Beaver <cellog@php.net>
+ * @copyright  2002-2006 Gregory Beaver
+ * @license    http://www.opensource.org/licenses/lgpl-license.php LGPL
+ * @version    CVS: $Id: Setup.inc.php 258122 2008-04-22 15:48:55Z ashnazg $
+ * @link       http://www.phpdoc.org
+ * @link       http://pear.php.net/PhpDocumentor
+ * @since      1.2
+ */
+error_reporting(E_ALL);
+
+/** ensure top-level PhpDocumentor dir is in include path */
+set_include_path(get_include_path() . PATH_SEPARATOR . dirname(dirname(__FILE__)));
+
+/** common settings */
+include_once("phpDocumentor/common.inc.php");
+
+include_once("phpDocumentor/Io.inc");
+include_once("phpDocumentor/Publisher.inc");
+include_once("phpDocumentor/Classes.inc");
+include_once("phpDocumentor/ProceduralPages.inc");
+include_once("phpDocumentor/IntermediateParser.inc");
+include_once("phpDocumentor/WordParser.inc");
+include_once("phpDocumentor/EventStack.inc");
+include_once("phpDocumentor/ParserData.inc");
+include_once("phpDocumentor/InlineTags.inc");
+include_once("phpDocumentor/DocBlockTags.inc");
+include_once("phpDocumentor/DescHTML.inc");
+include_once("phpDocumentor/ParserDocBlock.inc");
+include_once("phpDocumentor/ParserElements.inc");
+include_once("phpDocumentor/Parser.inc");
+include_once("phpDocumentor/phpDocumentorTWordParser.inc");
+include_once("phpDocumentor/phpDocumentorTParser.inc");
+include_once("phpDocumentor/HighlightParser.inc");
+include_once("phpDocumentor/TutorialHighlightParser.inc");
+include_once("phpDocumentor/ParserDescCleanup.inc");
+include_once("phpDocumentor/PackagePageElements.inc");
+include_once("phpDocumentor/XMLpackagePageParser.inc");
+include_once("phpDocumentor/LinkClasses.inc");
+include_once("phpDocumentor/Converter.inc");
+include_once("phpDocumentor/Errors.inc");
+if (isset($_GET))
+{
+/**
+ * $interface is either 'web' or is not set at all
+ * @global array $interface
+ */
+    if (isset($_GET['interface'])) $interface = $_GET['interface'];
+/**
+ * $_phpDocumentor_setting is either the value from the web interface, or is set up by {@link Io::parseArgv()}
+ * @global array $_phpDocumentor_setting
+ */
+    if (isset($_GET['setting'])) $_phpDocumentor_setting = $_GET['setting'];
+}
+
+/**
+ * default package name, set using -dn --defaultpackagename
+ * @global string $GLOBALS['phpDocumentor_DefaultPackageName']
+ * @name $phpDocumentor_DefaultPackageName
+ */
+$GLOBALS['phpDocumentor_DefaultPackageName'] = 'default';
+
+/**
+ * default package name, set using -dn --defaultcategoryname
+ * @global string $GLOBALS['phpDocumentor_DefaultCategoryName']
+ * @name $phpDocumentor_DefaultCategoryName
+ */
+$GLOBALS['phpDocumentor_DefaultCategoryName'] = 'default';
+
+/**
+ * @package phpDocumentor
+ */
+class phpDocumentor_setup
+{
+    /**
+     * The main parser
+     * @var Parser|phpDocumentorTParser
+     */
+    var $parse;
+    /**
+     * Used to parse command-line options
+     * @var Io
+     */
+    var $setup;
+    /**
+     * Used to organize output from the Parser before Conversion
+     * @var phpDocumentor_IntermediateParser
+     */
+    var $render = false;
+    /**
+     * Packages to create documentation for
+     * @var string
+     */
+    var $packages = false;
+    /**
+     * contents of --filename commandline
+     * @tutorial phpDocumentor.howto.pkg#using.command-line.filename
+     * @var string
+     */
+    var $files = '';
+    /**
+     * contents of --directory commandline
+     * @tutorial phpDocumentor.howto.pkg#using.command-line.directory
+     * @var string
+     */
+    var $dirs = '';
+    /**
+     * contents of --hidden commandline
+     * @tutorial phpDocumentor.howto.pkg#using.command-line.hidden
+     * @var boolean
+     */
+    var $hidden = false;
+    /**
+     * time that parsing was started, used for informative timing of output
+     * @access private
+     */
+    var $parse_start_time;
+    /**
+     * contents of --ignore commandline
+     * @tutorial phpDocumentor.howto.pkg#using.command-line.ignore
+     * @var string
+     */
+    var $ignore_files = array();
+    /**
+     * contents of --ignoresymlinks commandline
+     * @var boolean
+     */
+    var $ignoresymlinks = false;
+
+    /**
+     * Checks PHP version, makes sure it is 4.2.0+, and chooses the
+     * phpDocumentorTParser if version is 4.3.0+
+     * @uses parseIni()
+     */
+    function phpDocumentor_setup()
+    {
+        global $_phpDocumentor_cvsphpfile_exts, $_phpDocumentor_setting;
+        if (!function_exists('is_a'))
+        {
+            print "phpDocumentor requires PHP version 4.2.0 or greater to function";
+            exit;
+        }
+
+        $this->setup = new Io;
+        if (!isset($interface) && !isset($_GET['interface']) && !isset($_phpDocumentor_setting))
+        {
+            // Parse the argv settings
+            $_phpDocumentor_setting = $this->setup->parseArgv();
+        }
+        if (isset($_phpDocumentor_setting['useconfig']) &&
+             !empty($_phpDocumentor_setting['useconfig'])) {
+            $this->readConfigFile($_phpDocumentor_setting['useconfig']);
+        }
+
+        // set runtime to a large value since this can take quite a while
+        // we can only set_time_limit when not in safe_mode bug #912064
+        if (!ini_get('safe_mode'))
+        {
+            set_time_limit(0);    // unlimited runtime
+        } else
+        {
+            phpDocumentor_out("time_limit cannot be set since your in safe_mode, please edit time_limit in your php.ini to allow enough time for phpDocumentor to run"); 
+        }
+  
+        $phpver = phpversion();
+        $phpdocver = PHPDOCUMENTOR_VER;
+        if (isset($_GET['interface'])) {
+            $phpver = "<b>$phpver</b>";
+            $phpdocver = "<b>$phpdocver</b>";
+        }
+        phpDocumentor_out("PHP Version $phpver\n");
+        phpDocumentor_out("phpDocumentor version $phpdocver\n\n");
+
+        $this->parseIni();
+        $this->setMemoryLimit();
+
+        /*
+         * NOTE:  
+         * It is possible for the tokenizer extension to be loaded,
+         * but actually be broken in the OS, and therefore not working...
+         * the conditional below will NOT recognize this scenario.
+         * You can separately run the {@link tokenizer_test.php} to
+         * verify that the tokenizer library is working correctly
+         * from the OS perspective.
+         */
+        if (tokenizer_ext) {
+            phpDocumentor_out("using tokenizer Parser\n");
+            $this->parse = new phpDocumentorTParser;
+        } else {
+            phpDocumentor_out("No Tokenizer support detected, so using default (slower) Parser..." . PHP_EOL);
+
+            if (version_compare(phpversion(), '4.3.0', '<')) {
+                phpDocumentor_out("    for faster parsing, recompile PHP with --enable-tokenizer." . PHP_EOL );
+            } else {
+                phpDocumentor_out("    for faster parsing, recompile PHP without --disable-tokenizer." . PHP_EOL );
+            }
+
+            $this->parse = new Parser;
+        }
+    }
+    
+    /**
+     * Get phpDocumentor settings from a user configuration file
+     * @param string user configuration file
+     */
+    function readConfigFile($file)
+    {
+        global $_phpDocumentor_setting, $_phpDocumentor_options;
+        // security
+        $file = str_replace(array('..','.ini','\\'),array('','','/'),$file);
+        if (is_file($file . '.ini'))
+        {
+            $_phpDocumentor_setting = phpDocumentor_parse_ini_file($file.'.ini');
+        } else
+        {
+            if ('@DATA-DIR@' != '@'.'DATA-DIR@')
+            {
+                $configdir = str_replace('\\','/', '@DATA-DIR@/PhpDocumentor') . PATH_DELIMITER . 'user' . PATH_DELIMITER;
+            } else {
+                $configdir = str_replace('\\','/',$GLOBALS['_phpDocumentor_install_dir']) . PATH_DELIMITER . 'user' . PATH_DELIMITER;
+            }
+            if (isset($_phpDocumentor_options['userdir'])) $configdir = $_phpDocumentor_options['userdir'];
+            if (substr($configdir,-1) != '/')
+            {
+                $configdir .= '/';
+            }
+            $_phpDocumentor_setting = phpDocumentor_parse_ini_file( $configdir . $file . '.ini');
+            if (empty($_phpDocumentor_setting['defaultpackagename']))
+            {
+                $_phpDocumentor_setting['defaultpackagename'] = 'default';
+            }
+        }
+        // don't want a loop condition!
+        unset($_phpDocumentor_setting['useconfig']);
+    }
+    
+    /**
+     * Get phpDocumentor settings from command-line or web interface
+     */
+    function readCommandLineSettings()
+    {
+        global $_phpDocumentor_setting,$interface,$_phpDocumentor_RIC_files;
+        // subscribe $render class to $parse class events
+        if (!isset($_phpDocumentor_setting['junk'])) $_phpDocumentor_setting['junk'] = '';
+        if (!isset($_phpDocumentor_setting['title'])) $_phpDocumentor_setting['title'] = 'Generated Documentation';
+        $temp_title = $_phpDocumentor_setting['title'];
+        $this->render = new phpDocumentor_IntermediateParser($temp_title);
+        if (isset($_phpDocumentor_setting['help']) || $_phpDocumentor_setting['junk'] == "-h" || $_phpDocumentor_setting['junk'] == "--help")
+        {
+            echo $this->setup->displayHelpMsg();
+            die();
+        }
+
+        // set to parse hidden files
+        $this->hidden = (isset($_phpDocumentor_setting['hidden'])) ? decideOnOrOff($_phpDocumentor_setting['hidden']) : false;
+
+        // set to parse through symlinks
+        $this->ignoresymlinks = (isset($_phpDocumentor_setting['ignoresymlinks'])) ? decideOnOrOff($_phpDocumentor_setting['ignoresymlinks']) : false;
+        
+        // set to parse elements marked private with @access private
+        $this->render->setParsePrivate((isset($_phpDocumentor_setting['parseprivate'])) ? decideOnOrOff($_phpDocumentor_setting['parseprivate']) : false);
+
+        // set to print warnings when undocumented elements are spotted
+        $this->render->setUndocumentedElementWarningsMode((isset($_phpDocumentor_setting['undocumentedelements'])) ? decideOnOrOff($_phpDocumentor_setting['undocumentedelements']) : false);
+
+        if (isset($_phpDocumentor_setting['ignoretags']))
+        {
+            $ignoretags = explode(',', $_phpDocumentor_setting['ignoretags']);
+            $ignoretags = array_map('trim', $ignoretags);
+            $tags = array();
+            foreach($ignoretags as $tag)
+            {
+                if (!in_array($tag,array('@global', '@access', '@package', '@ignore', '@name', '@param', '@return', '@staticvar', '@var')))
+                    $tags[] = $tag;
+            }
+            $_phpDocumentor_setting['ignoretags'] = $tags;
+        }
+        
+        if (isset($_phpDocumentor_setting['readmeinstallchangelog']))
+        {
+            $_phpDocumentor_setting['readmeinstallchangelog'] = explode(',',str_replace(' ','',$_phpDocumentor_setting['readmeinstallchangelog']));
+            $rics = array();
+            foreach($_phpDocumentor_setting['readmeinstallchangelog'] as $ric)
+            {
+                $rics[] = strtoupper(trim($ric));
+            }
+            $_phpDocumentor_RIC_files = $rics;
+        }
+        
+        if (isset($_phpDocumentor_setting['javadocdesc']) && $_phpDocumentor_setting['javadocdesc'] == 'on')
+        {
+            $this->parse->eventHandlers[PARSER_EVENT_DOCBLOCK] = 'JavaDochandleDocblock';
+        }
+        if (tokenizer_ext)
+        {
+            if (isset($_phpDocumentor_setting['sourcecode']) && $_phpDocumentor_setting['sourcecode'] == 'on')
+            {
+                $_phpDocumentor_setting['sourcecode'] = true;
+            } else
+            {
+                $_phpDocumentor_setting['sourcecode'] = false;
+            }
+        } else
+        {
+            if (isset($_phpDocumentor_setting['sourcecode']) && $_phpDocumentor_setting['sourcecode'] == 'on')
+            {
+                addWarning(PDERROR_SOURCECODE_IGNORED);
+            }
+            $_phpDocumentor_setting['sourcecode'] = false;
+        }
+        if (isset($_phpDocumentor_setting['converterparams']))
+        {
+            $_phpDocumentor_setting['converterparams'] = explode($_phpDocumentor_setting['converterparams']);
+            foreach($_phpDocumentor_setting['converterparams'] as $i => $p)
+            {
+                $_phpDocumentor_setting['converterparams'][$i] = trim($p);
+            }
+        }
+        if (isset($_phpDocumentor_setting['customtags']) && !empty($_phpDocumentor_setting['customtags']))
+        {
+            $c = explode(',',$_phpDocumentor_setting['customtags']);
+            for($i=0;$i<count($c); $i++)
+            {
+                $GLOBALS['_phpDocumentor_tags_allowed'][] = trim($c[$i]);
+            }
+        }
+        if (isset($_phpDocumentor_setting['pear']))
+        {
+            if ($_phpDocumentor_setting['pear'] === 'off') $_phpDocumentor_setting['pear'] = false;
+            if ($_phpDocumentor_setting['pear'] === 'on') $_phpDocumentor_setting['pear'] = true;
+        }
+        if (!isset($_phpDocumentor_setting['pear'])) $_phpDocumentor_setting['pear'] = false;
+        // set to change the default package name from "default" to whatever you want
+        if (isset($_phpDocumentor_setting['defaultpackagename']))
+        {
+            $GLOBALS['phpDocumentor_DefaultPackageName'] = trim($_phpDocumentor_setting['defaultpackagename']);
+        }
+        // set to change the default category name from "default" to whatever you want
+        if (isset($_phpDocumentor_setting['defaultcategoryname']))
+        {
+            $GLOBALS['phpDocumentor_DefaultCategoryName'] = trim($_phpDocumentor_setting['defaultcategoryname']);
+        }
+        
+        // set the mode (quiet or verbose)
+        $this->render->setQuietMode((isset($_phpDocumentor_setting['quiet'])) ? decideOnOrOff($_phpDocumentor_setting['quiet']) : false);
+
+        // Setup the different classes
+        if (isset($_phpDocumentor_setting['templatebase']))
+        {
+            $this->render->setTemplateBase(trim($_phpDocumentor_setting['templatebase']));
+        }
+        if (isset($_phpDocumentor_setting['target']) && !empty($_phpDocumentor_setting['target']))
+        {
+            $this->render->setTargetDir(trim($_phpDocumentor_setting['target']));
+        }
+        else
+        {
+            echo "a target directory must be specified\n try phpdoc -h\n";
+            die();
+        }
+        if (!empty($_phpDocumentor_setting['packageoutput']))
+        {
+            $this->packages = explode(",",trim($_phpDocumentor_setting['packageoutput']));
+            foreach($this->packages as $p => $v)
+            {
+                $this->packages[$p] = trim($v);
+            }
+        }
+        if (!empty($_phpDocumentor_setting['filename'])) {
+            $this->files = trim($_phpDocumentor_setting['filename']);
+        }
+        if (!empty($_phpDocumentor_setting['directory'])) {
+            $this->dirs = trim($_phpDocumentor_setting['directory']);
+        }
+    }
+    
+    function checkIgnoreTag($tagname, $inline = false)
+    {
+        global $_phpDocumentor_setting;
+        $tagname = '@'.$tagname;
+        if (!isset($_phpDocumentor_setting['ignoretags'])) return false;
+        if ($inline) $tagname = '{'.$tagname.'}';
+        return in_array($tagname, $_phpDocumentor_setting['ignoretags']);
+    }
+
+    /**
+     * Allow a memory_limit setting in phpDocumentor.ini to override php.ini or default memory limit
+     * @todo recognize "K" and "G" in memory_limit settings, rather than just "M"
+     */
+    function setMemoryLimit() {
+        global $_phpDocumentor_options;
+        $DEFAULT_MEMORY_SIZE_MINIMUM = 256;
+        
+        // PhpDoc memory_limit from phpDocumentor.ini overrides all other considerations
+        if (isset($_phpDocumentor_options['memory_limit'])) {
+            $phpdoc_ini_setting = str_replace('M', '', $_phpDocumentor_options['memory_limit']);
+
+            // allow phpdoc.ini to DISABLE the setting via "= -1"
+            if ($phpdoc_ini_setting == -1)
+            {
+                $memory_setting_to_use = $phpdoc_ini_setting;
+                $max_mem_log_message = "setting disabled by phpDocumentor.ini...\n";
+            }
+            else
+            {
+                $memory_setting_to_use = $phpdoc_ini_setting . "M";
+                $max_mem_log_message = "set at " . $memory_setting_to_use . " by phpDocumentor.ini...\n";
+            }
+        } else {
+            $php_ini_setting = str_replace('M', '', ini_get('memory_limit'));
+
+            // allow php.ini to DISABLE the setting via "= -1"
+            if ($php_ini_setting == -1)
+            {
+                // allow it to remain disabled
+                $memory_setting_to_use = $php_ini_setting;
+                $max_mem_log_message = "setting disabled by php.ini...\n";
+            }
+            else
+            {
+                // memory_limit from php.ini must be at least the default minimum
+                $memory_setting_to_use = ($php_ini_setting > $DEFAULT_MEMORY_SIZE_MINIMUM) ? $php_ini_setting . "M" : $DEFAULT_MEMORY_SIZE_MINIMUM . "M";
+                $max_mem_log_message = "set at " . $memory_setting_to_use . " after considering php.ini...\n";                
+            }
+        }
+        if (ini_set("memory_limit", $memory_setting_to_use))
+        {
+            // PHP had to have been compiled with "--enable-memory-limit" to allow setting the value explicitly
+            phpDocumentor_out("Maximum memory usage " . $max_mem_log_message);
+        }
+        else
+        {
+            // PHP must not have been compiled with "--enable-memory-limit", so we cannot modify it...
+            // no need to notify user of this unless they tried using memory_limit in their phpDocumentor.ini...
+            if (isset($phpdoc_ini_setting))
+            {
+                phpDocumentor_out("Unable to alter memory_limit via your phpDocumentor.ini... perhaps PHP wasn't compiled with \"--enable-memory-limit\"?\n");
+            }
+        }
+    }
+    
+    function setJavadocDesc()
+    {
+           $this->parse->eventHandlers[PARSER_EVENT_DOCBLOCK] = 'JavaDochandleDocblock';
+    }
+    
+    function setParsePrivate($flag = true)
+    {
+        $this->render->setParsePrivate($flag);
+    }
+    
+    function setQuietMode($flag = true)
+    {
+        $this->render->setQuietMode($flag);
+    }
+
+    function setUndocumentedElementWarnings($flag = true)
+    {
+        $this->render->setUndocumentedElementWarnings($flag);
+    }
+    
+    function setTargetDir($target)
+    {
+        $this->render->setTargetDir($target);
+    }
+    
+    function setTemplateBase($dir)
+    {
+        $this->render->setTemplateBase($dir);
+    }
+    
+    function setPackageOutput($po)
+    {
+        $this->packages = explode(",",$po);
+        array_map('trim', $this->packages);
+    }
+    
+    function setTitle($ti)
+    {
+        $this->render = new phpDocumentor_IntermediateParser($ti);
+    }
+    
+    function setFilesToParse($files)
+    {
+        $this->files = $files;
+    }
+    
+    function setDirectoriesToParse($dirs)
+    {
+        $this->dirs = $dirs;
+    }
+    
+    function parseHiddenFiles($flag = true)
+    {
+        $this->hidden = $flag;
+    }
+    
+    function setIgnore($ig)
+    {
+        if (strstr($ig,","))
+        {
+            $this->ignore_files = explode(",",$ig);
+        } else {
+            if (!empty($ig))
+            $this->ignore_files = array($ig);
+        }
+        $this->ignore_files = array_map('trim', $this->ignore_files);
+    }
+    
+    function createDocs($title = false)
+    {
+        $this->parse_start_time = time();
+        global $_phpDocumentor_setting;
+        if (!$this->render)
+        {
+            $this->render = new phpDocumentor_IntermediateParser($title);
+        }
+        // setup ignore  list
+        $this->ignore_files =array();
+        if(isset($_phpDocumentor_setting['ignore']))
+        {
+            $this->setIgnore($_phpDocumentor_setting['ignore']);
+        }
+        $this->parse->subscribe("*",$this->render);
+        // parse the directory
+        if (!empty($this->files))
+        {
+            $files = explode(",",$this->files);
+            foreach($files as $file)
+            {
+                $file = trim($file);
+                $test = $this->setup->getAllFiles($file);
+                if ($test)
+                {
+                    foreach($test as $file)
+                    {
+                        $file = trim($file);
+                        $dir = realpath(dirname($file));
+                        $dir = strtr($dir, "\\", "/");
+                        $dir = str_replace('//','/',$dir);
+                        // strip trailing directory seperator
+                        if (substr($dir,-1) == "/" || substr($dir,-1) == "\\")
+                        {
+                            $dir = substr($dir,0,-1);
+                        }
+                        $file = strtr(realpath($file), "\\", "/");
+                        $file = str_replace('//','/',$file);
+
+                        if (!$this->setup->checkIgnore(basename($file),dirname($file),$this->ignore_files,true,$this->ignoresymlinks))
+                        {
+                            $filelist[] = str_replace('\\','/',$file);
+                        } else {
+                            phpDocumentor_out("File $file Ignored\n");
+                            flush();
+                        }
+                    }
+                } else
+                {
+                    $dir = dirname(realpath($file));
+                    $dir = strtr($dir, "\\", "/");
+                    $dir = str_replace('//','/',$dir);
+                    // strip trailing directory seperator
+                    if (substr($dir,-1) == "/" || substr($dir,-1) == "\\")
+                    {
+                        $dir = substr($dir,0,-1);
+                    }
+                    $base = count(explode("/",$dir));
+                    $file = strtr(realpath($file), "\\", "/");
+                    $file = str_replace('//','/',$file);
+                    flush();
+
+                    if (!$this->setup->checkIgnore(basename($file),dirname($file),$this->ignore_files,true,$this->ignoresymlinks))
+                    {
+                        $filelist[] = str_replace('\\','/',$file);
+                    } else {
+                        phpDocumentor_out("File $file Ignored\n");
+                        flush();
+                    }
+                }
+            }
+        }
+        if (!empty($this->dirs))
+        {
+            $dirs = explode(",",$this->dirs);
+            foreach($dirs as $dir)
+            {
+                $olddir = $dir;
+                $dir = realpath($dir);
+                if (!$dir) {
+                    phpDocumentor_out('ERROR: "' . $olddir . '" does not exist, skipping');
+                    continue;
+                }
+                $dir = trim($dir);
+                $dir = strtr($dir, "\\", "/");
+                $dir = str_replace('//','/',$dir);
+                // strip trailing directory seperator
+                if (substr($dir,-1) == "/" || substr($dir,-1) == "\\")
+                {
+                    $dir = substr($dir,0,-1);
+                }
+                $files = $this->setup->dirList($dir,$this->hidden,$this->ignoresymlinks);
+                if (is_array($files))
+                {
+                    foreach($files as $file)
+                    {
+                        $file = strtr($file, '\\', '/');
+                        // file's subpath, relative to $dir
+                        $file_subpath = str_replace('\\', '/', realpath(dirname($file)));
+                        $file_subpath = preg_replace('[\\/]', DIRECTORY_SEPARATOR, $file_subpath);
+                        $file_subpath = preg_replace('~^' . preg_quote($dir, '~') . '~', '', $file_subpath);
+
+                        if (!$this->setup->checkIgnore(basename($file), $file_subpath, $this->ignore_files,true,$this->ignoresymlinks))
+                        {
+                            $filelist[] = $file;
+                        } else {
+                            phpDocumentor_out("File $file Ignored\n");
+                            flush();
+                        }
+                    }
+                }
+            }
+        }
+        if (isset($filelist))
+        {
+            if (PHPDOCUMENTOR_WINDOWS)
+            {
+                // case insensitive array_unique
+                usort($filelist,'strnatcasecmp');
+                reset($filelist);
+                
+                $newarray = array();
+                $i = 0;
+                
+                $element = current($filelist);
+                for ($n=0;$n<sizeof($filelist);$n++)
+                {
+                    if (strtolower(next($filelist)) != strtolower($element))
+                    {
+                        $newarray[$i] = $element;
+                        $element = current($filelist);
+                        $i++;
+                    }
+                }
+                $filelist = $newarray; 
+            } else $filelist = array_unique($filelist);
+
+            $base = count(explode("/",$source_base = $this->setup->getBase($filelist)));
+            define("PHPDOCUMENTOR_BASE",$source_base);
+            list($filelist,$ric) = $this->setup->getReadmeInstallChangelog($source_base, $filelist);
+            phpDocumentor_out("\n\nGrabbing README/INSTALL/CHANGELOG\n");
+            flush();
+            foreach($ric as $file)
+            {
+                phpDocumentor_out(basename($file).'...');
+                flush();
+                $fp = fopen($file,'r');
+                $contents = fread($fp,filesize($file));
+                $this->render->HandleEvent(PHPDOCUMENTOR_EVENT_README_INSTALL_CHANGELOG, array(basename($file),$contents));
+                fclose($fp);
+            }
+            phpDocumentor_out("\ndone\n");
+            flush();
+            list($filelist,$tutorials) = $this->setup->getTutorials($filelist);
+            phpDocumentor_out("\n\nTutorial/Extended Documentation Parsing Stage\n\n");
+            flush();
+            if (count($tutorials))
+            {
+                $tuteparser = new XMLPackagePageParser;
+                $tuteparser->subscribe('*',$this->render);
+                foreach($tutorials as $tutorial)
+                {
+                    switch($tutorial['tutetype'])
+                    {
+                        case 'pkg' :
+                        case 'cls' :
+                        case 'proc' :
+                        switch($tutorial['tutetype'])
+                        {
+                            case 'pkg' :
+                                $ptext = 'Package-level Docs ';
+                                if (!empty($tutorial['subpackage']))
+                                $ptext = 'Sub-Package Docs ';
+                            break;
+                            case 'cls' :
+                                $ptext = 'Class-level Docs ';
+                            break;
+                            case 'proc' :
+                                $ptext = 'Procedural-level Docs ';
+                            break;
+                        }
+                        $fp = @fopen($tutorial['path'],"r");
+                        if ($fp)
+                        {
+                            $ret = fread($fp,filesize($tutorial['path']));
+                            // fix 1151650
+                            if (stristr($ret, "utf-8") !== "")
+                            {
+                                $ret = utf8_decode($ret);
+                            }
+                            fclose($fp);
+                            unset($fp);
+                            phpDocumentor_out('Parsing '.$ptext.$tutorial['path'].'...');
+                            flush();
+                            $tuteparser->parse($ret,$tutorial);
+                            phpDocumentor_out("done\n");
+                            flush();
+                        } else
+                        {
+                            phpDocumentor_out('Error '.$ptext.$tutorial['path'].' doesn\'t exist'."\n");
+                            flush();
+                        }
+                        default :
+                        break;
+                    }
+                }
+            }
+            phpDocumentor_out("done\n");
+            flush();
+            phpDocumentor_out("\n\nGeneral Parsing Stage\n\n");
+            flush();
+            foreach($filelist as $file)
+            {
+                phpDocumentor_out("Reading file $file");
+                flush();
+                $this->parse->parse($a = $this->setup->readPhpFile($file, $this->render->quietMode),$file,$base,$this->packages);
+    
+            }
+            $b = (time() - $this->parse_start_time);
+            phpDocumentor_out("done\n");
+            flush();
+            // render output
+            phpDocumentor_out("\nConverting From Abstract Parsed Data\n");
+            flush();
+            $this->render->output();
+            $a = (time() - $this->parse_start_time);
+            $c = ($a - $b);
+            phpDocumentor_out("\nParsing time: $b seconds\n");
+            phpDocumentor_out("\nConversion time: $c seconds\n");
+            phpDocumentor_out("\nTotal Documentation Time: $a seconds\n");
+            phpDocumentor_out("done\n");
+            flush();
+        } else
+        {
+            print "\nERROR: nothing parsed\n";
+            exit;
+        }
+    }
+    /**
+     * Parse configuration file phpDocumentor.ini
+     */
+    function parseIni()
+    {
+        phpDocumentor_out("Parsing configuration file phpDocumentor.ini...\n");
+        flush();
+        if ('@DATA-DIR@' != '@'.'DATA-DIR@')
+        {
+            $options = phpDocumentor_parse_ini_file(str_replace('\\','/', '@DATA-DIR@/PhpDocumentor') . PATH_DELIMITER . 'phpDocumentor.ini',true);
+            phpDocumentor_out("   (found in " . '@DATA-DIR@/PhpDocumentor' . PATH_DELIMITER . ")...\n");
+        } else {
+            $options = phpDocumentor_parse_ini_file(str_replace('\\','/',$GLOBALS['_phpDocumentor_install_dir']) . PATH_DELIMITER . 'phpDocumentor.ini',true);
+            phpDocumentor_out("   (found in " . $GLOBALS['_phpDocumentor_install_dir'] . PATH_DELIMITER . ")...\n");
+        }
+
+        if (!$options)
+        {
+            print "ERROR: cannot open phpDocumentor.ini in directory " . $GLOBALS['_phpDocumentor_install_dir']."\n";
+            print "-Is phpdoc in either the path or include_path in your php.ini file?";
+            exit;
+        }
+        
+        foreach($options as $var => $values)
+        {
+            if ($var != 'DEBUG')
+            {
+//                phpDocumentor_out("\n$var");
+                if ($var != '_phpDocumentor_setting' && $var != '_phpDocumentor_options' && $var != '_phpDocumentor_install_dir' ) $values = array_values($values);
+//                fancy_debug("\n$var",$values);
+                $GLOBALS[$var] = $values;
+            }
+        }
+        phpDocumentor_out("\ndone\n");
+        flush();
+        /** Debug Constant */
+        if (!defined('PHPDOCUMENTOR_DEBUG')) define("PHPDOCUMENTOR_DEBUG",$options['DEBUG']['PHPDOCUMENTOR_DEBUG']);
+        if (!defined('PHPDOCUMENTOR_KILL_WHITESPACE')) define("PHPDOCUMENTOR_KILL_WHITESPACE",$options['DEBUG']['PHPDOCUMENTOR_KILL_WHITESPACE']);
+        $GLOBALS['_phpDocumentor_cvsphpfile_exts'] = $GLOBALS['_phpDocumentor_phpfile_exts'];
+        foreach($GLOBALS['_phpDocumentor_cvsphpfile_exts'] as $key => $val)
+        {
+            $GLOBALS['_phpDocumentor_cvsphpfile_exts'][$key] = "$val,v";
+        }
+        // none of this stuff is used anymore
+        if (isset($GLOBALS['_phpDocumentor_html_allowed']))
+        {
+            $___htmltemp = array_flip($GLOBALS['_phpDocumentor_html_allowed']);
+            $___html1 = array();
+            foreach($___htmltemp as $tag => $trans)
+            {
+                $___html1['<'.$tag.'>'] = htmlentities('<'.$tag.'>');
+                $___html1['</'.$tag.'>'] = htmlentities('</'.$tag.'>');
+            }
+            $GLOBALS['phpDocumentor___html'] = array_flip($___html1);
+        }
+    }
+    
+    /**
+     * Performs character-based validation of Output Converter Template name pieces
+     * @param string the name piece (just ONE of either Output, Converter, or Template piece)
+     * @param string any extra characters to allow beyond the default character set
+     * @return string|bool the clean name, or FALSE if piece is deemed invalid
+     * @access private
+     */
+    function cleanConverterNamePiece($name, $extra_characters_to_allow = '')
+    {
+        $name = str_replace("\\", "/", $name);
+        // security:  ensure no opportunity exists to use "../.." pathing in this value
+        $name = preg_replace('/[^a-zA-Z0-9' . $extra_characters_to_allow . '_-]/', "", $name);
+
+        // absolutely positively do NOT allow two consecutive dots ".."
+        if (strpos($name, '..') > -1) $name = false;
+        return $name;
+    }
+
+    /**
+     * Figures out what output converter to use
+     * @param string Output Converter Template name
+     * @access private
+     * @global array
+     * @uses cleanConverterNamePieces
+     * @uses phpDocumentor_out
+     */    
+    function setupConverters($output = false)
+    {
+        global $_phpDocumentor_setting;
+        if ($output)
+        {
+            $_phpDocumentor_setting['output'] = $output;
+        }
+        if (isset($_phpDocumentor_setting['output']) && !empty($_phpDocumentor_setting['output']))
+        {
+            $c = explode(',',$_phpDocumentor_setting['output']);
+            for($i=0; $i< count($c); $i++)
+            {
+                $c[$i] = explode(':',$c[$i]);
+                $a = $c[$i][0];
+                if (isset($c[$i][0]))
+                {
+                    $a = $this->cleanConverterNamePiece($c[$i][0]);
+                }
+                else
+                {
+                    $a = false;
+                }
+                if (isset($c[$i][1]))
+                {
+                    /*
+                     * must allow "/" due to options like "DocBook/peardoc2"
+                     */
+                    $b = $this->cleanConverterNamePiece($c[$i][1], '\/');
+                }
+                else
+                {
+                    $b = false;
+                }
+                if (isset($c[$i][2]))
+                {
+                    /*
+                     * must allow "." due to options like "phpdoc.de"
+                     * must allow "/" due to options like "DOM/default"
+                     */
+                    $d = $this->cleanConverterNamePiece($c[$i][2], '.\/');
+                    if (substr($d,-1) != "/")
+                    {
+                        $d .= "/";
+                    }
+                    else 
+                    {
+                        $d = 'default/';
+                    }
+                }
+                if (strtoupper(trim($a)) == 'HTML' && (trim($b) == 'default'))
+                {
+                    phpDocumentor_out("WARNING: HTMLdefaultConverter is deprecated, using HTMLframesConverter.\n");
+                    phpDocumentor_out("WARNING: template output is identical, HTMLframes is more flexible.\n");
+                    phpDocumentor_out("WARNING: please adjust your usage\n");
+                    flush();
+                    $b = 'frames'; // change default to frames.
+                }
+                $this->render->addConverter(strtoupper(trim($a)),trim($b),trim($d));
+            }
+        } else
+        {
+            $this->render->addConverter('HTML','frames','default/');
+        }
+        if (empty($this->render->converters)) addErrorDie(PDERROR_NO_CONVERTERS);
+    }
+}
+
+/**
+ * Fuzzy logic to interpret the boolean args' intent
+ * @param string the command-line option to analyze
+ * @return boolean our best guess of the value's boolean intent
+ */
+function decideOnOrOff($value_to_guess = 'NO VALUE WAS PASSED')
+{
+    $these_probably_mean_yes = array(
+        '',             // "--hidden" with no value 
+        'on',           // "--hidden on"
+        'y', 'yes',     // "--hidden y"
+        'true',         // "--hidden true"
+        '1'             // "--hidden 1"
+    );
+    $best_guess = false;    // default to "false", "off", "no", "take a hike"
+
+    if (in_array(strtolower(trim($value_to_guess)), $these_probably_mean_yes))
+    {
+        $best_guess = true;
+    }
+    return $best_guess;
+}
+
+/**
+ * Print parse information if quiet setting is off
+ */
+function phpDocumentor_out($string)
+{
+    global $_phpDocumentor_setting;
+    if ((isset($_phpDocumentor_setting['quiet'])) ? !decideOnOrOff($_phpDocumentor_setting['quiet']) : true)
+    {
+        print $string;
+    }
+
+}
+
+/**
+ * Crash in case of known, dangerous bug condition
+ * 
+ * Checks the PHP version that is executing PhpDocumentor,
+ * in case a known PHP/PEAR bug condition could be triggered
+ * by the PhpDocumentor execution.
+ * @param string $php_version the PHP version that contains the bug
+ * @param string $php_bug_number the PHP bug number (if any)
+ * @param string $pear_bug_number the PEAR bug number (if any)
+ */
+function checkForBugCondition($php_version, $php_bug_number = 'none', $pear_bug_number = 'none')
+{
+    if (version_compare(phpversion(), $php_version) == 0)
+    {
+        addErrorDie(PDERROR_DANGEROUS_PHP_BUG_EXISTS, $php_version, $php_bug_number, $pear_bug_number);
+    }
+}
+?>