updating phpDocumentor, part 2: add new version

1 files changed, 992 insertions, 0 deletions

diff --git a/buildscripts/PhpDocumentor/phpDocumentor/Io.inc b/buildscripts/PhpDocumentor/phpDocumentor/Io.inc
new file mode 100755
index 00000000..17eb326b
--- /dev/null
+++ b/buildscripts/PhpDocumentor/phpDocumentor/Io.inc
@@ -0,0 +1,992 @@
+<?php
+/**
+ * File and input handling routines
+ * 
+ * This class parses command-line options, and works with files to
+ * generate lists of files to parse based on the ignore/include options
+ * 
+ * phpDocumentor :: automatic documentation generator
+ * 
+ * PHP versions 4 and 5
+ *
+ * Copyright (c) 2000-2006 Joshua Eichorn, 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     Joshua Eichorn <jeichorn@phpdoc.org>
+ * @author     Gregory Beaver <cellog@php.net>
+ * @copyright  2000-2006 Joshua Eichorn, Gregory Beaver
+ * @license    http://www.opensource.org/licenses/lgpl-license.php LGPL
+ * @version    CVS: $Id: Io.inc 286921 2009-08-08 05:01:24Z ashnazg $
+ * @filesource
+ * @link       http://www.phpdoc.org
+ * @link       http://pear.php.net/PhpDocumentor
+ * @since      0.1
+ */
+/**
+ * Class to handle file and user io opperations
+ *
+ * @author    Joshua Eichorn <jeichorn@phpdoc.org>
+ * @author     Gregory Beaver <cellog@php.net>
+ * @version    $Id: Io.inc 286921 2009-08-08 05:01:24Z ashnazg $
+ * @package     phpDocumentor
+ */
+class Io 
+{
+    
+    /**
+     * Holds all the options that are avaible to the cmd line interface
+     * and to the different web interfaces
+     */
+    var $phpDocOptions;
+    /**
+     * Format: array(array(regexp-ready string to search for whole path,
+     * regexp-ready string to search for basename of ignore strings),...)
+     * @var false|array
+     */
+    var $ignore;
+    /**
+     * A specific array of values that boolean-based arguments can understand,
+     * aided by the {@link decideOnOrOff()} helper method.
+     * 
+     * Use lowercase letters always, to simplify string comparisons
+     * @var array 
+     */
+    var $valid_booleans = array
+    (
+        '', ' ', 'on', 'y', 'yes', 'true', '1', 
+        'off', 'n', 'no', 'false', '0'
+
+    );
+    
+    /**
+     * creates an array $this->phpDocOptions and sets program options in it.
+     * Array is in the format of:
+     * <pre>
+     * [filename][tag][] = "f";
+     * [filename][tag][] = "-file";
+     * [filename][desc] "name of file to parse"
+     * </pre>
+     */
+    function Io()
+    {
+        $this->phpDocOptions['filename']['tag'] = array( "-f", "--filename");
+        $this->phpDocOptions['filename']['desc'] = "name of file(s) to parse ',' file1,file2.  Can contain complete path and * ? wildcards";
+        $this->phpDocOptions['filename']['type'] = "path";
+
+        $this->phpDocOptions['directory']['tag'] = array( "-d", "--directory");
+        $this->phpDocOptions['directory']['desc'] = "name of a directory(s) to parse directory1,directory2";
+        $this->phpDocOptions['directory']['type'] = "path";
+
+        $this->phpDocOptions['examplesdir']['tag'] = array( "-ed", "--examplesdir");
+        $this->phpDocOptions['examplesdir']['desc'] = "full path of the directory to look for example files from @example tags";
+        $this->phpDocOptions['examplesdir']['type'] = "path";
+
+        $this->phpDocOptions['templatebase']['tag'] = array( "-tb", "--templatebase");
+        $this->phpDocOptions['templatebase']['desc'] = "base location of all templates for this parse.";
+        $this->phpDocOptions['templatebase']['type'] = "path";
+
+        $this->phpDocOptions['target']['tag'] = array("-t", "--target");
+        $this->phpDocOptions['target']['desc'] = "path where to save the generated files";
+        $this->phpDocOptions['target']['type'] = "path";
+        
+        $this->phpDocOptions['ignore']['tag'] = array("-i", "--ignore");
+        $this->phpDocOptions['ignore']['desc'] = "file(s) that will be ignored, multiple separated by ','.  Wildcards * and ? are ok";
+        $this->phpDocOptions['ignore']['type'] = "path";
+
+        $this->phpDocOptions['ignoresymlinks']['tag'] = array("-is", "--ignoresymlinks");
+        $this->phpDocOptions['ignoresymlinks']['desc'] = "ignore symlinks to other files or directories, default is off";
+        $this->phpDocOptions['ignoresymlinks']['type'] = "set";
+        $this->phpDocOptions['ignoresymlinks']['validvalues'] = $this->valid_booleans;
+
+        $this->phpDocOptions['ignoretags']['tag'] = array("-it", "--ignore-tags");
+        $this->phpDocOptions['ignoretags']['desc'] = "tags to ignore for this parse.  @package, @subpackage, @access and @ignore may not be ignored.";
+        $this->phpDocOptions['ignoretags']['type'] = "value";
+
+        $this->phpDocOptions['hidden']['tag'] = array("-dh", "--hidden");
+        $this->phpDocOptions['hidden']['desc'] = "set equal to on (-dh on) to descend into hidden directories (directories starting with '.'), default is off";
+        $this->phpDocOptions['hidden']['type'] = "set";
+        $this->phpDocOptions['hidden']['validvalues'] = $this->valid_booleans;
+
+        $this->phpDocOptions['quiet']['tag'] = array("-q", "--quiet");
+        $this->phpDocOptions['quiet']['desc'] = "do not display parsing/conversion messages.  Useful for cron jobs on/off default off";
+        $this->phpDocOptions['quiet']['type'] = "set";
+        $this->phpDocOptions['quiet']['validvalues'] = $this->valid_booleans;
+
+        $this->phpDocOptions['undocumentedelements']['tag'] = array("-ue", "--undocumentedelements");
+        $this->phpDocOptions['undocumentedelements']['desc'] = "Control whether or not warnings will be shown for undocumented elements. Useful for identifying classes and methods that haven't yet been documented on/off default off";
+        $this->phpDocOptions['undocumentedelements']['type'] = "set";
+        $this->phpDocOptions['undocumentedelements']['validvalues'] = $this->valid_booleans;
+
+        $this->phpDocOptions['title']['tag'] = array("-ti","--title");
+        $this->phpDocOptions['title']['desc'] = "title of generated documentation, default is 'Generated Documentation'";
+        $this->phpDocOptions['title']['type'] = "value";
+
+        $this->phpDocOptions['help']['tag'] = array("-h", "--help");
+        $this->phpDocOptions['help']['desc'] = "    show this help message";
+
+        $this->phpDocOptions['useconfig']['tag'] = array("-c","--useconfig");
+        $this->phpDocOptions['useconfig']['desc'] = "Use a Config file in the users/ subdirectory for all command-line options";
+        $this->phpDocOptions['useconfig']['type'] = "value";
+
+        $this->phpDocOptions['parseprivate']['tag'] = array("-pp","--parseprivate");
+        $this->phpDocOptions['parseprivate']['desc'] = "parse @internal and elements marked private with @access.  Use on/off, default off";
+        $this->phpDocOptions['parseprivate']['type'] = "set";
+        $this->phpDocOptions['parseprivate']['validvalues'] = array('on', 'off');
+
+        $this->phpDocOptions['packageoutput']['tag'] = array("-po","--packageoutput");
+        $this->phpDocOptions['packageoutput']['desc'] = "output documentation only for selected packages.  Use a comma-delimited list";
+        $this->phpDocOptions['packageoutput']['type'] = "value";
+
+        $this->phpDocOptions['defaultpackagename']['tag'] = array("-dn","--defaultpackagename");
+        $this->phpDocOptions['defaultpackagename']['desc'] = "name to use for the default package.  If not specified, uses 'default'";
+        $this->phpDocOptions['defaultpackagename']['type'] = "value";
+
+        $this->phpDocOptions['defaultcategoryname']['tag'] = array("-dc","--defaultcategoryname");
+        $this->phpDocOptions['defaultcategoryname']['desc'] = "name to use for the default category.  If not specified, uses 'default'";
+        $this->phpDocOptions['defaultcategoryname']['type'] = "value";
+
+        $this->phpDocOptions['output']['tag'] = array("-o","--output");
+        $this->phpDocOptions['output']['desc'] = "output information to use separated by ','.  Format: output:converter:templatedir like \"HTML:frames:phpedit\"";
+        $this->phpDocOptions['output']['type'] = "value";
+
+        $this->phpDocOptions['converterparams']['tag'] = array("-cp","--converterparams");
+        $this->phpDocOptions['converterparams']['desc'] = "dynamic parameters for a converter, separate values with commas";
+        $this->phpDocOptions['converterparams']['type'] = "value";
+
+        $this->phpDocOptions['customtags']['tag'] = array("-ct","--customtags");
+        $this->phpDocOptions['customtags']['desc'] = "custom tags, will be recognized and put in tags[] instead of unknowntags[]";
+        $this->phpDocOptions['customtags']['type'] = "value";
+
+        $this->phpDocOptions['sourcecode']['tag'] = array("-s","--sourcecode");
+        $this->phpDocOptions['sourcecode']['desc'] = "generate highlighted sourcecode for every parsed file (PHP 4.3.0+ only) on/off default off";
+        $this->phpDocOptions['sourcecode']['type'] = "set";
+        $this->phpDocOptions['sourcecode']['validvalues'] = array('on', 'off');
+
+        $this->phpDocOptions['javadocdesc']['tag'] = array("-j","--javadocdesc");
+        $this->phpDocOptions['javadocdesc']['desc'] = "JavaDoc-compliant description parsing.  Use on/off, default off (more flexibility)";
+        $this->phpDocOptions['javadocdesc']['type'] = "set";
+        $this->phpDocOptions['javadocdesc']['validvalues'] = array('on', 'off');
+
+        $this->phpDocOptions['pear']['tag'] = array("-p","--pear");
+        $this->phpDocOptions['pear']['desc'] = "Parse a PEAR-style repository (package is directory, _members are @access private) on/off default off";
+        $this->phpDocOptions['pear']['type'] = "set";
+        $this->phpDocOptions['pear']['validvalues'] = array('on', 'off');
+
+        $this->phpDocOptions['readmeinstallchangelog']['tag'] = array("-ric","--readmeinstallchangelog");
+        $this->phpDocOptions['readmeinstallchangelog']['desc'] = "Specify custom filenames to parse like README, INSTALL or CHANGELOG files";
+        $this->phpDocOptions['readmeinstallchangelog']['type'] = "value";
+
+        $this->phpDocOptions['general']['message'] ="You can have multiple directories and multiple files, as well as a combination of both options";
+    }
+
+    
+    /**
+     * create the help message for display on the command-line
+     * @return string a string containing a help message
+     */
+    function displayHelpMsg()
+    {
+        unset($ret);
+        $ret = "\n";
+        foreach($this->phpDocOptions as $data)
+        {
+            unset($tag);
+            $tag = "";
+            if (isset($data['tag']))
+            {
+                if (is_array($data['tag'])) {
+                    foreach($data['tag'] as $param) {
+                        $tag .= "$param    ";
+                    }
+                }
+		$taglen = 34;
+		$outputwidth = 79;
+		$tagspace = str_repeat(" ",$taglen);
+                $tmp = "  ".trim($tag).$tagspace;
+                $tmp = substr($tmp,0,$taglen);
+                $d = wordwrap(ltrim($data['desc']),($outputwidth-$taglen));
+		$dt = explode("\n",$d);
+		$dt[0] = $tmp .$dt[0];
+		for($i=1;$i<count($dt);$i++)
+		{
+			$dt[$i] = $tagspace.$dt[$i];
+		}
+		$ret .= implode("\n",$dt)."\n\n";
+		
+            }
+        }
+        $ret .= "\n".wordwrap($data['message'],$outputwidth)."\n";
+        return $ret; 
+    }
+    
+    /**
+     * calls {@link file_exists()} for each value in include_path,
+     * then calls {@link is_readable()} when it finds the file
+     * @param string
+     * @return boolean
+     */
+    function isIncludeable($filename)
+    {
+        $test = realpath($filename);
+        if ($test && is_readable($test)) {
+            return true; // for absolute paths
+        }
+        $ip = get_include_path();
+        if (PHPDOCUMENTOR_WINDOWS)
+        {
+            $ip = explode(';', $ip);
+        } else {
+            $ip = explode(':', $ip);
+        }
+        foreach($ip as $path)
+        {
+            if ($a = realpath($path . DIRECTORY_SEPARATOR . $filename))
+            {
+                if (is_readable($a))
+                {
+                    return true;
+                }
+            }
+        }
+        return false;
+    }
+
+    /**
+     * Parses $_SERVER['argv'] and creates a setup array
+     * @return array a setup array
+     * @global array command-line arguments
+     * @todo replace with Console_* ?
+     */
+    function parseArgv()
+    {
+        global $argv;
+
+        // defaults for setting
+        $setting['hidden'] = "off";
+        $setting['ignoresymlinks'] = 'off';
+        $setting['template'] = 'templates' . PATH_DELIMITER .'default' . PATH_DELIMITER;
+
+        $valnext = "junk";
+        $data = array();
+        if(isset($argv) && is_array($argv))
+        {
+            foreach ($argv as $cmd)
+            {
+                if ($cmd == '--') {
+                    continue;
+                }
+                if ($cmd == '-h' || $cmd == '--help')
+                {
+                    echo $this->displayHelpMsg();
+                    die();
+                }
+
+                // at first, set the arg value as if we
+                // already know it's formatted normally, e.g.
+                //    -q on
+                $setting[$valnext] = $cmd;
+
+                if (isset($data['type']) && $data['type'] == 'set') {
+
+                    if ($valnext !== 'junk' && strpos(trim($cmd),'-') === 0) {
+                        // if valnext isn't 'junk' (i.e it was an arg option) 
+                        // then the first arg needs an implicit "" as its value, e.g.
+                        //     ... -q -pp ...  ===>  ... -q '' -pp ... 
+                        $setting[$valnext] = '';
+
+                    } else if (!in_array(strtolower($cmd), $data['validvalues'], true)) {
+                        // the arg value is not a valid value
+                        addErrorDie(PDERROR_INVALID_VALUES, $valnext, $cmd,
+                            '(' . implode(', ', $data['validvalues']) . ')');
+                    }
+                }
+
+                foreach( $this->phpDocOptions as $name => $data )
+                {
+                    if (!empty($data['tag']))
+                    {
+                        if (in_array($cmd,$data['tag']))
+                        {
+                            $valnext = $name;
+                            break;
+                        } 
+                        else
+                        {
+                            $valnext = "junk";
+                        }
+                    }
+                }
+
+                if ($valnext == 'junk' && (strpos(trim($cmd),'-') === 0)) {
+                    // this indicates the last arg of the command 
+                    // is an arg option (-) that was preceded by unrecognized "junk"
+                    addErrorDie(PDERROR_UNKNOWN_COMMANDLINE,$cmd);
+
+                } else if ($valnext != 'junk' && (strpos(trim($cmd),'-') === 0)) {
+                    // this indicates the last arg of the command 
+                    // is an arg option (-) without an arg value
+                    
+                    // add an empty arg "value" for this arg "option"
+                    $setting[$valnext] = '';
+                }
+
+
+            }
+        } else
+        {
+            echo "Please use php-cli.exe in windows, or set register_argc_argv On";
+            die;
+        }
+        /* $setting will always have at least 3 elements
+        [hidden] => off
+        [ignoresymlinks] => 'off'
+        [template] => templates/default
+         */
+        if (count($setting) < 4) {
+            echo $this->displayhelpMsg();
+            die();
+        }
+
+        return $setting;
+    }
+
+
+    /**
+     * @return array list of files in a directory
+     * @param string $directory full path to the directory you want the list of
+     * @param bool whether to list files that begin with . like .bash_history
+     * @param bool whether to ignore symlinks
+     */
+    function dirList($orig_directory, $hidden = false, $ignore_symlinks = false)
+    {
+        $directory = realpath($orig_directory);
+        $ret = false;
+        if (! @is_dir($directory))
+        {
+            die("directory: '$directory'  not found\n");
+        }
+        $ret = array();
+        $d = @dir($directory); // thanks to Jason E Sweat (jsweat@users.sourceforge.net) for fix
+        while($d && ($entry=$d->read()) !== false) {
+            if (strcmp($entry,".") == 0 || strcmp($entry,"..") == 0) {
+                continue;
+            }
+
+            // skip hidden files, if we're supposed to
+            if (!$hidden)
+            {
+                if (substr($entry,0,1) == ".")
+                {
+                    phpDocumentor_out("Hidden " . $directory . PATH_DELIMITER . $entry . " Ignored\n");
+                    continue;
+                }
+            }
+
+            // skip symlink files, if we're supposed to
+            if ($ignore_symlinks)
+            {
+                if (is_link($directory . PATH_DELIMITER . $entry))
+                {
+                    phpDocumentor_out("Symlink " . $directory . PATH_DELIMITER . $entry . " Ignored\n");
+                    continue;
+                }
+            }
+            
+            if (is_file($directory . PATH_DELIMITER . $entry)) {
+                $ret[] = $directory . PATH_DELIMITER . $entry;
+            }
+            if (is_dir($directory . PATH_DELIMITER . $entry)) {
+                $tmp = $this->dirList($directory . PATH_DELIMITER . $entry, $hidden, $ignore_symlinks);
+                if (is_array($tmp)) {
+                    foreach($tmp as $ent) {
+                        $ret[] = $ent;
+                    }
+                }
+            }
+        }
+        if ($d) $d->close();
+        return $ret;
+    }
+
+    /**
+     * Retrieve common directory (case-insensitive in windows)
+     *
+     * takes the list of files, and returns the subdirectory they share in common,
+     * so in this list:
+     *
+     * <code>
+     * array(
+     * "/dir1/dir2/subdir/dir3/filename.ext",
+     * "/dir1/dir2/subdir/dir4/filename.ext",
+     * "/dir1/dir2/mydir/dir5/filename.ext");
+     * </code>
+     *
+     * getBase will return "/dir1/dir2"
+     * @param array array of strings
+     */
+    function getBase($filelist)
+    {
+        $masterPath = false;
+        foreach($filelist as $path)
+        {
+            if (!$masterPath)
+            {
+                $masterPath = str_replace('\\','/',dirname($path));
+            } else
+            {
+                if (dirname($path) != $masterPath)
+                {
+                    $mp = explode(PATH_DELIMITER, $masterPath);
+                    $np = explode(PATH_DELIMITER, str_replace('\\', '/', dirname($path)));
+                    if (count($np) < count($mp))
+                    {
+                        $masterPath = join($np, PATH_DELIMITER);
+                    } else
+                    {
+                        $test = false;
+                        $found = false;
+                        for($i=0;$i < count($mp) && $i < count($np);$i++)
+                        {
+                            if (PHPDOCUMENTOR_WINDOWS)
+                            {
+                                if (strtolower($mp[$i]) != strtolower($np[$i])) $found = $i;
+                            } else
+                            {
+                                if ($mp[$i] != $np[$i]) $found = $i;
+                            }
+                        }
+                        if ($found !== false)
+                        {
+                            $mp = array_slice($mp,0,$found);
+                            $masterPath = join($mp,PATH_DELIMITER);
+                        }
+                    }
+                }
+            }
+        }
+        return $masterPath;
+    }
+    
+    /**
+     * Retrieve tutorial subdirectories and their contents from the list of
+     * files to parse
+     * @param array array of paths (strings)
+     * @return array array(filelist - tutorials, tutorials)
+     */
+    function getTutorials($filelist)
+    {
+        $list = $tutorials = array();
+        foreach($filelist as $file)
+        {
+            if (strpos($file,'tutorials/') !== false)
+            {
+                $tutedir = explode('/',substr($file,strpos($file,'tutorials/')));
+                array_shift($tutedir);
+                if (count($tutedir) <= 3)
+                {
+                    $res = array();
+                    // kludge - will need to fix for 2.0
+                    $res['category'] = $GLOBALS['phpDocumentor_DefaultCategoryName'];
+                    $res['package'] = array_shift($tutedir);
+                    $res['subpackage'] = '';
+                    if (count($tutedir) > 1)
+                    $res['subpackage'] = array_shift($tutedir);
+                    $f = array_shift($tutedir);
+                    $res['tutename'] = $f;
+                    $f = explode('.',$f);
+                    $res['tutetype'] = array_pop($f);
+                    if ($res['tutetype'] == 'ini') continue;
+                    $res['path'] = $file;
+                    if (@file_exists($file . '.ini'))
+                    {
+                        $res['ini'] = phpDocumentor_parse_ini_file($file . '.ini', true);
+                    } else
+                    {
+                        $res['ini'] = false;
+                    }
+                    $tutorials[] = $res;
+                }
+            } else $list[] = $file;
+        }
+        return array($list,$tutorials);
+    }
+    
+    /**
+     * @param string base directory from {@link getBase()}
+     * @param array file list from {@link dirList()}
+     * @return array array(filelist - README/INSTALL/CHANGELOG,
+     *                     README/INSTALL/CHANGELOG)
+     */
+    function getReadmeInstallChangelog($base,$filelist)
+    {
+        $list = $ric = array();
+        $names = $GLOBALS['_phpDocumentor_RIC_files'];
+        foreach($filelist as $file)
+        {
+            if ((dirname($file) == $base) && in_array(strtoupper(basename($file)), $names))
+            { // be sure to change $this->checkIgnore() if any other files are added here!!
+                $ric[] = $file;
+            } else
+            {
+                $list[] = $file;
+            }
+        }
+        return array($list,$ric);
+    }
+
+    /**
+     * @param string directory
+     * @param string base directory
+     * @param array array of ignored items
+     * @param boolean the "hidden" flag
+     * @param boolean the "ignoresymlinks" flag
+     * @uses dirList
+     * @uses checkIgnore
+     * @uses setup_dirs
+     */    
+    function getDirTree($dir, $base_dir, $ignore = array(), $hidden = false, $ignoresymlinks = false)
+    {
+        $allfiles = $this->dirList($dir,$hidden,$ignoresymlinks);
+        $struc = array();
+        foreach($allfiles as $file)
+        {
+            if ($this->checkIgnore(basename($file),dirname(realpath($file)),$ignore,$ignoresymlinks)) continue;
+            if (PHPDOCUMENTOR_WINDOWS) {
+                $path = substr(dirname($file),strlen(str_replace('\\','/',realpath($base_dir))));
+            } else {
+                $path = substr(dirname($file),strlen(str_replace('\\','/',realpath($base_dir)))+1);
+            }
+            if (!$path) $path = '/';
+            $parts = pathinfo($file);
+            if (!isset($parts['extension']))
+            {
+                $parts['extension'] = '';
+            }
+            $struc[$path][] = array(
+                'file' => $parts['basename'],
+                'ext' => $parts['extension'],
+                'path' => $file);
+        }
+        uksort($struc,'strnatcasecmp');
+        foreach($struc as $key => $ind)
+        {
+            usort($ind,'Ioinc_sortfiles');
+            $struc[$key] = $ind;
+            $save = $key;
+            if ($key != '/')
+            {
+                $key = explode('/',$key);
+                while (count($key))
+                {
+                    array_pop($key);
+                    if (isset($struc[join('/',$key)]))
+                    {
+                        $struc[join('/',$key)][substr($save,strlen(join('/',$key)) + 1)] = $ind;
+                        unset($struc[$save]);
+                    }
+                }
+            }
+        }
+        foreach($struc as $key => $ind)
+        {
+            if ($key != '/')
+            {
+                if (count(explode('/',$key)) == 1)
+                {
+                    $struc['/'][$key] = $struc[$key];
+                    unset($struc[$key]);
+                }
+            }
+        }
+        $tempstruc = $struc;
+        unset($tempstruc['/']);
+        $leftover_dirs = array_keys($tempstruc);
+        $splitdirs = array();
+        foreach($leftover_dirs as $dir)
+        {
+            $splitdirs[] = explode('/',$dir);
+        }
+        $leftover_dirs = array();
+
+        foreach($splitdirs as $dir)
+        {
+            $save = join($dir,'/');
+            $struc['/'] = setup_dirs($struc['/'], $dir, $tempstruc[$save]);
+            unset($struc[$save]);
+        }
+        @uksort($struc['/'],'Ioinc_mystrucsort');
+        return $struc;
+    }
+    
+    /**
+     * Reads a file and returns it as a string
+     * Does basic error checking
+     *
+     * file extensions are set in {@link phpdoc.inc}
+     *
+     * @global array PHP File extensions, used to validate that $path is a PHP File
+     * @global array PHP File extensions in a CVS repository, used to validate that $path is a PHP File
+     * @param    string    $path
+     */
+    function readPhpFile($path, $quietMode = false)
+    {
+        global $_phpDocumentor_cvsphpfile_exts, $_phpDocumentor_phpfile_exts;
+        // tiberiusblue addition
+        $cvsExt = $_phpDocumentor_cvsphpfile_exts; 
+        $ext = $_phpDocumentor_phpfile_exts;
+        if (file_exists($path))
+        {
+            if (is_file($path))
+            {
+                // check extension
+                $tmp = explode(".",$path);
+                // tiberiusblue addition
+                $tmp2 = $tmp;
+                if (in_array(array_pop($tmp),$ext))
+                {
+                    phpDocumentor_out(" -- Parsing file\n");
+                    flush();
+                    if (function_exists('file_get_contents')) {
+                        return file_get_contents($path);
+                    }
+                    $fp = fopen($path,"r");
+                    $ret = fread($fp,filesize($path));
+                    fclose($fp);
+                    return $ret;
+                } elseif (in_array(array_pop($tmp2),$cvsExt)) 
+                { 
+                    phpDocumentor_out(" CVS file [EXPERIMENTAL]\n"); 
+                    flush();
+                    if (function_exists('file_get_contents')) {
+                        $ret = file_get_contents($path);
+                    } else {
+                        $fp = fopen($path,"r"); 
+                        $ret = fread($fp,filesize($path)); 
+                        fclose($fp); 
+                    }
+                    $ret = strstr($ret,"<?");
+                    $ret = substr($ret,0,strpos($ret,"@\n"));
+                    $ret = str_replace("@@","@",$ret); 
+                    return $ret; 
+                } else
+                {
+                    phpDocumentor_out(" -- File not parsed, not a php file\n");
+                    flush();
+                }
+            } else {
+                phpDocumentor_out(" -- Unable to read file, not a file\n");
+                flush();
+            }
+        } else {
+            phpDocumentor_out(" -- Unable to read file, file does not exist\n");
+            flush();
+           }
+    }
+
+    /**
+     * Tell whether to ignore a file or a directory
+     * allows * and ? wildcards
+     *
+     * @author Greg Beaver <cellog@php.net>
+     * @param    string  $file    just the file name of the file or directory,
+     *                          in the case of directories this is the last dir
+     * @param    string  $path    the path to consider (should be checked by
+     *                            realpath() before, and may be relative)
+     * @param    array   $ignore
+     * @param    bool
+     * @param    bool    Ignore symlinks?
+     * @return   bool    true if $path should be ignored, false if it should not
+     */
+    function checkIgnore($file,$path,$ignore,$ignore_no_ext = true,$ignoresymlinks = false)
+    {
+        global $_phpDocumentor_RIC_files;
+
+        if ($ignoresymlinks && is_link($path . PATH_DELIMITER . $file)) return false;
+        
+        if (!count($ignore)) return false;
+
+        if (!isset($this->ignore))
+        {
+            $this->_setupIgnore($ignore);
+        }
+        if (!$this->ignore)
+        {
+            return false;
+        }
+
+        if ($ignore_no_ext && 
+            !in_array(strtoupper($file), $_phpDocumentor_RIC_files))
+        {
+            if (!is_numeric(strpos($file,'.'))) return true;
+        }
+        if (is_array($this->ignore))
+        {
+            foreach($this->ignore as $match)
+            {
+                // match is an array if the ignore parameter was a /path/to/pattern
+                if (is_array($match))
+                {
+                    // check to see if the path matches with a path delimiter appended
+                    preg_match('/^' . strtoupper($match[0]).'$/', strtoupper($path) . PATH_DELIMITER,$find);
+                    if (!count($find))
+                    {
+                        // check to see if it matches without an appended path delimiter
+                        preg_match('/^' . strtoupper($match[0]).'$/', strtoupper($path), $find);
+                    }
+                    if (count($find))
+                    {
+                        // check to see if the file matches the file portion of the regex string
+                        preg_match('/^' . strtoupper($match[1]).'$/', strtoupper($file), $find);
+                        if (count($find))
+                        {
+                            return true;
+                        }
+                    }
+                    // check to see if the full path matches the regex
+                    preg_match('/^' . strtoupper($match[0]).'$/',
+                               strtoupper($path . DIRECTORY_SEPARATOR . $file), $find);
+                    if (count($find))
+                    {
+                        return true;
+                    }
+                } else
+                {
+                    // ignore parameter was just a pattern with no path delimiters
+                    // check it against the path
+                    preg_match('/^' . strtoupper($match).'$/', strtoupper($path), $find);
+                    if (count($find))
+                    {
+                        return true;
+                    }
+                    // check it against the file only
+                    preg_match('/^' . strtoupper($match).'$/', strtoupper($file), $find);
+                    if (count($find))
+                    {
+                        return true;
+                    }
+                }
+            }
+        }
+        return false;
+    }
+    
+    /**
+     * Construct the {@link $ignore} array
+     * @author Greg Beaver <cellog@php.net>
+     * @param array strings of files/paths/wildcards to ignore
+     * @access protected
+     */
+    function _setupIgnore($ignore)
+    {
+        $ig = array();
+        if ( ! is_array($ignore))
+        {
+            $this->ignore = false;
+            return;
+        }
+        for($i=0; $i<count($ignore);$i++)
+        {
+            if (empty($ignore[$i]))
+                continue;
+
+            $ignore[$i] = strtr($ignore[$i], '\\', '/');
+            $ignore[$i] = str_replace('//','/',$ignore[$i]);
+
+            if (!is_numeric(strpos($ignore[$i],PATH_DELIMITER)))
+            {
+                $ig[] = $this->getRegExpableSearchString($ignore[$i]);
+            } else
+            {
+                if (basename($ignore[$i]) . PATH_DELIMITER == $ignore[$i])
+                $ig[] = $this->getRegExpableSearchString($ignore[$i]);
+                else
+                $ig[] = array($this->getRegExpableSearchString($ignore[$i]),$this->getRegExpableSearchString(basename($ignore[$i])));
+            }
+        }
+        if (count($ig)) $this->ignore = $ig;
+    }
+    
+    /**
+     * Converts $s into a string that can be used with preg_match
+     * @param string $s string with wildcards ? and *
+     * @author Greg Beaver <cellog@php.net>
+     * @return string converts * to .*, ? to ., etc.
+     */
+    function getRegExpableSearchString($s)
+    {
+        $y = '\/';
+        if (DIRECTORY_SEPARATOR == '\\')
+        {
+            $y = '\\\\';
+        }
+        $s = str_replace('/', DIRECTORY_SEPARATOR, $s);
+        $x = strtr($s, array('?' => '.','*' => '.*','.' => '\\.','\\' => '\\\\','/' => '\\/',
+                                '[' => '\\[',']' => '\\]','-' => '\\-'));
+        if (strpos($s, DIRECTORY_SEPARATOR) !== false &&
+            strrpos($s, DIRECTORY_SEPARATOR) === strlen($s) - 1)
+        {
+            $x = "(?:.*$y$x?.*|$x.*)";
+        }
+        return $x;
+    }
+    
+    /**
+     * Removes files from the $dir array that do not match the search string in
+     * $match
+     * @param array $dir array of filenames (full path)
+     * @param string $match search string with wildcards
+     * @author Greg Beaver <cellog@php.net>
+     * @return string|array listing of every file in a directory that matches
+     *                      the search string
+     */
+    function removeNonMatches($dir, $match)
+    {
+        $match = $this->getRegExpableSearchString($match);
+        $nodir = false;
+        if (!is_array($dir))
+        {
+            $dir = array($dir);
+            $nodir = true;
+        }
+        foreach($dir as $i => $file)
+        {
+            preg_match('/^'.$match.'$/',basename($file),$find);
+            if (!count($find)) unset($dir[$i]);
+        }
+        if ($nodir) return $dir[0];
+        return $dir;
+    }
+    
+    /**
+     * Take a filename with wildcards and return all files that match the
+     * wildcards
+     * @param string $file a full path from the -f command-line parameter, with
+     * potential * and ? wildcards.
+     * @return mixed if $file contains wildcards, returns an array of matching
+     *               files, otherwise returns false
+     * @author Greg Beaver <cellog@php.net>
+     * @uses dirList
+     * @uses removeNonMatches
+     */
+    function getAllFiles($file)
+    {
+        $path = realpath(dirname($file));
+        $file = basename($file);
+        // any wildcards?
+        if (is_numeric(strpos($file,'?')) || is_numeric(strpos($file,'*')))
+        {
+            $files = $this->dirList($path);
+            $a = $this->removeNonMatches($files,$file);
+            return $a;
+        }
+        return false;
+    }
+}
+
+/**#@+
+ * Sorting functions for the file list
+ * @param string
+ * @param string
+ */
+function Ioinc_sortfiles($a, $b)
+{
+    return strnatcasecmp($a['file'],$b['file']);
+}
+
+function Ioinc_mystrucsort($a, $b)
+{
+    if (is_numeric($a) && is_string($b)) return 1;
+    if (is_numeric($b) && is_string($a)) return -1;
+    if (is_numeric($a) && is_numeric($b))
+    {
+        if ($a > $b) return 1;
+        if ($a < $b) return -1;
+        if ($a == $b) return 0;
+    }
+    return strnatcasecmp($a,$b);
+}
+/**#@-*/
+
+/**
+ * Recursively add all the subdirectories of $contents to $dir without erasing anything in
+ * $dir
+ * @param array
+ * @param array
+ * @return array processed $dir
+ */
+function set_dir($dir,$contents)
+{
+    while(list($one,$two) = each($contents))
+    {
+        if (isset($dir[$one]))
+        {
+            $dir[$one] = set_dir($dir[$one],$contents[$one]);
+        } else $dir[$one] = $two;
+    }
+    return $dir;
+}
+
+/**
+ * Recursively move contents of $struc into associative array
+ *
+ * The contents of $struc have many indexes like 'dir/subdir/subdir2'.
+ * This function converts them to
+ * array('dir' => array('subdir' => array('subdir2')))
+ * @param array struc is array('dir' => array of files in dir,'dir/subdir' => array of files in dir/subdir,...)
+ * @param array array form of 'dir/subdir/subdir2' array('dir','subdir','subdir2')
+ * @return array same as struc but with array('dir' => array(file1,file2,'subdir' => array(file1,...)))
+ */
+function setup_dirs($struc,$dir,$contents)
+{
+    if (!count($dir))
+    {
+        foreach($contents as $dir => $files)
+        {
+            if (is_string($dir))
+            {
+                if (strpos($dir,'/'))
+                {
+                    $test = true;
+                    $a = $contents[$dir];
+                    unset($contents[$dir]);
+                    $b = explode('/',$dir);
+                    $c = array_shift($b);
+                    if (isset($contents[$c]))
+                    {
+                        $contents[$c] = set_dir($contents[$c],setup_dirs(array(),$b,$a));
+                    } else $contents[$c] = setup_dirs(array(),$b,$a);
+                }
+            }
+        }
+        return $contents;
+    }
+    $me = array_shift($dir);
+    if (!isset($struc[$me])) $struc[$me] = array();
+    $struc[$me] = setup_dirs($struc[$me],$dir,$contents);
+    return $struc;
+}
+
+if (!function_exists('get_include_path')) {
+function get_include_path()
+{
+    return ini_get('include_path');
+}
+}
+?>