MarkdownExtra_Parser

Complexity

Total Complexity

140

Size/Duplication

Total Lines	1556
Duplicated Lines	21.34 %

Coupling/Cohesion

Components	1
Dependencies	1

Importance

Changes

0

40 Methods

Rating	Name	Duplication	Size	Complexity
B	MarkdownExtra_Parser()	0	28	1
A	setup()	0	21	3
A	teardown()	0	13	1
C	doExtraAttributes()	0	34	8
B	stripLinkDefinitions()	35	35	1
A	_stripLinkDefinitions_callback()	0	8	2
B	hashHTMLBlocks()	0	25	2
D	_hashHTMLBlocks_inMarkdown()	24	244	24
D	_hashHTMLBlocks_inHTML()	2	173	19
A	hashClean()	0	8	1
A	doAnchors()	71	71	2
B	_doAnchors_reference_callback()	5	36	5
A	_doAnchors_inline_callback()	22	22	3
A	doImages()	56	56	1
B	_doImages_reference_callback()	5	30	5
A	_doImages_inline_callback()	19	19	3
B	doHeaders()	0	40	1
A	_doHeaders_callback_setext()	2	8	4
A	_doHeaders_callback_atx()	0	6	1
A	doTables()	0	61	1
A	_doTable_leadingPipe_callback()	0	10	1
B	_doTable_callback()	0	58	8
B	doDefLists()	0	42	1
A	_doDefLists_callback()	0	10	1
B	processDefListItems()	0	43	1
A	_processDefListItems_callback_dt()	0	9	2
A	_processDefListItems_callback_dd()	10	18	3
B	doFencedCodeBlocks()	39	39	1
B	_doFencedCodeBlocks_callback()	0	21	6
A	_doFencedCodeBlocks_newlines()	0	4	1
B	formParagraphs()	0	34	3
B	stripFootnotes()	27	27	1
A	_stripFootnotes_callback()	0	5	1
A	doFootnotes()	0	10	2
B	appendFootnotes()	0	64	7
B	_appendFootnotes_callback()	0	41	5
A	stripAbbreviations()	15	15	1
A	_stripAbbreviations_callback()	0	9	2
A	doAbbreviations()	0	16	2
A	_doAbbreviations_callback()	0	14	3

<?php
#
# Markdown Extra  -  A text-to-HTML conversion tool for web writers
#
# PHP Markdown & Extra  
# Copyright (c) 2004-2013 Michel Fortin  
# <http://michelf.ca/projects/php-markdown/>
#
# Original Markdown  
# Copyright (c) 2004-2006 John Gruber  
# <http://daringfireball.net/projects/markdown/>
#


define( 'MARKDOWN_VERSION',  "1.0.2" ); # 29 Nov 2013
define( 'MARKDOWNEXTRA_VERSION',  "1.2.8" ); # 29 Nov 2013


#
# Global default settings:
#

# Change to ">" for HTML output
@define( 'MARKDOWN_EMPTY_ELEMENT_SUFFIX',  " />");

It seems like you do not handle an error condition here. This can introduce security issues, and is generally not recommended.

# Define the width of a tab for code blocks.
@define( 'MARKDOWN_TAB_WIDTH',     4 );

It seems like you do not handle an error condition here. This can introduce security issues, and is generally not recommended.

# Optional title attribute for footnote links and backlinks.
@define( 'MARKDOWN_FN_LINK_TITLE',         "" );

It seems like you do not handle an error condition here. This can introduce security issues, and is generally not recommended.

@define( 'MARKDOWN_FN_BACKLINK_TITLE',     "" );

It seems like you do not handle an error condition here. This can introduce security issues, and is generally not recommended.

# Optional class attribute for footnote links and backlinks.
@define( 'MARKDOWN_FN_LINK_CLASS',         "" );

It seems like you do not handle an error condition here. This can introduce security issues, and is generally not recommended.

@define( 'MARKDOWN_FN_BACKLINK_CLASS',     "" );

It seems like you do not handle an error condition here. This can introduce security issues, and is generally not recommended.

# Optional class prefix for fenced code block.
@define( 'MARKDOWN_CODE_CLASS_PREFIX',     "" );

It seems like you do not handle an error condition here. This can introduce security issues, and is generally not recommended.

# Class attribute for code blocks goes on the `code` tag;
# setting this to true will put attributes on the `pre` tag instead.
@define( 'MARKDOWN_CODE_ATTR_ON_PRE',   false );

It seems like you do not handle an error condition here. This can introduce security issues, and is generally not recommended.

#
# WordPress settings:
#

# Change to false to remove Markdown from posts and/or comments.
@define( 'MARKDOWN_WP_POSTS',      true );

It seems like you do not handle an error condition here. This can introduce security issues, and is generally not recommended.

@define( 'MARKDOWN_WP_COMMENTS',   true );

It seems like you do not handle an error condition here. This can introduce security issues, and is generally not recommended.

### Standard Function Interface ###

@define( 'MARKDOWN_PARSER_CLASS',  'MarkdownExtra_Parser' );

It seems like you do not handle an error condition here. This can introduce security issues, and is generally not recommended.

function Markdown($text) {
#
# Initialize the parser and return the result of its transform method.
#
	# Setup static parser variable.
	static $parser;
	if (!isset($parser)) {
		$parser_class = MARKDOWN_PARSER_CLASS;
		$parser = new $parser_class;
	}

	# Transform text using parser.
	return $parser->transform($text);
}


### WordPress Plugin Interface ###

/*
Plugin Name: Markdown Extra
Plugin Name: Markdown
Plugin URI: http://michelf.ca/projects/php-markdown/
Description: <a href="http://daringfireball.net/projects/markdown/syntax">Markdown syntax</a> allows you to write using an easy-to-read, easy-to-write plain text format. Based on the original Perl version by <a href="http://daringfireball.net/">John Gruber</a>. <a href="http://michelf.ca/projects/php-markdown/">More...</a>
Version: 1.2.8
Author: Michel Fortin
Author URI: http://michelf.ca/
*/

if (isset($wp_version)) {
	# More details about how it works here:
	# <http://michelf.ca/weblog/2005/wordpress-text-flow-vs-markdown/>
	
	# Post content and excerpts
	# - Remove WordPress paragraph generator.
	# - Run Markdown on excerpt, then remove all tags.
	# - Add paragraph tag around the excerpt, but remove it for the excerpt rss.
	if (MARKDOWN_WP_POSTS) {
		remove_filter('the_content',     'wpautop');
        remove_filter('the_content_rss', 'wpautop');
		remove_filter('the_excerpt',     'wpautop');
		add_filter('the_content',     'mdwp_MarkdownPost', 6);
        add_filter('the_content_rss', 'mdwp_MarkdownPost', 6);
		add_filter('get_the_excerpt', 'mdwp_MarkdownPost', 6);
		add_filter('get_the_excerpt', 'trim', 7);
		add_filter('the_excerpt',     'mdwp_add_p');
		add_filter('the_excerpt_rss', 'mdwp_strip_p');
		
		remove_filter('content_save_pre',  'balanceTags', 50);
		remove_filter('excerpt_save_pre',  'balanceTags', 50);
		add_filter('the_content',  	  'balanceTags', 50);
		add_filter('get_the_excerpt', 'balanceTags', 9);
	}
	
	# Add a footnote id prefix to posts when inside a loop.
	function mdwp_MarkdownPost($text) {
		static $parser;
		if (!$parser) {
			$parser_class = MARKDOWN_PARSER_CLASS;
			$parser = new $parser_class;
		}
		if (is_single() || is_page() || is_feed()) {
			$parser->fn_id_prefix = "";
		} else {
			$parser->fn_id_prefix = get_the_ID() . ".";
		}
		return $parser->transform($text);
	}
	
	# Comments
	# - Remove WordPress paragraph generator.
	# - Remove WordPress auto-link generator.
	# - Scramble important tags before passing them to the kses filter.
	# - Run Markdown on excerpt then remove paragraph tags.
	if (MARKDOWN_WP_COMMENTS) {
		remove_filter('comment_text', 'wpautop', 30);
		remove_filter('comment_text', 'make_clickable');
		add_filter('pre_comment_content', 'Markdown', 6);
		add_filter('pre_comment_content', 'mdwp_hide_tags', 8);
		add_filter('pre_comment_content', 'mdwp_show_tags', 12);
		add_filter('get_comment_text',    'Markdown', 6);
		add_filter('get_comment_excerpt', 'Markdown', 6);
		add_filter('get_comment_excerpt', 'mdwp_strip_p', 7);
	
		global $mdwp_hidden_tags, $mdwp_placeholders;
		$mdwp_hidden_tags = explode(' ',
			'<p> </p> <pre> </pre> <ol> </ol> <ul> </ul> <li> </li>');
		$mdwp_placeholders = explode(' ', str_rot13(
			'pEj07ZbbBZ U1kqgh4w4p pre2zmeN6K QTi31t9pre ol0MP1jzJR '.
			'ML5IjmbRol ulANi1NsGY J7zRLJqPul liA8ctl16T K9nhooUHli'));
	}
	
	function mdwp_add_p($text) {
		if (!preg_match('{^$|^<(p|ul|ol|dl|pre|blockquote)>}i', $text)) {
			$text = '<p>'.$text.'</p>';
			$text = preg_replace('{\n{2,}}', "</p>\n\n<p>", $text);
		}
		return $text;
	}
	
	function mdwp_strip_p($t) { return preg_replace('{</?p>}i', '', $t); }

	function mdwp_hide_tags($text) {
		global $mdwp_hidden_tags, $mdwp_placeholders;
		return str_replace($mdwp_hidden_tags, $mdwp_placeholders, $text);
	}
	function mdwp_show_tags($text) {
		global $mdwp_hidden_tags, $mdwp_placeholders;
		return str_replace($mdwp_placeholders, $mdwp_hidden_tags, $text);
	}
}


### bBlog Plugin Info ###

function identify_modifier_markdown() {
	return array(
		'name' => 'markdown',
		'type' => 'modifier',
		'nicename' => 'PHP Markdown Extra',
		'description' => 'A text-to-HTML conversion tool for web writers',
		'authors' => 'Michel Fortin and John Gruber',
		'licence' => 'GPL',
		'version' => MARKDOWNEXTRA_VERSION,
		'help' => '<a href="http://daringfireball.net/projects/markdown/syntax">Markdown syntax</a> allows you to write using an easy-to-read, easy-to-write plain text format. Based on the original Perl version by <a href="http://daringfireball.net/">John Gruber</a>. <a href="http://michelf.ca/projects/php-markdown/">More...</a>',
		);
}


### Smarty Modifier Interface ###

function smarty_modifier_markdown($text) {
	return Markdown($text);
}


### Textile Compatibility Mode ###

# Rename this file to "classTextile.php" and it can replace Textile everywhere.

if (strcasecmp(substr(__FILE__, -16), "classTextile.php") == 0) {
	# Try to include PHP SmartyPants. Should be in the same directory.
	@include_once 'smartypants.php';

It seems like you do not handle an error condition here. This can introduce security issues, and is generally not recommended.

	# Fake Textile class. It calls Markdown instead.
	class Textile {
		function TextileThis($text, $lite='', $encode='') {

It is generally recommended to explicitly declare the visibility for methods.

			if ($lite == '' && $encode == '')    $text = Markdown($text);
			if (function_exists('SmartyPants'))  $text = SmartyPants($text);
			return $text;
		}
		# Fake restricted version: restrictions are not supported for now.
		function TextileRestricted($text, $lite='', $noimage='') {

It is generally recommended to explicitly declare the visibility for methods.

			return $this->TextileThis($text, $lite);
		}
		# Workaround to ensure compatibility with TextPattern 4.0.3.
		function blockLite($text) { return $text; }

It is generally recommended to explicitly declare the visibility for methods.

	}
}



#
# Markdown Parser Class
#

class Markdown_Parser {

	### Configuration Variables ###

	# Change to ">" for HTML output.
	var $empty_element_suffix = MARKDOWN_EMPTY_ELEMENT_SUFFIX;
	var $tab_width = MARKDOWN_TAB_WIDTH;
	
	# Change to `true` to disallow markup or entities.
	var $no_markup = false;
	var $no_entities = false;
	
	# Predefined urls and titles for reference links and images.
	var $predef_urls = array();
	var $predef_titles = array();


	### Parser Implementation ###

	# Regex to match balanced [brackets].
	# Needed to insert a maximum bracked depth while converting to PHP.
	var $nested_brackets_depth = 6;
	var $nested_brackets_re;
	
	var $nested_url_parenthesis_depth = 4;
	var $nested_url_parenthesis_re;

	# Table of hash values for escaped characters:
	var $escape_chars = '\`*_{}[]()>#+-.!';
	var $escape_chars_re;


	function Markdown_Parser() {

It is generally recommended to explicitly declare the visibility for methods.

	#
	# Constructor function. Initialize appropriate member variables.
	#
		$this->_initDetab();
		$this->prepareItalicsAndBold();
	
		$this->nested_brackets_re = 
			str_repeat('(?>[^\[\]]+|\[', $this->nested_brackets_depth).
			str_repeat('\])*', $this->nested_brackets_depth);
	
		$this->nested_url_parenthesis_re = 
			str_repeat('(?>[^()\s]+|\(', $this->nested_url_parenthesis_depth).
			str_repeat('(?>\)))*', $this->nested_url_parenthesis_depth);
		
		$this->escape_chars_re = '['.preg_quote($this->escape_chars).']';
		
		# Sort document, block, and span gamut in ascendent priority order.
		asort($this->document_gamut);
		asort($this->block_gamut);
		asort($this->span_gamut);
	}


	# Internal hashes used during transformation.
	var $urls = array();
	var $titles = array();
	var $html_hashes = array();
	
	# Status flag to avoid invalid nesting.
	var $in_anchor = false;
	
	
	function setup() {

It is generally recommended to explicitly declare the visibility for methods.

	#
	# Called before the transformation process starts to setup parser 
	# states.
	#
		# Clear global hashes.
		$this->urls = $this->predef_urls;
		$this->titles = $this->predef_titles;
		$this->html_hashes = array();
		
		$this->in_anchor = false;
	}
	
	function teardown() {

It is generally recommended to explicitly declare the visibility for methods.

	#
	# Called after the transformation process to clear any variable 
	# which may be taking up memory unnecessarly.
	#
		$this->urls = array();
		$this->titles = array();
		$this->html_hashes = array();
	}


	function transform($text) {

It is generally recommended to explicitly declare the visibility for methods.

	#
	# Main function. Performs some preprocessing on the input text
	# and pass it through the document gamut.
	#
		$this->setup();
	
		# Remove UTF-8 BOM and marker character in input, if present.
		$text = preg_replace('{^\xEF\xBB\xBF|\x1A}', '', $text);

		# Standardize line endings:
		#   DOS to Unix and Mac to Unix
		$text = preg_replace('{\r\n?}', "\n", $text);

		# Make sure $text ends with a couple of newlines:
		$text .= "\n\n";

		# Convert all tabs to spaces.
		$text = $this->detab($text);

		# Turn block-level HTML blocks into hash entries
		$text = $this->hashHTMLBlocks($text);

		# Strip any lines consisting only of spaces and tabs.
		# This makes subsequent regexen easier to write, because we can
		# match consecutive blank lines with /\n+/ instead of something
		# contorted like /[ ]*\n+/ .
		$text = preg_replace('/^[ ]+$/m', '', $text);

		# Run document gamut methods.
		foreach ($this->document_gamut as $method => $priority) {
			$text = $this->$method($text);
		}
		
		$this->teardown();

		return $text . "\n";
	}
	
	var $document_gamut = array(
		# Strip link definitions, store in hashes.
		"stripLinkDefinitions" => 20,
		
		"runBasicBlockGamut"   => 30,
		);


	function stripLinkDefinitions($text) {

It is generally recommended to explicitly declare the visibility for methods.

This method seems to be duplicated in your project.

	#
	# Strips link definitions from text, stores the URLs and titles in
	# hash references.
	#
		$less_than_tab = $this->tab_width - 1;

		# Link defs are in the form: ^[id]: url "optional title"
		$text = preg_replace_callback('{
							^[ ]{0,'.$less_than_tab.'}\[(.+)\][ ]?:	# id = $1
							  [ ]*
							  \n?				# maybe *one* newline
							  [ ]*
							(?:
							  <(.+?)>			# url = $2
							|
							  (\S+?)			# url = $3
							)
							  [ ]*
							  \n?				# maybe one newline
							  [ ]*
							(?:
								(?<=\s)			# lookbehind for whitespace
								["(]
								(.*?)			# title = $4
								[")]
								[ ]*
							)?	# title is optional
							(?:\n+|\Z)
			}xm',
			array(&$this, '_stripLinkDefinitions_callback'),
			$text);
		return $text;
	}
	function _stripLinkDefinitions_callback($matches) {

It is generally recommended to explicitly declare the visibility for methods.

		$link_id = strtolower($matches[1]);
		$url = $matches[2] == '' ? $matches[3] : $matches[2];
		$this->urls[$link_id] = $url;
		$this->titles[$link_id] =& $matches[4];
		return ''; # String that will replace the block
	}


	function hashHTMLBlocks($text) {

It is generally recommended to explicitly declare the visibility for methods.

		if ($this->no_markup)  return $text;

		$less_than_tab = $this->tab_width - 1;

		# Hashify HTML blocks:
		# We only want to do this for block-level HTML tags, such as headers,
		# lists, and tables. That's because we still want to wrap <p>s around
		# "paragraphs" that are wrapped in non-block-level tags, such as anchors,
		# phrase emphasis, and spans. The list of tags we're looking for is
		# hard-coded:
		#
		# *  List "a" is made of tags which can be both inline or block-level.
		#    These will be treated block-level when the start tag is alone on 
		#    its line, otherwise they're not matched here and will be taken as 
		#    inline later.
		# *  List "b" is made of tags which are always block-level;
		#
		$block_tags_a_re = 'ins|del';
		$block_tags_b_re = 'p|div|h[1-6]|blockquote|pre|table|dl|ol|ul|address|'.
						   'script|noscript|form|fieldset|iframe|math|svg|'.
						   'article|section|nav|aside|hgroup|header|footer|'.
						   'figure';

		# Regular expression for the content of a block tag.
		$nested_tags_level = 4;
		$attr = '
			(?>				# optional tag attributes
			  \s			# starts with whitespace
			  (?>
				[^>"/]+		# text outside quotes
			  |
				/+(?!>)		# slash not followed by ">"
			  |
				"[^"]*"		# text inside double quotes (tolerate ">")
			  |
				\'[^\']*\'	# text inside single quotes (tolerate ">")
			  )*
			)?	
			';
		$content =
			str_repeat('
				(?>
				  [^<]+			# content without tag
				|
				  <\2			# nested opening tag
					'.$attr.'	# attributes
					(?>
					  />
					|
					  >', $nested_tags_level).	# end of opening tag
					  '.*?'.					# last level nested tag content
			str_repeat('
					  </\2\s*>	# closing nested tag
					)
				  |				
					<(?!/\2\s*>	# other tags with a different name
				  )
				)*',
				$nested_tags_level);
		$content2 = str_replace('\2', '\3', $content);

		# First, look for nested blocks, e.g.:
		# 	<div>
		# 		<div>
		# 		tags for inner block must be indented.
		# 		</div>
		# 	</div>
		#
		# The outermost tags must start at the left margin for this to match, and
		# the inner nested divs must be indented.
		# We need to do this before the next, more liberal match, because the next
		# match will start at the first `<div>` and stop at the first `</div>`.
		$text = preg_replace_callback('{(?>
			(?>
				(?<=\n\n)		# Starting after a blank line
				|				# or
				\A\n?			# the beginning of the doc
			)
			(						# save in $1

			  # Match from `\n<tag>` to `</tag>\n`, handling nested tags 
			  # in between.
					
						[ ]{0,'.$less_than_tab.'}
						<('.$block_tags_b_re.')# start tag = $2
						'.$attr.'>			# attributes followed by > and \n
						'.$content.'		# content, support nesting
						</\2>				# the matching end tag
						[ ]*				# trailing spaces/tabs
						(?=\n+|\Z)	# followed by a newline or end of document

			| # Special version for tags of group a.

						[ ]{0,'.$less_than_tab.'}
						<('.$block_tags_a_re.')# start tag = $3
						'.$attr.'>[ ]*\n	# attributes followed by >
						'.$content2.'		# content, support nesting
						</\3>				# the matching end tag
						[ ]*				# trailing spaces/tabs
						(?=\n+|\Z)	# followed by a newline or end of document
					
			| # Special case just for <hr />. It was easier to make a special 
			  # case than to make the other regex more complicated.
			
						[ ]{0,'.$less_than_tab.'}
						<(hr)				# start tag = $2
						'.$attr.'			# attributes
						/?>					# the matching end tag
						[ ]*
						(?=\n{2,}|\Z)		# followed by a blank line or end of document
			
			| # Special case for standalone HTML comments:
			
					[ ]{0,'.$less_than_tab.'}
					(?s:
						<!-- .*? -->
					)
					[ ]*
					(?=\n{2,}|\Z)		# followed by a blank line or end of document
			
			| # PHP and ASP-style processor instructions (<? and <%)
			
					[ ]{0,'.$less_than_tab.'}
					(?s:
						<([?%])			# $2
						.*?
						\2>
					)
					[ ]*
					(?=\n{2,}|\Z)		# followed by a blank line or end of document
					
			)
			)}Sxmi',
			array(&$this, '_hashHTMLBlocks_callback'),
			$text);

		return $text;
	}
	function _hashHTMLBlocks_callback($matches) {

It is generally recommended to explicitly declare the visibility for methods.

		$text = $matches[1];
		$key  = $this->hashBlock($text);
		return "\n\n$key\n\n";
	}
	
	
	function hashPart($text, $boundary = 'X') {

It is generally recommended to explicitly declare the visibility for methods.

	#
	# Called whenever a tag must be hashed when a function insert an atomic 
	# element in the text stream. Passing $text to through this function gives
	# a unique text-token which will be reverted back when calling unhash.
	#
	# The $boundary argument specify what character should be used to surround
	# the token. By convension, "B" is used for block elements that needs not
	# to be wrapped into paragraph tags at the end, ":" is used for elements
	# that are word separators and "X" is used in the general case.
	#
		# Swap back any tag hash found in $text so we do not have to `unhash`
		# multiple times at the end.
		$text = $this->unhash($text);
		
		# Then hash the block.
		static $i = 0;
		$key = "$boundary\x1A" . ++$i . $boundary;
		$this->html_hashes[$key] = $text;
		return $key; # String that will replace the tag.
	}


	function hashBlock($text) {

It is generally recommended to explicitly declare the visibility for methods.

	#
	# Shortcut function for hashPart with block-level boundaries.
	#
		return $this->hashPart($text, 'B');
	}


	var $block_gamut = array(
	#
	# These are all the transformations that form block-level
	# tags like paragraphs, headers, and list items.
	#
		"doHeaders"         => 10,
		"doHorizontalRules" => 20,
		
		"doLists"           => 40,
		"doCodeBlocks"      => 50,
		"doBlockQuotes"     => 60,
		);

	function runBlockGamut($text) {

It is generally recommended to explicitly declare the visibility for methods.

	#
	# Run block gamut tranformations.
	#
		# We need to escape raw HTML in Markdown source before doing anything 
		# else. This need to be done for each block, and not only at the 
		# begining in the Markdown function since hashed blocks can be part of
		# list items and could have been indented. Indented blocks would have 
		# been seen as a code block in a previous pass of hashHTMLBlocks.
		$text = $this->hashHTMLBlocks($text);
		
		return $this->runBasicBlockGamut($text);
	}
	
	function runBasicBlockGamut($text) {

It is generally recommended to explicitly declare the visibility for methods.

	#
	# Run block gamut tranformations, without hashing HTML blocks. This is 
	# useful when HTML blocks are known to be already hashed, like in the first
	# whole-document pass.
	#
		foreach ($this->block_gamut as $method => $priority) {
			$text = $this->$method($text);
		}
		
		# Finally form paragraph and restore hashed blocks.
		$text = $this->formParagraphs($text);

		return $text;
	}
	
	
	function doHorizontalRules($text) {

It is generally recommended to explicitly declare the visibility for methods.

		# Do Horizontal Rules:
		return preg_replace(
			'{
				^[ ]{0,3}	# Leading space
				([-*_])		# $1: First marker
				(?>			# Repeated marker group
					[ ]{0,2}	# Zero, one, or two spaces.
					\1			# Marker character
				){2,}		# Group repeated at least twice
				[ ]*		# Tailing spaces
				$			# End of line.
			}mx',
			"\n".$this->hashBlock("<hr$this->empty_element_suffix")."\n", 
			$text);
	}


	var $span_gamut = array(
	#
	# These are all the transformations that occur *within* block-level
	# tags like paragraphs, headers, and list items.
	#
		# Process character escapes, code spans, and inline HTML
		# in one shot.
		"parseSpan"           => -30,

		# Process anchor and image tags. Images must come first,
		# because ![foo][f] looks like an anchor.
		"doImages"            =>  10,
		"doAnchors"           =>  20,
		
		# Make links out of things like `<http://example.com/>`
		# Must come after doAnchors, because you can use < and >
		# delimiters in inline links like [this](<url>).
		"doAutoLinks"         =>  30,
		"encodeAmpsAndAngles" =>  40,

		"doItalicsAndBold"    =>  50,
		"doHardBreaks"        =>  60,
		);

	function runSpanGamut($text) {

It is generally recommended to explicitly declare the visibility for methods.

	#
	# Run span gamut tranformations.
	#
		foreach ($this->span_gamut as $method => $priority) {
			$text = $this->$method($text);
		}

		return $text;
	}
	
	
	function doHardBreaks($text) {

It is generally recommended to explicitly declare the visibility for methods.

		# Do hard breaks:
		return preg_replace_callback('/ {2,}\n/', 
			array(&$this, '_doHardBreaks_callback'), $text);
	}
	function _doHardBreaks_callback($matches) {

It is generally recommended to explicitly declare the visibility for methods.

		return $this->hashPart("<br$this->empty_element_suffix\n");
	}


	function doAnchors($text) {

It is generally recommended to explicitly declare the visibility for methods.

This method seems to be duplicated in your project.

	#
	# Turn Markdown link shortcuts into XHTML <a> tags.
	#
		if ($this->in_anchor) return $text;
		$this->in_anchor = true;
		
		#
		# First, handle reference-style links: [link text] [id]
		#
		$text = preg_replace_callback('{
			(					# wrap whole match in $1
			  \[
				('.$this->nested_brackets_re.')	# link text = $2
			  \]

			  [ ]?				# one optional space
			  (?:\n[ ]*)?		# one optional newline followed by spaces

			  \[
				(.*?)		# id = $3
			  \]
			)
			}xs',
			array(&$this, '_doAnchors_reference_callback'), $text);

		#
		# Next, inline-style links: [link text](url "optional title")
		#
		$text = preg_replace_callback('{
			(				# wrap whole match in $1
			  \[
				('.$this->nested_brackets_re.')	# link text = $2
			  \]
			  \(			# literal paren
				[ \n]*
				(?:
					<(.+?)>	# href = $3
				|
					('.$this->nested_url_parenthesis_re.')	# href = $4
				)
				[ \n]*
				(			# $5
				  ([\'"])	# quote char = $6
				  (.*?)		# Title = $7
				  \6		# matching quote
				  [ \n]*	# ignore any spaces/tabs between closing quote and )
				)?			# title is optional
			  \)
			)
			}xs',
			array(&$this, '_doAnchors_inline_callback'), $text);

		#
		# Last, handle reference-style shortcuts: [link text]
		# These must come last in case you've also got [link text][1]
		# or [link text](/foo)
		#
		$text = preg_replace_callback('{
			(					# wrap whole match in $1
			  \[
				([^\[\]]+)		# link text = $2; can\'t contain [ or ]
			  \]
			)
			}xs',
			array(&$this, '_doAnchors_reference_callback'), $text);

		$this->in_anchor = false;
		return $text;
	}
	function _doAnchors_reference_callback($matches) {

It is generally recommended to explicitly declare the visibility for methods.

		$whole_match =  $matches[1];
		$link_text   =  $matches[2];
		$link_id     =& $matches[3];

		if ($link_id == "") {
			# for shortcut links like [this][] or [this].
			$link_id = $link_text;
		}
		
		# lower-case and turn embedded newlines into spaces
		$link_id = strtolower($link_id);
		$link_id = preg_replace('{[ ]?\n}', ' ', $link_id);

		if (isset($this->urls[$link_id])) {
			$url = $this->urls[$link_id];
			$url = $this->encodeAttribute($url);
			
			$result = "<a href=\"$url\"";
			if ( isset( $this->titles[$link_id] ) ) {
				$title = $this->titles[$link_id];
				$title = $this->encodeAttribute($title);
				$result .=  " title=\"$title\"";
			}
		
			$link_text = $this->runSpanGamut($link_text);
			$result .= ">$link_text</a>";
			$result = $this->hashPart($result);
		}
		else {
			$result = $whole_match;
		}
		return $result;
	}
	function _doAnchors_inline_callback($matches) {

It is generally recommended to explicitly declare the visibility for methods.

This method seems to be duplicated in your project.

		$whole_match	=  $matches[1];

$whole_match is not used, you could remove the assignment.

		$link_text		=  $this->runSpanGamut($matches[2]);
		$url			=  $matches[3] == '' ? $matches[4] : $matches[3];
		$title			=& $matches[7];

		$url = $this->encodeAttribute($url);

		$result = "<a href=\"$url\"";
		if (isset($title)) {
			$title = $this->encodeAttribute($title);
			$result .=  " title=\"$title\"";
		}
		
		$link_text = $this->runSpanGamut($link_text);
		$result .= ">$link_text</a>";

		return $this->hashPart($result);
	}


	function doImages($text) {

It is generally recommended to explicitly declare the visibility for methods.

This method seems to be duplicated in your project.

	#
	# Turn Markdown image shortcuts into <img> tags.
	#
		#
		# First, handle reference-style labeled images: ![alt text][id]
		#
		$text = preg_replace_callback('{
			(				# wrap whole match in $1
			  !\[
				('.$this->nested_brackets_re.')		# alt text = $2
			  \]

			  [ ]?				# one optional space
			  (?:\n[ ]*)?		# one optional newline followed by spaces

			  \[
				(.*?)		# id = $3
			  \]

			)
			}xs', 
			array(&$this, '_doImages_reference_callback'), $text);

		#
		# Next, handle inline images:  ![alt text](url "optional title")
		# Don't forget: encode * and _
		#
		$text = preg_replace_callback('{
			(				# wrap whole match in $1
			  !\[
				('.$this->nested_brackets_re.')		# alt text = $2
			  \]
			  \s?			# One optional whitespace character
			  \(			# literal paren
				[ \n]*
				(?:
					<(\S*)>	# src url = $3
				|
					('.$this->nested_url_parenthesis_re.')	# src url = $4
				)
				[ \n]*
				(			# $5
				  ([\'"])	# quote char = $6
				  (.*?)		# title = $7
				  \6		# matching quote
				  [ \n]*
				)?			# title is optional
			  \)
			)
			}xs',
			array(&$this, '_doImages_inline_callback'), $text);

		return $text;
	}
	function _doImages_reference_callback($matches) {

It is generally recommended to explicitly declare the visibility for methods.

		$whole_match = $matches[1];
		$alt_text    = $matches[2];
		$link_id     = strtolower($matches[3]);

		if ($link_id == "") {
			$link_id = strtolower($alt_text); # for shortcut links like ![this][].
		}

		$alt_text = $this->encodeAttribute($alt_text);
		if (isset($this->urls[$link_id])) {
			$url = $this->encodeAttribute($this->urls[$link_id]);
			$result = "<img src=\"$url\" alt=\"$alt_text\"";
			if (isset($this->titles[$link_id])) {
				$title = $this->titles[$link_id];
				$title = $this->encodeAttribute($title);
				$result .=  " title=\"$title\"";
			}
			$result .= $this->empty_element_suffix;
			$result = $this->hashPart($result);
		}
		else {
			# If there's no such link ID, leave intact:
			$result = $whole_match;
		}

		return $result;
	}
	function _doImages_inline_callback($matches) {

It is generally recommended to explicitly declare the visibility for methods.

This method seems to be duplicated in your project.

		$whole_match	= $matches[1];

$whole_match is not used, you could remove the assignment.

		$alt_text		= $matches[2];
		$url			= $matches[3] == '' ? $matches[4] : $matches[3];
		$title			=& $matches[7];

		$alt_text = $this->encodeAttribute($alt_text);
		$url = $this->encodeAttribute($url);
		$result = "<img src=\"$url\" alt=\"$alt_text\"";
		if (isset($title)) {
			$title = $this->encodeAttribute($title);
			$result .=  " title=\"$title\""; # $title already quoted
		}
		$result .= $this->empty_element_suffix;

		return $this->hashPart($result);
	}


	function doHeaders($text) {

It is generally recommended to explicitly declare the visibility for methods.

		# Setext-style headers:
		#	  Header 1
		#	  ========
		#  
		#	  Header 2
		#	  --------
		#
		$text = preg_replace_callback('{ ^(.+?)[ ]*\n(=+|-+)[ ]*\n+ }mx',
			array(&$this, '_doHeaders_callback_setext'), $text);

		# atx-style headers:
		#	# Header 1
		#	## Header 2
		#	## Header 2 with closing hashes ##
		#	...
		#	###### Header 6
		#
		$text = preg_replace_callback('{
				^(\#{1,6})	# $1 = string of #\'s
				[ ]*
				(.+?)		# $2 = Header text
				[ ]*
				\#*			# optional closing #\'s (not counted)
				\n+
			}xm',
			array(&$this, '_doHeaders_callback_atx'), $text);

		return $text;
	}
	function _doHeaders_callback_setext($matches) {

It is generally recommended to explicitly declare the visibility for methods.

		# Terrible hack to check we haven't found an empty list item.
		if ($matches[2] == '-' && preg_match('{^-(?: |$)}', $matches[1]))
			return $matches[0];
		
		$level = $matches[2]{0} == '=' ? 1 : 2;
		$block = "<h$level>".$this->runSpanGamut($matches[1])."</h$level>";
		return "\n" . $this->hashBlock($block) . "\n\n";
	}
	function _doHeaders_callback_atx($matches) {

It is generally recommended to explicitly declare the visibility for methods.

		$level = strlen($matches[1]);
		$block = "<h$level>".$this->runSpanGamut($matches[2])."</h$level>";
		return "\n" . $this->hashBlock($block) . "\n\n";
	}


	function doLists($text) {

It is generally recommended to explicitly declare the visibility for methods.

	#
	# Form HTML ordered (numbered) and unordered (bulleted) lists.
	#
		$less_than_tab = $this->tab_width - 1;

		# Re-usable patterns to match list item bullets and number markers:
		$marker_ul_re  = '[*+-]';
		$marker_ol_re  = '\d+[\.]';
		$marker_any_re = "(?:$marker_ul_re|$marker_ol_re)";

$marker_any_re is not used, you could remove the assignment.

		$markers_relist = array(
			$marker_ul_re => $marker_ol_re,
			$marker_ol_re => $marker_ul_re,
			);

		foreach ($markers_relist as $marker_re => $other_marker_re) {
			# Re-usable pattern to match any entirel ul or ol list:
			$whole_list_re = '
				(								# $1 = whole list
				  (								# $2
					([ ]{0,'.$less_than_tab.'})	# $3 = number of spaces
					('.$marker_re.')			# $4 = first list item marker
					[ ]+
				  )
				  (?s:.+?)
				  (								# $5
					  \z
					|
					  \n{2,}
					  (?=\S)
					  (?!						# Negative lookahead for another list item marker
						[ ]*
						'.$marker_re.'[ ]+
					  )
					|
					  (?=						# Lookahead for another kind of list
					    \n
						\3						# Must have the same indentation
						'.$other_marker_re.'[ ]+
					  )
				  )
				)
			'; // mx
			
			# We use a different prefix before nested lists than top-level lists.
			# See extended comment in _ProcessListItems().
		
			if ($this->list_level) {
				$text = preg_replace_callback('{
						^
						'.$whole_list_re.'
					}mx',
					array(&$this, '_doLists_callback'), $text);
			}
			else {
				$text = preg_replace_callback('{
						(?:(?<=\n)\n|\A\n?) # Must eat the newline
						'.$whole_list_re.'
					}mx',
					array(&$this, '_doLists_callback'), $text);
			}
		}

		return $text;
	}
	function _doLists_callback($matches) {

It is generally recommended to explicitly declare the visibility for methods.

		# Re-usable patterns to match list item bullets and number markers:
		$marker_ul_re  = '[*+-]';
		$marker_ol_re  = '\d+[\.]';
		$marker_any_re = "(?:$marker_ul_re|$marker_ol_re)";

$marker_any_re is not used, you could remove the assignment.

		
		$list = $matches[1];
		$list_type = preg_match("/$marker_ul_re/", $matches[4]) ? "ul" : "ol";
		
		$marker_any_re = ( $list_type == "ul" ? $marker_ul_re : $marker_ol_re );
		
		$list .= "\n";
		$result = $this->processListItems($list, $marker_any_re);
		
		$result = $this->hashBlock("<$list_type>\n" . $result . "</$list_type>");
		return "\n". $result ."\n\n";
	}

	var $list_level = 0;

	function processListItems($list_str, $marker_any_re) {

It is generally recommended to explicitly declare the visibility for methods.

	#
	#	Process the contents of a single ordered or unordered list, splitting it
	#	into individual list items.
	#
		# The $this->list_level global keeps track of when we're inside a list.
		# Each time we enter a list, we increment it; when we leave a list,
		# we decrement. If it's zero, we're not in a list anymore.
		#
		# We do this because when we're not inside a list, we want to treat
		# something like this:
		#
		#		I recommend upgrading to version
		#		8. Oops, now this line is treated
		#		as a sub-list.
		#
		# As a single paragraph, despite the fact that the second line starts
		# with a digit-period-space sequence.
		#
		# Whereas when we're inside a list (or sub-list), that line will be
		# treated as the start of a sub-list. What a kludge, huh? This is
		# an aspect of Markdown's syntax that's hard to parse perfectly
		# without resorting to mind-reading. Perhaps the solution is to
		# change the syntax rules such that sub-lists must start with a
		# starting cardinal number; e.g. "1." or "a.".
		
		$this->list_level++;

		# trim trailing blank lines:
		$list_str = preg_replace("/\n{2,}\\z/", "\n", $list_str);

		$list_str = preg_replace_callback('{
			(\n)?							# leading line = $1
			(^[ ]*)							# leading whitespace = $2
			('.$marker_any_re.'				# list marker and space = $3
				(?:[ ]+|(?=\n))	# space only required if item is not empty
			)
			((?s:.*?))						# list item text   = $4
			(?:(\n+(?=\n))|\n)				# tailing blank line = $5
			(?= \n* (\z | \2 ('.$marker_any_re.') (?:[ ]+|(?=\n))))
			}xm',
			array(&$this, '_processListItems_callback'), $list_str);

		$this->list_level--;
		return $list_str;
	}
	function _processListItems_callback($matches) {

It is generally recommended to explicitly declare the visibility for methods.

		$item = $matches[4];
		$leading_line =& $matches[1];
		$leading_space =& $matches[2];
		$marker_space = $matches[3];
		$tailing_blank_line =& $matches[5];

		if ($leading_line || $tailing_blank_line || 
			preg_match('/\n{2,}/', $item))
		{
			# Replace marker with the appropriate whitespace indentation
			$item = $leading_space . str_repeat(' ', strlen($marker_space)) . $item;
			$item = $this->runBlockGamut($this->outdent($item)."\n");
		}
		else {
			# Recursion for sub-lists:
			$item = $this->doLists($this->outdent($item));
			$item = preg_replace('/\n+$/', '', $item);
			$item = $this->runSpanGamut($item);
		}

		return "<li>" . $item . "</li>\n";
	}


	function doCodeBlocks($text) {

It is generally recommended to explicitly declare the visibility for methods.

	#
	#	Process Markdown `<pre><code>` blocks.
	#
		$text = preg_replace_callback('{
				(?:\n\n|\A\n?)
				(	            # $1 = the code block -- one or more lines, starting with a space/tab
				  (?>
					[ ]{'.$this->tab_width.'}  # Lines must start with a tab or a tab-width of spaces
					.*\n+
				  )+
				)
				((?=^[ ]{0,'.$this->tab_width.'}\S)|\Z)	# Lookahead for non-space at line-start, or end of doc
			}xm',
			array(&$this, '_doCodeBlocks_callback'), $text);

		return $text;
	}
	function _doCodeBlocks_callback($matches) {

It is generally recommended to explicitly declare the visibility for methods.

		$codeblock = $matches[1];

		$codeblock = $this->outdent($codeblock);
		$codeblock = htmlspecialchars($codeblock, ENT_NOQUOTES);

		# trim leading newlines and trailing newlines
		$codeblock = preg_replace('/\A\n+|\n+\z/', '', $codeblock);

		$codeblock = "<pre><code>$codeblock\n</code></pre>";
		return "\n\n".$this->hashBlock($codeblock)."\n\n";
	}


	function makeCodeSpan($code) {

It is generally recommended to explicitly declare the visibility for methods.

	#
	# Create a code span markup for $code. Called from handleSpanToken.
	#
		$code = htmlspecialchars(trim($code), ENT_NOQUOTES);
		return $this->hashPart("<code>$code</code>");
	}


	var $em_relist = array(
		''  => '(?:(?<!\*)\*(?!\*)|(?<!_)_(?!_))(?=\S|$)(?![\.,:;]\s)',
		'*' => '(?<=\S|^)(?<!\*)\*(?!\*)',
		'_' => '(?<=\S|^)(?<!_)_(?!_)',
		);
	var $strong_relist = array(
		''   => '(?:(?<!\*)\*\*(?!\*)|(?<!_)__(?!_))(?=\S|$)(?![\.,:;]\s)',
		'**' => '(?<=\S|^)(?<!\*)\*\*(?!\*)',
		'__' => '(?<=\S|^)(?<!_)__(?!_)',
		);
	var $em_strong_relist = array(
		''    => '(?:(?<!\*)\*\*\*(?!\*)|(?<!_)___(?!_))(?=\S|$)(?![\.,:;]\s)',
		'***' => '(?<=\S|^)(?<!\*)\*\*\*(?!\*)',
		'___' => '(?<=\S|^)(?<!_)___(?!_)',
		);
	var $em_strong_prepared_relist;
	
	function prepareItalicsAndBold() {

It is generally recommended to explicitly declare the visibility for methods.

	#
	# Prepare regular expressions for searching emphasis tokens in any
	# context.
	#
		foreach ($this->em_relist as $em => $em_re) {
			foreach ($this->strong_relist as $strong => $strong_re) {
				# Construct list of allowed token expressions.
				$token_relist = array();
				if (isset($this->em_strong_relist["$em$strong"])) {
					$token_relist[] = $this->em_strong_relist["$em$strong"];
				}
				$token_relist[] = $em_re;
				$token_relist[] = $strong_re;
				
				# Construct master expression from list.
				$token_re = '{('. implode('|', $token_relist) .')}';
				$this->em_strong_prepared_relist["$em$strong"] = $token_re;
			}
		}
	}
	
	function doItalicsAndBold($text) {

It is generally recommended to explicitly declare the visibility for methods.

		$token_stack = array('');
		$text_stack = array('');
		$em = '';
		$strong = '';
		$tree_char_em = false;
		
		while (1) {
			#
			# Get prepared regular expression for seraching emphasis tokens
			# in current context.
			#
			$token_re = $this->em_strong_prepared_relist["$em$strong"];
			
			#
			# Each loop iteration search for the next emphasis token. 
			# Each token is then passed to handleSpanToken.
			#
			$parts = preg_split($token_re, $text, 2, PREG_SPLIT_DELIM_CAPTURE);
			$text_stack[0] .= $parts[0];
			$token =& $parts[1];
			$text =& $parts[2];
			
			if (empty($token)) {
				# Reached end of text span: empty stack without emitting.
				# any more emphasis.
				while ($token_stack[0]) {
					$text_stack[1] .= array_shift($token_stack);
					$text_stack[0] .= array_shift($text_stack);
				}
				break;
			}
			
			$token_len = strlen($token);
			if ($tree_char_em) {
				# Reached closing marker while inside a three-char emphasis.
				if ($token_len == 3) {
					# Three-char closing marker, close em and strong.
					array_shift($token_stack);
					$span = array_shift($text_stack);
					$span = $this->runSpanGamut($span);
					$span = "<strong><em>$span</em></strong>";
					$text_stack[0] .= $this->hashPart($span);
					$em = '';
					$strong = '';
				} else {
					# Other closing marker: close one em or strong and
					# change current token state to match the other
					$token_stack[0] = str_repeat($token{0}, 3-$token_len);
					$tag = $token_len == 2 ? "strong" : "em";
					$span = $text_stack[0];
					$span = $this->runSpanGamut($span);
					$span = "<$tag>$span</$tag>";
					$text_stack[0] = $this->hashPart($span);
					$$tag = ''; # $$tag stands for $em or $strong
				}
				$tree_char_em = false;
			} else if ($token_len == 3) {
				if ($em) {
					# Reached closing marker for both em and strong.
					# Closing strong marker:
					for ($i = 0; $i < 2; ++$i) {
						$shifted_token = array_shift($token_stack);
						$tag = strlen($shifted_token) == 2 ? "strong" : "em";
						$span = array_shift($text_stack);
						$span = $this->runSpanGamut($span);
						$span = "<$tag>$span</$tag>";
						$text_stack[0] .= $this->hashPart($span);
						$$tag = ''; # $$tag stands for $em or $strong
					}
				} else {
					# Reached opening three-char emphasis marker. Push on token 
					# stack; will be handled by the special condition above.
					$em = $token{0};
					$strong = "$em$em";
					array_unshift($token_stack, $token);
					array_unshift($text_stack, '');
					$tree_char_em = true;
				}
			} else if ($token_len == 2) {
				if ($strong) {
					# Unwind any dangling emphasis marker:
					if (strlen($token_stack[0]) == 1) {
						$text_stack[1] .= array_shift($token_stack);
						$text_stack[0] .= array_shift($text_stack);
					}
					# Closing strong marker:
					array_shift($token_stack);
					$span = array_shift($text_stack);
					$span = $this->runSpanGamut($span);
					$span = "<strong>$span</strong>";
					$text_stack[0] .= $this->hashPart($span);
					$strong = '';
				} else {
					array_unshift($token_stack, $token);
					array_unshift($text_stack, '');
					$strong = $token;
				}
			} else {
				# Here $token_len == 1
				if ($em) {
					if (strlen($token_stack[0]) == 1) {
						# Closing emphasis marker:
						array_shift($token_stack);
						$span = array_shift($text_stack);
						$span = $this->runSpanGamut($span);
						$span = "<em>$span</em>";
						$text_stack[0] .= $this->hashPart($span);
						$em = '';
					} else {
						$text_stack[0] .= $token;
					}
				} else {
					array_unshift($token_stack, $token);
					array_unshift($text_stack, '');
					$em = $token;
				}
			}
		}
		return $text_stack[0];
	}


	function doBlockQuotes($text) {

It is generally recommended to explicitly declare the visibility for methods.

		$text = preg_replace_callback('/
			  (								# Wrap whole match in $1
				(?>
				  ^[ ]*>[ ]?			# ">" at the start of a line
					.+\n					# rest of the first line
				  (.+\n)*					# subsequent consecutive lines
				  \n*						# blanks
				)+
			  )
			/xm',
			array(&$this, '_doBlockQuotes_callback'), $text);

		return $text;
	}
	function _doBlockQuotes_callback($matches) {

It is generally recommended to explicitly declare the visibility for methods.

		$bq = $matches[1];
		# trim one level of quoting - trim whitespace-only lines
		$bq = preg_replace('/^[ ]*>[ ]?|^[ ]+$/m', '', $bq);
		$bq = $this->runBlockGamut($bq);		# recurse

		$bq = preg_replace('/^/m', "  ", $bq);
		# These leading spaces cause problem with <pre> content, 
		# so we need to fix that:
		$bq = preg_replace_callback('{(\s*<pre>.+?</pre>)}sx', 
			array(&$this, '_doBlockQuotes_callback2'), $bq);

		return "\n". $this->hashBlock("<blockquote>\n$bq\n</blockquote>")."\n\n";
	}
	function _doBlockQuotes_callback2($matches) {

It is generally recommended to explicitly declare the visibility for methods.

		$pre = $matches[1];
		$pre = preg_replace('/^  /m', '', $pre);
		return $pre;
	}


	function formParagraphs($text) {

It is generally recommended to explicitly declare the visibility for methods.

	#
	#	Params:
	#		$text - string to process with html <p> tags
	#
		# Strip leading and trailing lines:
		$text = preg_replace('/\A\n+|\n+\z/', '', $text);

		$grafs = preg_split('/\n{2,}/', $text, -1, PREG_SPLIT_NO_EMPTY);

		#
		# Wrap <p> tags and unhashify HTML blocks
		#
		foreach ($grafs as $key => $value) {
			if (!preg_match('/^B\x1A[0-9]+B$/', $value)) {
				# Is a paragraph.
				$value = $this->runSpanGamut($value);
				$value = preg_replace('/^([ ]*)/', "<p>", $value);
				$value .= "</p>";
				$grafs[$key] = $this->unhash($value);
			}
			else {
				# Is a block.
				# Modify elements of @grafs in-place...
				$graf = $value;
				$block = $this->html_hashes[$graf];
				$graf = $block;
//				if (preg_match('{
//					\A
//					(							# $1 = <div> tag
//					  <div  \s+
//					  [^>]*
//					  \b
//					  markdown\s*=\s*  ([\'"])	#	$2 = attr quote char
//					  1
//					  \2
//					  [^>]*
//					  >
//					)
//					(							# $3 = contents
//					.*
//					)
//					(</div>)					# $4 = closing tag
//					\z
//					}xs', $block, $matches))
//				{
//					list(, $div_open, , $div_content, $div_close) = $matches;
//
//					# We can't call Markdown(), because that resets the hash;
//					# that initialization code should be pulled into its own sub, though.
//					$div_content = $this->hashHTMLBlocks($div_content);
//					
//					# Run document gamut methods on the content.
//					foreach ($this->document_gamut as $method => $priority) {
//						$div_content = $this->$method($div_content);
//					}
//
//					$div_open = preg_replace(
//						'{\smarkdown\s*=\s*([\'"]).+?\1}', '', $div_open);
//
//					$graf = $div_open . "\n" . $div_content . "\n" . $div_close;
//				}
				$grafs[$key] = $graf;
			}
		}

		return implode("\n\n", $grafs);
	}


	function encodeAttribute($text) {

It is generally recommended to explicitly declare the visibility for methods.

	#
	# Encode text for a double-quoted HTML attribute. This function
	# is *not* suitable for attributes enclosed in single quotes.
	#
		$text = $this->encodeAmpsAndAngles($text);
		$text = str_replace('"', '"', $text);
		return $text;
	}
	
	
	function encodeAmpsAndAngles($text) {

It is generally recommended to explicitly declare the visibility for methods.

	#
	# Smart processing for ampersands and angle brackets that need to 
	# be encoded. Valid character entities are left alone unless the
	# no-entities mode is set.
	#
		if ($this->no_entities) {
			$text = str_replace('&', '&', $text);
		} else {
			# Ampersand-encoding based entirely on Nat Irons's Amputator
			# MT plugin: <http://bumppo.net/projects/amputator/>
			$text = preg_replace('/&(?!#?[xX]?(?:[0-9a-fA-F]+|\w+);)/', 
								'&amp;', $text);;
		}
		# Encode remaining <'s
		$text = str_replace('<', '&lt;', $text);

		return $text;
	}


	function doAutoLinks($text) {

It is generally recommended to explicitly declare the visibility for methods.

		$text = preg_replace_callback('{<((https?|ftp|dict):[^\'">\s]+)>}i', 
			array(&$this, '_doAutoLinks_url_callback'), $text);

		# Email addresses: <address@domain.foo>
		$text = preg_replace_callback('{
			<
			(?:mailto:)?
			(
				(?:
					[-!#$%&\'*+/=?^_`.{|}~\w\x80-\xFF]+
				|
					".*?"
				)
				\@
				(?:
					[-a-z0-9\x80-\xFF]+(\.[-a-z0-9\x80-\xFF]+)*\.[a-z]+
				|
					\[[\d.a-fA-F:]+\]	# IPv4 & IPv6
				)
			)
			>
			}xi',
			array(&$this, '_doAutoLinks_email_callback'), $text);
		$text = preg_replace_callback('{<(tel:([^\'">\s]+))>}i',array(&$this, '_doAutoLinks_tel_callback'), $text);

		return $text;
	}
	function _doAutoLinks_tel_callback($matches) {

It is generally recommended to explicitly declare the visibility for methods.

		$url = $this->encodeAttribute($matches[1]);
		$tel = $this->encodeAttribute($matches[2]);
		$link = "<a href=\"$url\">$tel</a>";
		return $this->hashPart($link);
	}
	function _doAutoLinks_url_callback($matches) {

It is generally recommended to explicitly declare the visibility for methods.

		$url = $this->encodeAttribute($matches[1]);
		$link = "<a href=\"$url\">$url</a>";
		return $this->hashPart($link);
	}
	function _doAutoLinks_email_callback($matches) {

It is generally recommended to explicitly declare the visibility for methods.

		$address = $matches[1];
		$link = $this->encodeEmailAddress($address);
		return $this->hashPart($link);
	}


	function encodeEmailAddress($addr) {

It is generally recommended to explicitly declare the visibility for methods.

	#
	#	Input: an email address, e.g. "foo@example.com"
	#
	#	Output: the email address as a mailto link, with each character
	#		of the address encoded as either a decimal or hex entity, in
	#		the hopes of foiling most address harvesting spam bots. E.g.:
	#
	#	  <p><a href="&#109;&#x61;&#105;&#x6c;&#116;&#x6f;&#58;&#x66;o&#111;
	#        &#x40;&#101;&#x78;&#97;&#x6d;&#112;&#x6c;&#101;&#46;&#x63;&#111;
	#        &#x6d;">&#x66;o&#111;&#x40;&#101;&#x78;&#97;&#x6d;&#112;&#x6c;
	#        &#101;&#46;&#x63;&#111;&#x6d;</a></p>
	#
	#	Based by a filter by Matthew Wickline, posted to BBEdit-Talk.
	#   With some optimizations by Milian Wolff.
	#
		$addr = "mailto:" . $addr;
		$chars = preg_split('/(?<!^)(?!$)/', $addr);
		$seed = (int)abs(crc32($addr) / strlen($addr)); # Deterministic seed.
		
		foreach ($chars as $key => $char) {
			$ord = ord($char);
			# Ignore non-ascii chars.
			if ($ord < 128) {
				$r = ($seed * (1 + $key)) % 100; # Pseudo-random function.
				# roughly 10% raw, 45% hex, 45% dec
				# '@' *must* be encoded. I insist.
				if ($r > 90 && $char != '@') /* do nothing */;
				else if ($r < 45) $chars[$key] = '&#x'.dechex($ord).';';
				else              $chars[$key] = '&#'.$ord.';';
			}
		}
		
		$addr = implode('', $chars);
		$text = implode('', array_slice($chars, 7)); # text without `mailto:`
		$addr = "<a href=\"$addr\">$text</a>";

		return $addr;
	}


	function parseSpan($str) {

It is generally recommended to explicitly declare the visibility for methods.

	#
	# Take the string $str and parse it into tokens, hashing embeded HTML,
	# escaped characters and handling code spans.
	#
		$output = '';
		
		$span_re = '{
				(
					\\\\'.$this->escape_chars_re.'
				|
					(?<![`\\\\])
					`+						# code span marker
			'.( $this->no_markup ? '' : '
				|
					<!--    .*?     -->		# comment
				|
					<\?.*?\?> | <%.*?%>		# processing instruction
				|
					<[!$]?[-a-zA-Z0-9:_]+	# regular tags
					(?>
						\s
						(?>[^"\'>]+|"[^"]*"|\'[^\']*\')*
					)?
					>
				|
					<[-a-zA-Z0-9:_]+\s*/> # xml-style empty tag
				|
					</[-a-zA-Z0-9:_]+\s*> # closing tag
			').'
				)
				}xs';

		while (1) {
			#
			# Each loop iteration seach for either the next tag, the next 
			# openning code span marker, or the next escaped character. 
			# Each token is then passed to handleSpanToken.
			#
			$parts = preg_split($span_re, $str, 2, PREG_SPLIT_DELIM_CAPTURE);
			
			# Create token from text preceding tag.
			if ($parts[0] != "") {
				$output .= $parts[0];
			}
			
			# Check if we reach the end.
			if (isset($parts[1])) {
				$output .= $this->handleSpanToken($parts[1], $parts[2]);
				$str = $parts[2];
			}
			else {
				break;
			}
		}
		
		return $output;
	}
	
	
	function handleSpanToken($token, &$str) {

It is generally recommended to explicitly declare the visibility for methods.

	#
	# Handle $token provided by parseSpan by determining its nature and 
	# returning the corresponding value that should replace it.
	#
		switch ($token{0}) {
			case "\\":
				return $this->hashPart("&#". ord($token{1}). ";");
			case "`":
				# Search for end marker in remaining text.
				if (preg_match('/^(.*?[^`])'.preg_quote($token).'(?!`)(.*)$/sm', 
					$str, $matches))
				{
					$str = $matches[2];
					$codespan = $this->makeCodeSpan($matches[1]);
					return $this->hashPart($codespan);
				}
				return $token; // return as text since no ending marker found.
			default:
				return $this->hashPart($token);
		}
	}


	function outdent($text) {

It is generally recommended to explicitly declare the visibility for methods.

	#
	# Remove one level of line-leading tabs or spaces
	#
		return preg_replace('/^(\t|[ ]{1,'.$this->tab_width.'})/m', '', $text);
	}


	# String length function for detab. `_initDetab` will create a function to 
	# hanlde UTF-8 if the default function does not exist.
	var $utf8_strlen = 'mb_strlen';
	
	function detab($text) {

It is generally recommended to explicitly declare the visibility for methods.

	#
	# Replace tabs with the appropriate amount of space.
	#
		# For each line we separate the line in blocks delemited by
		# tab characters. Then we reconstruct every line by adding the 
		# appropriate number of space between each blocks.
		
		$text = preg_replace_callback('/^.*\t.*$/m',
			array(&$this, '_detab_callback'), $text);

		return $text;
	}
	function _detab_callback($matches) {

It is generally recommended to explicitly declare the visibility for methods.

		$line = $matches[0];
		$strlen = $this->utf8_strlen; # strlen function for UTF-8.
		
		# Split in blocks.
		$blocks = explode("\t", $line);
		# Add each blocks to the line.
		$line = $blocks[0];
		unset($blocks[0]); # Do not add first block twice.
		foreach ($blocks as $block) {
			# Calculate amount of space, insert spaces, insert block.
			$amount = $this->tab_width - 
				$strlen($line, 'UTF-8') % $this->tab_width;
			$line .= str_repeat(" ", $amount) . $block;
		}
		return $line;
	}
	function _initDetab() {

It is generally recommended to explicitly declare the visibility for methods.

	#
	# Check for the availability of the function in the `utf8_strlen` property
	# (initially `mb_strlen`). If the function is not available, create a 
	# function that will loosely count the number of UTF-8 characters with a
	# regular expression.
	#
		if (function_exists($this->utf8_strlen)) return;
		$this->utf8_strlen = create_function('$text', 'return preg_match_all(
			"/[\\\\x00-\\\\xBF]|[\\\\xC0-\\\\xFF][\\\\x80-\\\\xBF]*/", 
			$text, $m);');
	}


	function unhash($text) {

It is generally recommended to explicitly declare the visibility for methods.

	#
	# Swap back in all the tags hashed by _HashHTMLBlocks.
	#
		return preg_replace_callback('/(.)\x1A[0-9]+\1/', 
			array(&$this, '_unhash_callback'), $text);
	}
	function _unhash_callback($matches) {

It is generally recommended to explicitly declare the visibility for methods.

		return $this->html_hashes[$matches[0]];
	}

}


#
# Markdown Extra Parser Class
#

class MarkdownExtra_Parser extends Markdown_Parser {

	### Configuration Variables ###

	# Prefix for footnote ids.
	var $fn_id_prefix = "";
	
	# Optional title attribute for footnote links and backlinks.
	var $fn_link_title = MARKDOWN_FN_LINK_TITLE;
	var $fn_backlink_title = MARKDOWN_FN_BACKLINK_TITLE;
	
	# Optional class attribute for footnote links and backlinks.
	var $fn_link_class = MARKDOWN_FN_LINK_CLASS;
	var $fn_backlink_class = MARKDOWN_FN_BACKLINK_CLASS;

	# Optional class prefix for fenced code block.
	var $code_class_prefix = MARKDOWN_CODE_CLASS_PREFIX;
	# Class attribute for code blocks goes on the `code` tag;
	# setting this to true will put attributes on the `pre` tag instead.
	var $code_attr_on_pre = MARKDOWN_CODE_ATTR_ON_PRE;
	
	# Predefined abbreviations.
	var $predef_abbr = array();


	### Parser Implementation ###

	function MarkdownExtra_Parser() {

It is generally recommended to explicitly declare the visibility for methods.

	#
	# Constructor function. Initialize the parser object.
	#
		# Add extra escapable characters before parent constructor 
		# initialize the table.
		$this->escape_chars .= ':|';
		
		# Insert extra document, block, and span transformations. 
		# Parent constructor will do the sorting.
		$this->document_gamut += array(
			"doFencedCodeBlocks" => 5,
			"stripFootnotes"     => 15,
			"stripAbbreviations" => 25,
			"appendFootnotes"    => 50,
			);
		$this->block_gamut += array(
			"doFencedCodeBlocks" => 5,
			"doTables"           => 15,
			"doDefLists"         => 45,
			);
		$this->span_gamut += array(
			"doFootnotes"        => 5,
			"doAbbreviations"    => 70,
			);
		
		parent::Markdown_Parser();

It seems like you call parent on a different method (Markdown_Parser() instead of MarkdownExtra_Parser()). Are you sure this is correct? If so, you might want to change this to $this->Markdown_Parser().

	}
	
	
	# Extra variables used during extra transformations.
	var $footnotes = array();
	var $footnotes_ordered = array();
	var $footnotes_ref_count = array();
	var $footnotes_numbers = array();
	var $abbr_desciptions = array();
	var $abbr_word_re = '';
	
	# Give the current footnote number.
	var $footnote_counter = 1;
	
	
	function setup() {

It is generally recommended to explicitly declare the visibility for methods.

	#
	# Setting up Extra-specific variables.
	#
		parent::setup();
		
		$this->footnotes = array();
		$this->footnotes_ordered = array();
		$this->footnotes_ref_count = array();
		$this->footnotes_numbers = array();
		$this->abbr_desciptions = array();
		$this->abbr_word_re = '';
		$this->footnote_counter = 1;
		
		foreach ($this->predef_abbr as $abbr_word => $abbr_desc) {
			if ($this->abbr_word_re)
				$this->abbr_word_re .= '|';
			$this->abbr_word_re .= preg_quote($abbr_word);
			$this->abbr_desciptions[$abbr_word] = trim($abbr_desc);
		}
	}
	
	function teardown() {

It is generally recommended to explicitly declare the visibility for methods.

	#
	# Clearing Extra-specific variables.
	#
		$this->footnotes = array();
		$this->footnotes_ordered = array();
		$this->footnotes_ref_count = array();
		$this->footnotes_numbers = array();
		$this->abbr_desciptions = array();
		$this->abbr_word_re = '';
		
		parent::teardown();
	}
	
	
	### Extra Attribute Parser ###

	# Expression to use to catch attributes (includes the braces)
	var $id_class_attr_catch_re = '\{((?:[ ]*[#.][-_:a-zA-Z0-9]+){1,})[ ]*\}';
	# Expression to use when parsing in a context when no capture is desired
	var $id_class_attr_nocatch_re = '\{(?:[ ]*[#.][-_:a-zA-Z0-9]+){1,}[ ]*\}';

	function doExtraAttributes($tag_name, $attr) {

It is generally recommended to explicitly declare the visibility for methods.

	#
	# Parse attributes caught by the $this->id_class_attr_catch_re expression
	# and return the HTML-formatted list of attributes.
	#
	# Currently supported attributes are .class and #id.
	#
		if (empty($attr)) return "";
		
		# Split on components
		preg_match_all('/[#.][-_:a-zA-Z0-9]+/', $attr, $matches);
		$elements = $matches[0];

		# handle classes and ids (only first id taken into account)
		$classes = array();
		$id = false;
		foreach ($elements as $element) {
			if ($element{0} == '.') {
				$classes[] = substr($element, 1);
			} else if ($element{0} == '#') {
				if ($id === false) $id = substr($element, 1);
			}
		}

		# compose attributes as string
		$attr_str = "";
		if (!empty($id)) {
			$attr_str .= ' id="'.$id.'"';
		}
		if (!empty($classes)) {
			$attr_str .= ' class="'.implode(" ", $classes).'"';
		}
		return $attr_str;
	}


	function stripLinkDefinitions($text) {

It is generally recommended to explicitly declare the visibility for methods.

This method seems to be duplicated in your project.

	#
	# Strips link definitions from text, stores the URLs and titles in
	# hash references.
	#
		$less_than_tab = $this->tab_width - 1;

		# Link defs are in the form: ^[id]: url "optional title"
		$text = preg_replace_callback('{
							^[ ]{0,'.$less_than_tab.'}\[(.+)\][ ]?:	# id = $1
							  [ ]*
							  \n?				# maybe *one* newline
							  [ ]*
							(?:
							  <(.+?)>			# url = $2
							|
							  (\S+?)			# url = $3
							)
							  [ ]*
							  \n?				# maybe one newline
							  [ ]*
							(?:
								(?<=\s)			# lookbehind for whitespace
								["(]
								(.*?)			# title = $4
								[")]
								[ ]*
							)?	# title is optional
					(?:[ ]* '.$this->id_class_attr_catch_re.' )?  # $5 = extra id & class attr
							(?:\n+|\Z)
			}xm',
			array(&$this, '_stripLinkDefinitions_callback'),
			$text);
		return $text;
	}
	function _stripLinkDefinitions_callback($matches) {

It is generally recommended to explicitly declare the visibility for methods.

		$link_id = strtolower($matches[1]);
		$url = $matches[2] == '' ? $matches[3] : $matches[2];
		$this->urls[$link_id] = $url;
		$this->titles[$link_id] =& $matches[4];
		$this->ref_attr[$link_id] = $this->doExtraAttributes("", $dummy =& $matches[5]);

The property ref_attr does not exist. Did you maybe forget to declare it?

		return ''; # String that will replace the block
	}


	### HTML Block Parser ###
	
	# Tags that are always treated as block tags:
	var $block_tags_re = 'p|div|h[1-6]|blockquote|pre|table|dl|ol|ul|address|form|fieldset|iframe|hr|legend|article|section|nav|aside|hgroup|header|footer|figcaption';
						   
	# Tags treated as block tags only if the opening tag is alone on its line:
	var $context_block_tags_re = 'script|noscript|ins|del|iframe|object|source|track|param|math|svg|canvas|audio|video';
	
	# Tags where markdown="1" default to span mode:
	var $contain_span_tags_re = 'p|h[1-6]|li|dd|dt|td|th|legend|address';
	
	# Tags which must not have their contents modified, no matter where 
	# they appear:
	var $clean_tags_re = 'script|math|svg';
	
	# Tags that do not need to be closed.
	var $auto_close_tags_re = 'hr|img|param|source|track';
	

	function hashHTMLBlocks($text) {

It is generally recommended to explicitly declare the visibility for methods.

	#
	# Hashify HTML Blocks and "clean tags".
	#
	# We only want to do this for block-level HTML tags, such as headers,
	# lists, and tables. That's because we still want to wrap <p>s around
	# "paragraphs" that are wrapped in non-block-level tags, such as anchors,
	# phrase emphasis, and spans. The list of tags we're looking for is
	# hard-coded.
	#
	# This works by calling _HashHTMLBlocks_InMarkdown, which then calls
	# _HashHTMLBlocks_InHTML when it encounter block tags. When the markdown="1" 
	# attribute is found within a tag, _HashHTMLBlocks_InHTML calls back
	#  _HashHTMLBlocks_InMarkdown to handle the Markdown syntax within the tag.
	# These two functions are calling each other. It's recursive!
	#
		if ($this->no_markup)  return $text;

		#
		# Call the HTML-in-Markdown hasher.
		#
		list($text, ) = $this->_hashHTMLBlocks_inMarkdown($text);
		
		return $text;
	}
	function _hashHTMLBlocks_inMarkdown($text, $indent = 0, 

It is generally recommended to explicitly declare the visibility for methods.

										$enclosing_tag_re = '', $span = false)
	{
	#
	# Parse markdown text, calling _HashHTMLBlocks_InHTML for block tags.
	#
	# *   $indent is the number of space to be ignored when checking for code 
	#     blocks. This is important because if we don't take the indent into 
	#     account, something like this (which looks right) won't work as expected:
	#
	#     <div>
	#         <div markdown="1">
	#         Hello World.  <-- Is this a Markdown code block or text?
	#         </div>  <-- Is this a Markdown code block or a real tag?
	#     <div>
	#
	#     If you don't like this, just don't indent the tag on which
	#     you apply the markdown="1" attribute.
	#
	# *   If $enclosing_tag_re is not empty, stops at the first unmatched closing 
	#     tag with that name. Nested tags supported.
	#
	# *   If $span is true, text inside must treated as span. So any double 
	#     newline will be replaced by a single newline so that it does not create 
	#     paragraphs.
	#
	# Returns an array of that form: ( processed text , remaining text )
	#
		if ($text === '') return array('', '');

		# Regex to check for the presense of newlines around a block tag.
		$newline_before_re = '/(?:^\n?|\n\n)*$/';
		$newline_after_re = 
			'{
				^						# Start of text following the tag.
				(?>[ ]*<!--.*?-->)?		# Optional comment.
				[ ]*\n					# Must be followed by newline.
			}xs';
		
		# Regex to match any tag.
		$block_tag_re =
			'{
				(					# $2: Capture whole tag.
					</?					# Any opening or closing tag.
						(?>				# Tag name.
							'.$this->block_tags_re.'			|
							'.$this->context_block_tags_re.'	|
							'.$this->clean_tags_re.'        	|
							(?!\s)'.$enclosing_tag_re.'
						)
						(?:
							(?=[\s"\'/a-zA-Z0-9])	# Allowed characters after tag name.
							(?>
								".*?"		|	# Double quotes (can contain `>`)
								\'.*?\'   	|	# Single quotes (can contain `>`)
								.+?				# Anything but quotes and `>`.
							)*?
						)?
					>					# End of tag.
				|
					<!--    .*?     -->	# HTML Comment
				|
					<\?.*?\?> | <%.*?%>	# Processing instruction
				|
					<!\[CDATA\[.*?\]\]>	# CData Block
				'. ( !$span ? ' # If not in span.
				|
					# Indented code block
					(?: ^[ ]*\n | ^ | \n[ ]*\n )
					[ ]{'.($indent+4).'}[^\n]* \n
					(?>
						(?: [ ]{'.($indent+4).'}[^\n]* | [ ]* ) \n
					)*
				|
					# Fenced code block marker
					(?<= ^ | \n )
					[ ]{0,'.($indent+3).'}(?:~{3,}|`{3,})
									[ ]*
					(?:
					\.?[-_:a-zA-Z0-9]+ # standalone class name
					|
						'.$this->id_class_attr_nocatch_re.' # extra attributes
					)?
					[ ]*
					(?= \n )
				' : '' ). ' # End (if not is span).
				|
					# Code span marker
					# Note, this regex needs to go after backtick fenced
					# code blocks but it should also be kept outside of the
					# "if not in span" condition adding backticks to the parser
					`+
				)
			}xs';

		
		$depth = 0;		# Current depth inside the tag tree.
		$parsed = "";	# Parsed text that will be returned.

		#
		# Loop through every tag until we find the closing tag of the parent
		# or loop until reaching the end of text if no parent tag specified.
		#
		do {
			#
			# Split the text using the first $tag_match pattern found.
			# Text before  pattern will be first in the array, text after
			# pattern will be at the end, and between will be any catches made 
			# by the pattern.
			#
			$parts = preg_split($block_tag_re, $text, 2, 
								PREG_SPLIT_DELIM_CAPTURE);
			
			# If in Markdown span mode, add a empty-string span-level hash 
			# after each newline to prevent triggering any block element.
			if ($span) {
				$void = $this->hashPart("", ':');
				$newline = "$void\n";
				$parts[0] = $void . str_replace("\n", $newline, $parts[0]) . $void;
			}
			
			$parsed .= $parts[0]; # Text before current tag.
			
			# If end of $text has been reached. Stop loop.
			if (count($parts) < 3) {
				$text = "";
				break;
			}
			
			$tag  = $parts[1]; # Tag to handle.
			$text = $parts[2]; # Remaining text after current tag.
			$tag_re = preg_quote($tag); # For use in a regular expression.

$tag_re is not used, you could remove the assignment.

			
			#
			# Check for: Fenced code block marker.
			# Note: need to recheck the whole tag to disambiguate backtick
			# fences from code spans
			#
			if (preg_match('{^\n?([ ]{0,'.($indent+3).'})(~{3,}|`{3,})[ ]*(?:\.?[-_:a-zA-Z0-9]+|'.$this->id_class_attr_nocatch_re.')?[ ]*\n?$}', $tag, $capture)) {
				# Fenced code block marker: find matching end marker.
				$fence_indent = strlen($capture[1]); # use captured indent in re
				$fence_re = $capture[2]; # use captured fence in re
				if (preg_match('{^(?>.*\n)*?[ ]{'.($fence_indent).'}'.$fence_re.'[ ]*(?:\n|$)}', $text,
					$matches)) 
				{
					# End marker found: pass text unchanged until marker.
					$parsed .= $tag . $matches[0];
					$text = substr($text, strlen($matches[0]));
				}
				else {
					# No end marker: just skip it.
					$parsed .= $tag;
				}
			}
			#
			# Check for: Indented code block.
			#
			else if ($tag{0} == "\n" || $tag{0} == " ") {
				# Indented code block: pass it unchanged, will be handled 
				# later.
				$parsed .= $tag;
			}
			#
			# Check for: Code span marker
			# Note: need to check this after backtick fenced code blocks
			#
			else if ($tag{0} == "`") {
				# Find corresponding end marker.
				$tag_re = preg_quote($tag);
				if (preg_match('{^(?>.+?|\n(?!\n))*?(?<!`)'.$tag_re.'(?!`)}',
					$text, $matches))
				{
					# End marker found: pass text unchanged until marker.
					$parsed .= $tag . $matches[0];
					$text = substr($text, strlen($matches[0]));
				}
				else {
					# Unmatched marker: just skip it.
					$parsed .= $tag;
				}
			}
			#
			# Check for: Opening Block level tag or
			#            Opening Context Block tag (like ins and del) 
			#               used as a block tag (tag is alone on it's line).
			#
			else if (preg_match('{^<(?:'.$this->block_tags_re.')\b}', $tag) ||
				(	preg_match('{^<(?:'.$this->context_block_tags_re.')\b}', $tag) &&
					preg_match($newline_before_re, $parsed) &&
					preg_match($newline_after_re, $text)	)
				)
			{
				# Need to parse tag and following text using the HTML parser.
				list($block_text, $text) = 
					$this->_hashHTMLBlocks_inHTML($tag . $text, "hashBlock", true);
				
				# Make sure it stays outside of any paragraph by adding newlines.
				$parsed .= "\n\n$block_text\n\n";
			}
			#
			# Check for: Clean tag (like script, math)
			#            HTML Comments, processing instructions.
			#
			else if (preg_match('{^<(?:'.$this->clean_tags_re.')\b}', $tag) ||
				$tag{1} == '!' || $tag{1} == '?')
			{
				# Need to parse tag and following text using the HTML parser.
				# (don't check for markdown attribute)
				list($block_text, $text) = 
					$this->_hashHTMLBlocks_inHTML($tag . $text, "hashClean", false);
				
				$parsed .= $block_text;
			}
			#
			# Check for: Tag with same name as enclosing tag.
			#
			else if ($enclosing_tag_re !== '' &&
				# Same name as enclosing tag.
				preg_match('{^</?(?:'.$enclosing_tag_re.')\b}', $tag))
			{
				#
				# Increase/decrease nested tag count.
				#
				if ($tag{1} == '/')						$depth--;
				else if ($tag{strlen($tag)-2} != '/')	$depth++;

				if ($depth < 0) {
					#
					# Going out of parent element. Clean up and break so we
					# return to the calling function.
					#
					$text = $tag . $text;
					break;
				}
				
				$parsed .= $tag;
			}
			else {
				$parsed .= $tag;
			}
		} while ($depth >= 0);
		
		return array($parsed, $text);
	}
	function _hashHTMLBlocks_inHTML($text, $hash_method, $md_attr) {

It is generally recommended to explicitly declare the visibility for methods.

	#
	# Parse HTML, calling _HashHTMLBlocks_InMarkdown for block tags.
	#
	# *   Calls $hash_method to convert any blocks.
	# *   Stops when the first opening tag closes.
	# *   $md_attr indicate if the use of the `markdown="1"` attribute is allowed.
	#     (it is not inside clean tags)
	#
	# Returns an array of that form: ( processed text , remaining text )
	#
		if ($text === '') return array('', '');
		
		# Regex to match `markdown` attribute inside of a tag.
		$markdown_attr_re = '
			{
				\s*			# Eat whitespace before the `markdown` attribute
				markdown
				\s*=\s*
				(?>
					(["\'])		# $1: quote delimiter		
					(.*?)		# $2: attribute value
					\1			# matching delimiter	
				|
					([^\s>]*)	# $3: unquoted attribute value
				)
				()				# $4: make $3 always defined (avoid warnings)
			}xs';
		
		# Regex to match any tag.
		$tag_re = '{
				(					# $2: Capture whole tag.
					</?					# Any opening or closing tag.
						[\w:$]+			# Tag name.
						(?:
							(?=[\s"\'/a-zA-Z0-9])	# Allowed characters after tag name.
							(?>
								".*?"		|	# Double quotes (can contain `>`)
								\'.*?\'   	|	# Single quotes (can contain `>`)
								.+?				# Anything but quotes and `>`.
							)*?
						)?
					>					# End of tag.
				|
					<!--    .*?     -->	# HTML Comment
				|
					<\?.*?\?> | <%.*?%>	# Processing instruction
				|
					<!\[CDATA\[.*?\]\]>	# CData Block
				)
			}xs';
		
		$original_text = $text;		# Save original text in case of faliure.
		
		$depth		= 0;	# Current depth inside the tag tree.
		$block_text	= "";	# Temporary text holder for current text.
		$parsed		= "";	# Parsed text that will be returned.

		#
		# Get the name of the starting tag.
		# (This pattern makes $base_tag_name_re safe without quoting.)
		#
		if (preg_match('/^<([\w:$]*)\b/', $text, $matches))
			$base_tag_name_re = $matches[1];

		#
		# Loop through every tag until we find the corresponding closing tag.
		#
		do {
			#
			# Split the text using the first $tag_match pattern found.
			# Text before  pattern will be first in the array, text after
			# pattern will be at the end, and between will be any catches made 
			# by the pattern.
			#
			$parts = preg_split($tag_re, $text, 2, PREG_SPLIT_DELIM_CAPTURE);
			
			if (count($parts) < 3) {
				#
				# End of $text reached with unbalenced tag(s).
				# In that case, we return original text unchanged and pass the
				# first character as filtered to prevent an infinite loop in the 
				# parent function.
				#
				return array($original_text{0}, substr($original_text, 1));
			}
			
			$block_text .= $parts[0]; # Text before current tag.
			$tag         = $parts[1]; # Tag to handle.
			$text        = $parts[2]; # Remaining text after current tag.
			
			#
			# Check for: Auto-close tag (like <hr/>)
			#			 Comments and Processing Instructions.
			#
			if (preg_match('{^</?(?:'.$this->auto_close_tags_re.')\b}', $tag) ||
				$tag{1} == '!' || $tag{1} == '?')
			{
				# Just add the tag to the block as if it was text.
				$block_text .= $tag;
			}
			else {
				#
				# Increase/decrease nested tag count. Only do so if
				# the tag's name match base tag's.
				#
				if (preg_match('{^</?'.$base_tag_name_re.'\b}', $tag)) {

The variable $base_tag_name_re does not seem to be defined for all execution paths leading up to this point.

					if ($tag{1} == '/')						$depth--;
					else if ($tag{strlen($tag)-2} != '/')	$depth++;
				}
				
				#
				# Check for `markdown="1"` attribute and handle it.
				#
				if ($md_attr && 
					preg_match($markdown_attr_re, $tag, $attr_m) &&
					preg_match('/^1|block|span$/', $attr_m[2] . $attr_m[3]))
				{
					# Remove `markdown` attribute from opening tag.
					$tag = preg_replace($markdown_attr_re, '', $tag);
					
					# Check if text inside this tag must be parsed in span mode.
					$this->mode = $attr_m[2] . $attr_m[3];

The property mode does not exist. Did you maybe forget to declare it?

					$span_mode = $this->mode == 'span' || $this->mode != 'block' &&
						preg_match('{^<(?:'.$this->contain_span_tags_re.')\b}', $tag);
					
					# Calculate indent before tag.
					if (preg_match('/(?:^|\n)( *?)(?! ).*?$/', $block_text, $matches)) {
						$strlen = $this->utf8_strlen;
						$indent = $strlen($matches[1], 'UTF-8');
					} else {
						$indent = 0;
					}
					
					# End preceding block with this tag.
					$block_text .= $tag;
					$parsed .= $this->$hash_method($block_text);
					
					# Get enclosing tag name for the ParseMarkdown function.
					# (This pattern makes $tag_name_re safe without quoting.)
					preg_match('/^<([\w:$]*)\b/', $tag, $matches);
					$tag_name_re = $matches[1];
					
					# Parse the content using the HTML-in-Markdown parser.
					list ($block_text, $text)
						= $this->_hashHTMLBlocks_inMarkdown($text, $indent, 
							$tag_name_re, $span_mode);
					
					# Outdent markdown text.
					if ($indent > 0) {
						$block_text = preg_replace("/^[ ]{1,$indent}/m", "", 
													$block_text);
					}
					
					# Append tag content to parsed text.
					if (!$span_mode)	$parsed .= "\n\n$block_text\n\n";
					else				$parsed .= "$block_text";
					
					# Start over with a new block.
					$block_text = "";
				}
				else $block_text .= $tag;
			}
			
		} while ($depth > 0);
		
		#
		# Hash last block text that wasn't processed inside the loop.
		#
		$parsed .= $this->$hash_method($block_text);
		
		return array($parsed, $text);
	}


	function hashClean($text) {

It is generally recommended to explicitly declare the visibility for methods.

	#
	# Called whenever a tag must be hashed when a function inserts a "clean" tag
	# in $text, it passes through this function and is automaticaly escaped, 
	# blocking invalid nested overlap.
	#
		return $this->hashPart($text, 'C');
	}


	function doAnchors($text) {

It is generally recommended to explicitly declare the visibility for methods.

This method seems to be duplicated in your project.

	#
	# Turn Markdown link shortcuts into XHTML <a> tags.
	#
		if ($this->in_anchor) return $text;
		$this->in_anchor = true;
		
		#
		# First, handle reference-style links: [link text] [id]
		#
		$text = preg_replace_callback('{
			(					# wrap whole match in $1
			  \[
				('.$this->nested_brackets_re.')	# link text = $2
			  \]

			  [ ]?				# one optional space
			  (?:\n[ ]*)?		# one optional newline followed by spaces

			  \[
				(.*?)		# id = $3
			  \]
			)
			}xs',
			array(&$this, '_doAnchors_reference_callback'), $text);

		#
		# Next, inline-style links: [link text](url "optional title")
		#
		$text = preg_replace_callback('{
			(				# wrap whole match in $1
			  \[
				('.$this->nested_brackets_re.')	# link text = $2
			  \]
			  \(			# literal paren
				[ \n]*
				(?:
					<(.+?)>	# href = $3
				|
					('.$this->nested_url_parenthesis_re.')	# href = $4
				)
				[ \n]*
				(			# $5
				  ([\'"])	# quote char = $6
				  (.*?)		# Title = $7
				  \6		# matching quote
				  [ \n]*	# ignore any spaces/tabs between closing quote and )
				)?			# title is optional
			  \)
			  (?:[ ]? '.$this->id_class_attr_catch_re.' )?	 # $8 = id/class attributes
			)
			}xs',
			array(&$this, '_doAnchors_inline_callback'), $text);

		#
		# Last, handle reference-style shortcuts: [link text]
		# These must come last in case you've also got [link text][1]
		# or [link text](/foo)
		#
		$text = preg_replace_callback('{
			(					# wrap whole match in $1
			  \[
				([^\[\]]+)		# link text = $2; can\'t contain [ or ]
			  \]
			)
			}xs',
			array(&$this, '_doAnchors_reference_callback'), $text);

		$this->in_anchor = false;
		return $text;
	}
	function _doAnchors_reference_callback($matches) {

It is generally recommended to explicitly declare the visibility for methods.

		$whole_match =  $matches[1];
		$link_text   =  $matches[2];
		$link_id     =& $matches[3];

		if ($link_id == "") {
			# for shortcut links like [this][] or [this].
			$link_id = $link_text;
		}
		
		# lower-case and turn embedded newlines into spaces
		$link_id = strtolower($link_id);
		$link_id = preg_replace('{[ ]?\n}', ' ', $link_id);

		if (isset($this->urls[$link_id])) {
			$url = $this->urls[$link_id];
			$url = $this->encodeAttribute($url);
			
			$result = "<a href=\"$url\"";
			if ( isset( $this->titles[$link_id] ) ) {
				$title = $this->titles[$link_id];
				$title = $this->encodeAttribute($title);
				$result .=  " title=\"$title\"";
			}
			if (isset($this->ref_attr[$link_id]))
				$result .= $this->ref_attr[$link_id];
		
			$link_text = $this->runSpanGamut($link_text);
			$result .= ">$link_text</a>";
			$result = $this->hashPart($result);
		}
		else {
			$result = $whole_match;
		}
		return $result;
	}
	function _doAnchors_inline_callback($matches) {

It is generally recommended to explicitly declare the visibility for methods.

This method seems to be duplicated in your project.

		$whole_match	=  $matches[1];

$whole_match is not used, you could remove the assignment.

		$link_text		=  $this->runSpanGamut($matches[2]);
		$url			=  $matches[3] == '' ? $matches[4] : $matches[3];
		$title			=& $matches[7];
		$attr  = $this->doExtraAttributes("a", $dummy =& $matches[8]);


		$url = $this->encodeAttribute($url);

		$result = "<a href=\"$url\"";
		if (isset($title)) {
			$title = $this->encodeAttribute($title);
			$result .=  " title=\"$title\"";
		}
		$result .= $attr;
		
		$link_text = $this->runSpanGamut($link_text);
		$result .= ">$link_text</a>";

		return $this->hashPart($result);
	}


	function doImages($text) {

It is generally recommended to explicitly declare the visibility for methods.

This method seems to be duplicated in your project.

	#
	# Turn Markdown image shortcuts into <img> tags.
	#
		#
		# First, handle reference-style labeled images: ![alt text][id]
		#
		$text = preg_replace_callback('{
			(				# wrap whole match in $1
			  !\[
				('.$this->nested_brackets_re.')		# alt text = $2
			  \]

			  [ ]?				# one optional space
			  (?:\n[ ]*)?		# one optional newline followed by spaces

			  \[
				(.*?)		# id = $3
			  \]

			)
			}xs', 
			array(&$this, '_doImages_reference_callback'), $text);

		#
		# Next, handle inline images:  ![alt text](url "optional title")
		# Don't forget: encode * and _
		#
		$text = preg_replace_callback('{
			(				# wrap whole match in $1
			  !\[
				('.$this->nested_brackets_re.')		# alt text = $2
			  \]
			  \s?			# One optional whitespace character
			  \(			# literal paren
				[ \n]*
				(?:
					<(\S*)>	# src url = $3
				|
					('.$this->nested_url_parenthesis_re.')	# src url = $4
				)
				[ \n]*
				(			# $5
				  ([\'"])	# quote char = $6
				  (.*?)		# title = $7
				  \6		# matching quote
				  [ \n]*
				)?			# title is optional
			  \)
			  (?:[ ]? '.$this->id_class_attr_catch_re.' )?	 # $8 = id/class attributes
			)
			}xs',
			array(&$this, '_doImages_inline_callback'), $text);

		return $text;
	}
	function _doImages_reference_callback($matches) {

It is generally recommended to explicitly declare the visibility for methods.

		$whole_match = $matches[1];
		$alt_text    = $matches[2];
		$link_id     = strtolower($matches[3]);

		if ($link_id == "") {
			$link_id = strtolower($alt_text); # for shortcut links like ![this][].
		}

		$alt_text = $this->encodeAttribute($alt_text);
		if (isset($this->urls[$link_id])) {
			$url = $this->encodeAttribute($this->urls[$link_id]);
			$result = "<img src=\"$url\" alt=\"$alt_text\"";
			if (isset($this->titles[$link_id])) {
				$title = $this->titles[$link_id];
				$title = $this->encodeAttribute($title);
				$result .=  " title=\"$title\"";
			}
			if (isset($this->ref_attr[$link_id]))
				$result .= $this->ref_attr[$link_id];
			$result .= $this->empty_element_suffix;
			$result = $this->hashPart($result);
		}
		else {
			# If there's no such link ID, leave intact:
			$result = $whole_match;
		}

		return $result;
	}
	function _doImages_inline_callback($matches) {

It is generally recommended to explicitly declare the visibility for methods.

This method seems to be duplicated in your project.

		$whole_match	= $matches[1];

$whole_match is not used, you could remove the assignment.

		$alt_text		= $matches[2];
		$url			= $matches[3] == '' ? $matches[4] : $matches[3];
		$title			=& $matches[7];
		$attr  = $this->doExtraAttributes("img", $dummy =& $matches[8]);

		$alt_text = $this->encodeAttribute($alt_text);
		$url = $this->encodeAttribute($url);
		$result = "<img src=\"$url\" alt=\"$alt_text\"";
		if (isset($title)) {
			$title = $this->encodeAttribute($title);
			$result .=  " title=\"$title\""; # $title already quoted
		}
		$result .= $attr;
		$result .= $this->empty_element_suffix;

		return $this->hashPart($result);
	}


	function doHeaders($text) {

It is generally recommended to explicitly declare the visibility for methods.

	#
	# Redefined to add id and class attribute support.
	#
		# Setext-style headers:
		#	  Header 1  {#header1}
		#	  ========
		#  
		#	  Header 2  {#header2 .class1 .class2}
		#	  --------
		#
		$text = preg_replace_callback(
			'{
				(^.+?)								# $1: Header text
				(?:[ ]+ '.$this->id_class_attr_catch_re.' )?	 # $3 = id/class attributes
				[ ]*\n(=+|-+)[ ]*\n+				# $3: Header footer
			}mx',
			array(&$this, '_doHeaders_callback_setext'), $text);

		# atx-style headers:
		#	# Header 1        {#header1}
		#	## Header 2       {#header2}
		#	## Header 2 with closing hashes ##  {#header3.class1.class2}
		#	...
		#	###### Header 6   {.class2}
		#
		$text = preg_replace_callback('{
				^(\#{1,6})	# $1 = string of #\'s
				[ ]*
				(.+?)		# $2 = Header text
				[ ]*
				\#*			# optional closing #\'s (not counted)
				(?:[ ]+ '.$this->id_class_attr_catch_re.' )?	 # $3 = id/class attributes
				[ ]*
				\n+
			}xm',
			array(&$this, '_doHeaders_callback_atx'), $text);

		return $text;
	}
	function _doHeaders_callback_setext($matches) {

It is generally recommended to explicitly declare the visibility for methods.

		if ($matches[3] == '-' && preg_match('{^- }', $matches[1]))
			return $matches[0];
		$level = $matches[3]{0} == '=' ? 1 : 2;
		$attr  = $this->doExtraAttributes("h$level", $dummy =& $matches[2]);
		$block = "<h$level$attr>".$this->runSpanGamut($matches[1])."</h$level>";
		return "\n" . $this->hashBlock($block) . "\n\n";
	}
	function _doHeaders_callback_atx($matches) {

It is generally recommended to explicitly declare the visibility for methods.

		$level = strlen($matches[1]);
		$attr  = $this->doExtraAttributes("h$level", $dummy =& $matches[3]);
		$block = "<h$level$attr>".$this->runSpanGamut($matches[2])."</h$level>";
		return "\n" . $this->hashBlock($block) . "\n\n";
	}


	function doTables($text) {

It is generally recommended to explicitly declare the visibility for methods.

	#
	# Form HTML tables.
	#
		$less_than_tab = $this->tab_width - 1;
		#
		# Find tables with leading pipe.
		#
		#	| Header 1 | Header 2
		#	| -------- | --------
		#	| Cell 1   | Cell 2
		#	| Cell 3   | Cell 4
		#
		$text = preg_replace_callback('
			{
				^							# Start of a line
				[ ]{0,'.$less_than_tab.'}	# Allowed whitespace.
				[|]							# Optional leading pipe (present)
				(.+) \n						# $1: Header row (at least one pipe)
				
				[ ]{0,'.$less_than_tab.'}	# Allowed whitespace.
				[|] ([ ]*[-:]+[-| :]*) \n	# $2: Header underline
				
				(							# $3: Cells
					(?>
						[ ]*				# Allowed whitespace.
						[|] .* \n			# Row content.
					)*
				)
				(?=\n|\Z)					# Stop at final double newline.
			}xm',
			array(&$this, '_doTable_leadingPipe_callback'), $text);
		
		#
		# Find tables without leading pipe.
		#
		#	Header 1 | Header 2
		#	-------- | --------
		#	Cell 1   | Cell 2
		#	Cell 3   | Cell 4
		#
		$text = preg_replace_callback('
			{
				^							# Start of a line
				[ ]{0,'.$less_than_tab.'}	# Allowed whitespace.
				(\S.*[|].*) \n				# $1: Header row (at least one pipe)
				
				[ ]{0,'.$less_than_tab.'}	# Allowed whitespace.
				([-:]+[ ]*[|][-| :]*) \n	# $2: Header underline
				
				(							# $3: Cells
					(?>
						.* [|] .* \n		# Row content
					)*
				)
				(?=\n|\Z)					# Stop at final double newline.
			}xm',
			array(&$this, '_DoTable_callback'), $text);

		return $text;
	}
	function _doTable_leadingPipe_callback($matches) {

It is generally recommended to explicitly declare the visibility for methods.

		$head		= $matches[1];
		$underline	= $matches[2];
		$content	= $matches[3];
		
		# Remove leading pipe for each row.
		$content	= preg_replace('/^ *[|]/m', '', $content);
		
		return $this->_doTable_callback(array($matches[0], $head, $underline, $content));
	}
	function _doTable_callback($matches) {

It is generally recommended to explicitly declare the visibility for methods.

		$head		= $matches[1];
		$underline	= $matches[2];
		$content	= $matches[3];

		# Remove any tailing pipes for each line.
		$head		= preg_replace('/[|] *$/m', '', $head);
		$underline	= preg_replace('/[|] *$/m', '', $underline);
		$content	= preg_replace('/[|] *$/m', '', $content);
		
		# Reading alignement from header underline.
		$separators	= preg_split('/ *[|] */', $underline);
		foreach ($separators as $n => $s) {
			if (preg_match('/^ *-+: *$/', $s))		$attr[$n] = ' align="right"';

$attr was never initialized. Although not strictly required by PHP, it is generally a good practice to add $attr = array(); before regardless.

			else if (preg_match('/^ *:-+: *$/', $s))$attr[$n] = ' align="center"';

The variable $attr does not seem to be defined for all execution paths leading up to this point.

			else if (preg_match('/^ *:-+ *$/', $s))	$attr[$n] = ' align="left"';
			else									$attr[$n] = '';
		}
		
		# Parsing span elements, including code spans, character escapes, 
		# and inline HTML tags, so that pipes inside those gets ignored.
		$head		= $this->parseSpan($head);
		$headers	= preg_split('/ *[|] */', $head);
		$col_count	= count($headers);
		$attr       = array_pad($attr, $col_count, '');
		
		# Write column headers.
		$text = "<table>\n";
		$text .= "<thead>\n";
		$text .= "<tr>\n";
		foreach ($headers as $n => $header)
			$text .= "  <th$attr[$n]>".$this->runSpanGamut(trim($header))."</th>\n";
		$text .= "</tr>\n";
		$text .= "</thead>\n";
		
		# Split content by row.
		$rows = explode("\n", trim($content, "\n"));
		
		$text .= "<tbody>\n";
		foreach ($rows as $row) {
			# Parsing span elements, including code spans, character escapes, 
			# and inline HTML tags, so that pipes inside those gets ignored.
			$row = $this->parseSpan($row);
			
			# Split row by cell.
			$row_cells = preg_split('/ *[|] */', $row, $col_count);
			$row_cells = array_pad($row_cells, $col_count, '');
			
			$text .= "<tr>\n";
			foreach ($row_cells as $n => $cell)
				$text .= "  <td$attr[$n]>".$this->runSpanGamut(trim($cell))."</td>\n";
			$text .= "</tr>\n";
		}
		$text .= "</tbody>\n";
		$text .= "</table>";
		
		return $this->hashBlock($text) . "\n";
	}

	
	function doDefLists($text) {

It is generally recommended to explicitly declare the visibility for methods.

	#
	# Form HTML definition lists.
	#
		$less_than_tab = $this->tab_width - 1;

		# Re-usable pattern to match any entire dl list:
		$whole_list_re = '(?>
			(								# $1 = whole list
			  (								# $2
				[ ]{0,'.$less_than_tab.'}
				((?>.*\S.*\n)+)				# $3 = defined term
				\n?
				[ ]{0,'.$less_than_tab.'}:[ ]+ # colon starting definition
			  )
			  (?s:.+?)
			  (								# $4
				  \z
				|
				  \n{2,}
				  (?=\S)
				  (?!						# Negative lookahead for another term
					[ ]{0,'.$less_than_tab.'}
					(?: \S.*\n )+?			# defined term
					\n?
					[ ]{0,'.$less_than_tab.'}:[ ]+ # colon starting definition
				  )
				  (?!						# Negative lookahead for another definition
					[ ]{0,'.$less_than_tab.'}:[ ]+ # colon starting definition
				  )
			  )
			)
		)'; // mx

		$text = preg_replace_callback('{
				(?>\A\n?|(?<=\n\n))
				'.$whole_list_re.'
			}mx',
			array(&$this, '_doDefLists_callback'), $text);

		return $text;
	}
	function _doDefLists_callback($matches) {

It is generally recommended to explicitly declare the visibility for methods.

		# Re-usable patterns to match list item bullets and number markers:
		$list = $matches[1];
		
		# Turn double returns into triple returns, so that we can make a
		# paragraph for the last item in a list, if necessary:
		$result = trim($this->processDefListItems($list));
		$result = "<dl>\n" . $result . "\n</dl>";
		return $this->hashBlock($result) . "\n\n";
	}


	function processDefListItems($list_str) {

It is generally recommended to explicitly declare the visibility for methods.

	#
	#	Process the contents of a single definition list, splitting it
	#	into individual term and definition list items.
	#
		$less_than_tab = $this->tab_width - 1;
		
		# trim trailing blank lines:
		$list_str = preg_replace("/\n{2,}\\z/", "\n", $list_str);

		# Process definition terms.
		$list_str = preg_replace_callback('{
			(?>\A\n?|\n\n+)					# leading line
			(								# definition terms = $1
				[ ]{0,'.$less_than_tab.'}	# leading whitespace
				(?!\:[ ]|[ ])				# negative lookahead for a definition
											#   mark (colon) or more whitespace.
				(?> \S.* \n)+?				# actual term (not whitespace).	
			)			
			(?=\n?[ ]{0,3}:[ ])				# lookahead for following line feed 
											#   with a definition mark.
			}xm',
			array(&$this, '_processDefListItems_callback_dt'), $list_str);

		# Process actual definitions.
		$list_str = preg_replace_callback('{
			\n(\n+)?						# leading line = $1
			(								# marker space = $2
				[ ]{0,'.$less_than_tab.'}	# whitespace before colon
				\:[ ]+						# definition mark (colon)
			)
			((?s:.+?))						# definition text = $3
			(?= \n+ 						# stop at next definition mark,
				(?:							# next term or end of text
					[ ]{0,'.$less_than_tab.'} \:[ ]	|
					<dt> | \z
				)						
			)					
			}xm',
			array(&$this, '_processDefListItems_callback_dd'), $list_str);

		return $list_str;
	}
	function _processDefListItems_callback_dt($matches) {

It is generally recommended to explicitly declare the visibility for methods.

		$terms = explode("\n", trim($matches[1]));
		$text = '';
		foreach ($terms as $term) {
			$term = $this->runSpanGamut(trim($term));
			$text .= "\n<dt>" . $term . "</dt>";
		}
		return $text . "\n";
	}
	function _processDefListItems_callback_dd($matches) {

It is generally recommended to explicitly declare the visibility for methods.

		$leading_line	= $matches[1];
		$marker_space	= $matches[2];
		$def			= $matches[3];

		if ($leading_line || preg_match('/\n{2,}/', $def)) {
			# Replace marker with the appropriate whitespace indentation
			$def = str_repeat(' ', strlen($marker_space)) . $def;
			$def = $this->runBlockGamut($this->outdent($def . "\n\n"));
			$def = "\n". $def ."\n";
		}
		else {
			$def = rtrim($def);
			$def = $this->runSpanGamut($this->outdent($def));
		}

		return "\n<dd>" . $def . "</dd>\n";
	}


	function doFencedCodeBlocks($text) {

It is generally recommended to explicitly declare the visibility for methods.

This method seems to be duplicated in your project.

	#
	# Adding the fenced code block syntax to regular Markdown:
	#
	# ~~~
	# Code block
	# ~~~
	#
		$less_than_tab = $this->tab_width;

$less_than_tab is not used, you could remove the assignment.

		
		$text = preg_replace_callback('{
				(?:\n|\A)
				# 1: Opening marker
				(
					(?:~{3,}|`{3,}) # 3 or more tildes/backticks.
				)
				[ ]*
				(?:
					\.?([-_:a-zA-Z0-9]+) # 2: standalone class name
				|
					'.$this->id_class_attr_catch_re.' # 3: Extra attributes
				)?
				[ ]* \n # Whitespace and newline following marker.
				
				# 4: Content
				(
					(?>
						(?!\1 [ ]* \n)	# Not a closing marker.
						.*\n+
					)+
				)
				
				# Closing marker.
				\1 [ ]* (?= \n )
			}xm',
			array(&$this, '_doFencedCodeBlocks_callback'), $text);

		return $text;
	}
	function _doFencedCodeBlocks_callback($matches) {

It is generally recommended to explicitly declare the visibility for methods.

		$classname =& $matches[2];
		$attrs     =& $matches[3];
		$codeblock = $matches[4];
		$codeblock = htmlspecialchars($codeblock, ENT_NOQUOTES);
		$codeblock = preg_replace_callback('/^\n+/',
			array(&$this, '_doFencedCodeBlocks_newlines'), $codeblock);

		if ($classname != "") {
			if ($classname{0} == '.')
				$classname = substr($classname, 1);
			$attr_str = ' class="'.$this->code_class_prefix.$classname.'"';
		} else {
			$attr_str = $this->doExtraAttributes($this->code_attr_on_pre ? "pre" : "code", $attrs);
		}
		$pre_attr_str  = $this->code_attr_on_pre ? $attr_str : '';
		$code_attr_str = $this->code_attr_on_pre ? '' : $attr_str;
		$codeblock  = "<pre$pre_attr_str><code$code_attr_str>$codeblock</code></pre>";
		
		return "\n\n".$this->hashBlock($codeblock)."\n\n";
	}
	function _doFencedCodeBlocks_newlines($matches) {

It is generally recommended to explicitly declare the visibility for methods.

		return str_repeat("<br$this->empty_element_suffix", 
			strlen($matches[0]));
	}


	#
	# Redefining emphasis markers so that emphasis by underscore does not
	# work in the middle of a word.
	#
	var $em_relist = array(
		''  => '(?:(?<!\*)\*(?!\*)|(?<![a-zA-Z0-9_])_(?!_))(?=\S|$)(?![\.,:;]\s)',
		'*' => '(?<=\S|^)(?<!\*)\*(?!\*)',
		'_' => '(?<=\S|^)(?<!_)_(?![a-zA-Z0-9_])',
		);
	var $strong_relist = array(
		''   => '(?:(?<!\*)\*\*(?!\*)|(?<![a-zA-Z0-9_])__(?!_))(?=\S|$)(?![\.,:;]\s)',
		'**' => '(?<=\S|^)(?<!\*)\*\*(?!\*)',
		'__' => '(?<=\S|^)(?<!_)__(?![a-zA-Z0-9_])',
		);
	var $em_strong_relist = array(
		''    => '(?:(?<!\*)\*\*\*(?!\*)|(?<![a-zA-Z0-9_])___(?!_))(?=\S|$)(?![\.,:;]\s)',
		'***' => '(?<=\S|^)(?<!\*)\*\*\*(?!\*)',
		'___' => '(?<=\S|^)(?<!_)___(?![a-zA-Z0-9_])',
		);


	function formParagraphs($text) {

It is generally recommended to explicitly declare the visibility for methods.

	#
	#	Params:
	#		$text - string to process with html <p> tags
	#
		# Strip leading and trailing lines:
		$text = preg_replace('/\A\n+|\n+\z/', '', $text);
		
		$grafs = preg_split('/\n{2,}/', $text, -1, PREG_SPLIT_NO_EMPTY);

		#
		# Wrap <p> tags and unhashify HTML blocks
		#
		foreach ($grafs as $key => $value) {
			$value = trim($this->runSpanGamut($value));
			
			# Check if this should be enclosed in a paragraph.
			# Clean tag hashes & block tag hashes are left alone.
			$is_p = !preg_match('/^B\x1A[0-9]+B|^C\x1A[0-9]+C$/', $value);
			
			if ($is_p) {
				$value = "<p>$value</p>";
			}
			$grafs[$key] = $value;
		}
		
		# Join grafs in one text, then unhash HTML tags. 
		$text = implode("\n\n", $grafs);
		
		# Finish by removing any tag hashes still present in $text.
		$text = $this->unhash($text);
		
		return $text;
	}
	
	
	### Footnotes
	
	function stripFootnotes($text) {

It is generally recommended to explicitly declare the visibility for methods.

This method seems to be duplicated in your project.

	#
	# Strips link definitions from text, stores the URLs and titles in
	# hash references.
	#
		$less_than_tab = $this->tab_width - 1;

		# Link defs are in the form: [^id]: url "optional title"
		$text = preg_replace_callback('{
			^[ ]{0,'.$less_than_tab.'}\[\^(.+?)\][ ]?:	# note_id = $1
			  [ ]*
			  \n?					# maybe *one* newline
			(						# text = $2 (no blank lines allowed)
				(?:					
					.+				# actual text
				|
					\n				# newlines but 
					(?!\[\^.+?\]:\s)# negative lookahead for footnote marker.
					(?!\n+[ ]{0,3}\S)# ensure line is not blank and followed 
									# by non-indented content
				)*
			)		
			}xm',
			array(&$this, '_stripFootnotes_callback'),
			$text);
		return $text;
	}
	function _stripFootnotes_callback($matches) {

It is generally recommended to explicitly declare the visibility for methods.

		$note_id = $this->fn_id_prefix . $matches[1];
		$this->footnotes[$note_id] = $this->outdent($matches[2]);
		return ''; # String that will replace the block
	}


	function doFootnotes($text) {

It is generally recommended to explicitly declare the visibility for methods.

	#
	# Replace footnote references in $text [^id] with a special text-token 
	# which will be replaced by the actual footnote marker in appendFootnotes.
	#
		if (!$this->in_anchor) {
			$text = preg_replace('{\[\^(.+?)\]}', "F\x1Afn:\\1\x1A:", $text);
		}
		return $text;
	}

	
	function appendFootnotes($text) {

It is generally recommended to explicitly declare the visibility for methods.

	#
	# Append footnote list to text.
	#
		$text = preg_replace_callback('{F\x1Afn:(.*?)\x1A:}', 
			array(&$this, '_appendFootnotes_callback'), $text);
	
		if (!empty($this->footnotes_ordered)) {
			$text .= "\n\n";
			$text .= "<div class=\"footnotes\">\n";
			$text .= "<hr". $this->empty_element_suffix ."\n";
			$text .= "<ol>\n\n";
			
			$attr = " rev=\"footnote\"";
			if ($this->fn_backlink_class != "") {
				$class = $this->fn_backlink_class;
				$class = $this->encodeAttribute($class);
				$attr .= " class=\"$class\"";
			}
			if ($this->fn_backlink_title != "") {
				$title = $this->fn_backlink_title;
				$title = $this->encodeAttribute($title);
				$attr .= " title=\"$title\"";
			}
			$num = 0;
			
			while (!empty($this->footnotes_ordered)) {
				$footnote = reset($this->footnotes_ordered);
				$note_id = key($this->footnotes_ordered);
				unset($this->footnotes_ordered[$note_id]);
				$ref_count = $this->footnotes_ref_count[$note_id];
				unset($this->footnotes_ref_count[$note_id]);
				unset($this->footnotes[$note_id]);
				
				$footnote .= "\n"; # Need to append newline before parsing.
				$footnote = $this->runBlockGamut("$footnote\n");				
				$footnote = preg_replace_callback('{F\x1Afn:(.*?)\x1A:}', 
					array(&$this, '_appendFootnotes_callback'), $footnote);
				
				$attr = str_replace("%%", ++$num, $attr);
				$note_id = $this->encodeAttribute($note_id);

				# Prepare backlink, multiple backlinks if multiple references
				$backlink = "<a href=\"#fnref:$note_id\"$attr>&#8617;</a>";
				for ($ref_num = 2; $ref_num <= $ref_count; ++$ref_num) {
					$backlink .= " <a href=\"#fnref$ref_num:$note_id\"$attr>&#8617;</a>";
				}
				# Add backlink to last paragraph; create new paragraph if needed.
				if (preg_match('{</p>$}', $footnote)) {
					$footnote = substr($footnote, 0, -4) . "&#160;$backlink</p>";
				} else {
					$footnote .= "\n\n<p>$backlink</p>";
				}
				
				$text .= "<li id=\"fn:$note_id\">\n";
				$text .= $footnote . "\n";
				$text .= "</li>\n\n";
			}
			
			$text .= "</ol>\n";
			$text .= "</div>";
		}
		return $text;
	}
	function _appendFootnotes_callback($matches) {

It is generally recommended to explicitly declare the visibility for methods.

		$node_id = $this->fn_id_prefix . $matches[1];
		
		# Create footnote marker only if it has a corresponding footnote *and*
		# the footnote hasn't been used by another marker.
		if (isset($this->footnotes[$node_id])) {
			$num =& $this->footnotes_numbers[$node_id];
			if (!isset($num)) {
				# Transfer footnote content to the ordered list and give it its
				# number
				$this->footnotes_ordered[$node_id] = $this->footnotes[$node_id];
				$this->footnotes_ref_count[$node_id] = 1;
				$num = $this->footnote_counter++;
				$ref_count_mark = '';
			} else {
				$ref_count_mark = $this->footnotes_ref_count[$node_id] += 1;
			}
			
			$attr = " rel=\"footnote\"";
			if ($this->fn_link_class != "") {
				$class = $this->fn_link_class;
				$class = $this->encodeAttribute($class);
				$attr .= " class=\"$class\"";
			}
			if ($this->fn_link_title != "") {
				$title = $this->fn_link_title;
				$title = $this->encodeAttribute($title);
				$attr .= " title=\"$title\"";
			}
			
			$attr = str_replace("%%", $num, $attr);
			$node_id = $this->encodeAttribute($node_id);
			
			return
				"<sup id=\"fnref$ref_count_mark:$node_id\">".
				"<a href=\"#fn:$node_id\"$attr>$num</a>".
				"</sup>";
		}
		
		return "[^".$matches[1]."]";
	}
		
	
	### Abbreviations ###
	
	function stripAbbreviations($text) {

It is generally recommended to explicitly declare the visibility for methods.

This method seems to be duplicated in your project.

	#
	# Strips abbreviations from text, stores titles in hash references.
	#
		$less_than_tab = $this->tab_width - 1;

		# Link defs are in the form: [id]*: url "optional title"
		$text = preg_replace_callback('{
			^[ ]{0,'.$less_than_tab.'}\*\[(.+?)\][ ]?:	# abbr_id = $1
			(.*)					# text = $2 (no blank lines allowed)	
			}xm',
			array(&$this, '_stripAbbreviations_callback'),
			$text);
		return $text;
	}
	function _stripAbbreviations_callback($matches) {

It is generally recommended to explicitly declare the visibility for methods.

		$abbr_word = $matches[1];
		$abbr_desc = $matches[2];
		if ($this->abbr_word_re)
			$this->abbr_word_re .= '|';
		$this->abbr_word_re .= preg_quote($abbr_word);
		$this->abbr_desciptions[$abbr_word] = trim($abbr_desc);
		return ''; # String that will replace the block
	}
	
	
	function doAbbreviations($text) {

It is generally recommended to explicitly declare the visibility for methods.

	#
	# Find defined abbreviations in text and wrap them in <abbr> elements.
	#
		if ($this->abbr_word_re) {
			// cannot use the /x modifier because abbr_word_re may 
			// contain significant spaces:
			$text = preg_replace_callback('{'.
				'(?<![\w\x1A])'.
				'(?:'.$this->abbr_word_re.')'.
				'(?![\w\x1A])'.
				'}', 
				array(&$this, '_doAbbreviations_callback'), $text);
		}
		return $text;
	}
	function _doAbbreviations_callback($matches) {

It is generally recommended to explicitly declare the visibility for methods.

		$abbr = $matches[0];
		if (isset($this->abbr_desciptions[$abbr])) {
			$desc = $this->abbr_desciptions[$abbr];
			if (empty($desc)) {
				return $this->hashPart("<abbr>$abbr</abbr>");
			} else {
				$desc = $this->encodeAttribute($desc);
				return $this->hashPart("<abbr title=\"$desc\">$abbr</abbr>");
			}
		} else {
			return $matches[0];
		}
	}

}


/*

PHP Markdown Extra
==================

Description
-----------

This is a PHP port of the original Markdown formatter written in Perl 
by John Gruber. This special "Extra" version of PHP Markdown features 
further enhancements to the syntax for making additional constructs 
such as tables and definition list.

Markdown is a text-to-HTML filter; it translates an easy-to-read /
easy-to-write structured text format into HTML. Markdown's text format
is mostly similar to that of plain text email, and supports features such
as headers, *emphasis*, code blocks, blockquotes, and links.

Markdown's syntax is designed not as a generic markup language, but
specifically to serve as a front-end to (X)HTML. You can use span-level
HTML tags anywhere in a Markdown document, and you can use block level
HTML tags (like <div> and <table> as well).

For more information about Markdown's syntax, see:

<http://daringfireball.net/projects/markdown/>


Bugs
----

To file bug reports please send email to:

<michel.fortin@michelf.ca>

Please include with your report: (1) the example input; (2) the output you
expected; (3) the output Markdown actually produced.


Version History
--------------- 

See the readme file for detailed release notes for this version.


Copyright and License
---------------------

PHP Markdown & Extra
Copyright (c) 2004-2013 Michel Fortin
<http://michelf.ca/>  
All rights reserved.

Based on Markdown  
Copyright (c) 2003-2006 John Gruber   
<http://daringfireball.net/>   
All rights reserved.

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
met:

*	Redistributions of source code must retain the above copyright notice,
	this list of conditions and the following disclaimer.

*	Redistributions in binary form must reproduce the above copyright
	notice, this list of conditions and the following disclaimer in the
	documentation and/or other materials provided with the distribution.

*	Neither the name "Markdown" nor the names of its contributors may
	be used to endorse or promote products derived from this software
	without specific prior written permission.

This software is provided by the copyright holders and contributors "as
is" and any express or implied warranties, including, but not limited
to, the implied warranties of merchantability and fitness for a
particular purpose are disclaimed. In no event shall the copyright owner
or contributors be liable for any direct, indirect, incidental, special,
exemplary, or consequential damages (including, but not limited to,
procurement of substitute goods or services; loss of use, data, or
profits; or business interruption) however caused and on any theory of
liability, whether in contract, strict liability, or tort (including
negligence or otherwise) arising in any way out of the use of this
software, even if advised of the possibility of such damage.

*/
?>

It is not recommended to use PHP's closing tag ?> in files other than templates.