--- markdown.php.orig	2008-03-18 21:39:44.000000000 -0400
+++ markdown.php	2008-03-18 22:15:51.000000000 -0400
@@ -708,6 +708,7 @@
 
 		if (isset($this->urls[$link_id])) {
 			$url = $this->urls[$link_id];
+			$url = $this->urlWrapper($url);
 			$url = $this->encodeAmpsAndAngles($url);
 			
 			$result = "<a href=\"$url\"";
@@ -732,6 +733,7 @@
 		$url			=  $matches[3] == '' ? $matches[4] : $matches[3];
 		$title			=& $matches[7];
 
+		$url = $this->urlWrapper($url);
 		$url = $this->encodeAmpsAndAngles($url);
 
 		$result = "<a href=\"$url\"";
@@ -747,6 +749,13 @@
 		return $this->hashPart($result);
 	}
 
+	function urlWrapper($url) {
+	# urlWrapper gets called whenever Markdown creates a link
+	# subclasses can override this function to convert internal urls to ordinary html (like for drupal)
+	# by default we just return the unadultered url
+
+	  return $url;
+	}
 
 	function doImages($text) {
 	#
@@ -2633,4 +2642,4 @@
 software, even if advised of the possibility of such damage.
 
 */
-?>
\ No newline at end of file
+?>
--- marksmarty.module.orig	2008-01-22 17:25:27.000000000 -0500
+++ marksmarty.module	2008-03-18 22:14:37.000000000 -0400
@@ -111,7 +111,45 @@
  * Module Functions
  ********************************************************************/
 
+ /*
+  * We subclass the Markdown parser to implement support for drupal internal links
+  */
+
+class DrupalMarkdownParser {
+
+  /* urlWrapper gets called when the Markdown parser creates a link. By default the parser does no
+   * transformation, so links are ordinary absolute or relative html links. Here, we transform
+   * drupal internal links to ordinary html links
+  */
+  function urlWrapper($original_url) {
+    $frag = null;
+    $query = null;
+
+	$url = $original_url;
+
+    // support ordinary query strings and marks
+    if( strrpos($url, '#') !== FALSE ) {
+      list($url,$frag) = explode('#', $url, 2);
+    }
+
+    if( strpos($url, '?') !== FALSE ) {
+      list($url,$query) = explode('?', $url, 2);
+    }
+
+	/* We use drupal_get_path_alias to sniff whether drupal thinks this is an internal link.
+	 * If it isn't then we return the original link. This lets us support both drupal internal links
+	 * and ordinary absolute and relative html links, such as /path/file
+	*/
+	if( drupal_get_path_alias($url) === $url ) {
+	  return $original_url;
+	}
+
+    return url($url, $query, $frag);
+  }
+}
+
 function _marksmarty_process($text, $format) {
+  @define( 'MARKDOWN_PARSER_CLASS', 'DrupalMarkdownParser' ); // specify class that Markdown will declare for a parser
   require_once(dirname(__FILE__) .'/markdown.php');
   require_once(dirname(__FILE__) .'/smartypants.php');
   if (variable_get("marksmarty_is_markdown_on_$format", 1) == 1) {
@@ -169,4 +207,4 @@
   );
 
   return $form;
-}
\ No newline at end of file
+}