Only in filter: .DS_Store
Common subdirectories: filter-old/CVS and filter/CVS
diff -up filter-old/filter.module filter/filter.module
--- filter-old/filter.module	2008-12-30 11:43:17.000000000 -0500
+++ filter/filter.module	2009-01-16 17:49:57.000000000 -0500
@@ -732,7 +732,7 @@ function _filter_url($text, $format) {
   $text = ' ' . $text . ' ';
 
   // Match absolute URLs.
-  $text = preg_replace_callback("`(<p>|<li>|<br\s*/?>|[ \n\r\t\(])((http://|https://|ftp://|mailto:|smb://|afp://|file://|gopher://|news://|ssl://|sslv2://|sslv3://|tls://|tcp://|udp://)([a-zA-Z0-9@:%_+*~#?&=.,/;-]*[a-zA-Z0-9@:%_+*~#&=/;-]))([.,?!]*?)(?=(</p>|</li>|<br\s*/?>|[ \n\r\t\)]))`i", '_filter_url_parse_full_links', $text);
+  $text = preg_replace_callback("`(<p>|<li>|<br\s*/?>|[ \n\r\t\(])((http://|https://|ftp://|mailto:|smb://|afp://|file://|gopher://|news://|ssl://|sslv2://|sslv3://|tls://|tcp://|udp://)([][a-zA-Z0-9@:%_+*~#?&=.,/;-]*[a-zA-Z0-9@:%_+*~#&=/;-]))([.,?!]*?)(?=(</p>|</li>|<br\s*/?>|[ \n\r\t\)]))`i", '_filter_url_parse_full_links', $text);
 
   // Match e-mail addresses.
   $text = preg_replace("`(<p>|<li>|<br\s*/?>|[ \n\r\t\(])([A-Za-z0-9._-]+@[A-Za-z0-9._+-]+\.[A-Za-z]{2,4})([.,?!]*?)(?=(</p>|</li>|<br\s*/?>|[ \n\r\t\)]))`i", '\1<a href="mailto:\2">\2</a>\3', $text);
diff -up filter-old/filter.test filter/filter.test
--- filter-old/filter.test	2008-12-28 14:30:36.000000000 -0500
+++ filter/filter.test	2009-01-16 17:52:19.000000000 -0500
@@ -214,7 +214,8 @@ class FilterTestCase extends DrupalWebTe
    * Test the HTML filter
    */
   function testHtmlFilter() {
-
+    $filtered = _filter_url('http://www.example.com/index.php?a[]=1', 'f');
+    $this->assertEqual($filtered, '<a href="http://www.example.com/index.php?a[]=1" title="http://www.example.com/index.php?a[]=1">http://www.example.com/index.php?a[]=1</a>', t('Converting URLs -- addresses with square brackets.'));
   }
 
   function createFormat($filter) {