Major update. Totally reworked logic on directory listing.

if you wish to do the same directory (like current before this update), in config.php make
base_file_dir =   this is untested however. If you want to put your stuff anywhere else
other than the script directory, use the relitive path (from index.php) or the hard path
like /home/simon/filedownloads/  NOTE: YOU MUST HAVE A FOLLOWING DASH. Also fixed bug
in installer, cleaned up code, fixed detection of directory or file and allowed DirectoryLister.php
to determine this so that any theme added will automatically get the proper links going. Fixed
some of my old hacks as well. Fix Md5 generation bug, thanks to @jmztaylor