[Bioperl-l] cvs updates

[Jason Stajich]

Updated to handle newer scripts, retrieval in batch mode, more expasy
mirrors.  Thanks to Alexandre Gattiker <gattiker@isb-sib.ch> for pointing
me to newer scripts. 

Also updated Bio/Tools/Run modules that were not calling _initialize_io in
new.  I belive this was preventing tempfile cleanup.

Changes committed to main trunk and 07 branch. 

Jason Stajich
jason@chg.mc.duke.edu
Center for Human Genetics
Duke University Medical Center 
http://www.chg.duke.edu/