Per the wiki:

http://wiki.opensymphony.com/display/WW/Prototype

"Do you forsee adding a configuration file so we can keep our own directory structure, etc.. ? If that were the case, I could/weould like to start using it today but I have my structure already set in my SVN repository. I would like to start prototyping right from there."

I would like to be able to specify:

SRC.DIR (or even the classes dir and have the users IDE do the compilation?)
LIB.DIR
WEB-INF.DIR
JSP.DIR

..and I think that would cover everything we would need.