I only jar the wt and com packages (folders) under codebase as separate jar files. You can zip them and change file extension to jar - works the same. The only jar file you will need if you create custom webject in Info*Engine is the ie.jar under WEB-INF/lib
Jar idea is good otherwise if you revise a class it may try to resolve your old version of the class on the classpath. Be careful whatever you do because the auto builds will try and compile and/or copy the entire codebase to a build directory which wastes a lot of time and can eat up CPU.
I don't know how many ANT guru's are on here, but you can still achieve code completion and have a custo. build and deployment script with ANT and just disable all the auto builds, etc. I cannot share mine, but can provide insight into windchill and ant if anyone is interested.
I manage all customizations in a project like setup and typically will use a source code repository like Subversion, CVS, SourceSafeto manage the details.
David