When you have confirmed that your webMathematica site is running correctly and you start to develop your own material, you may wish to strip out all of the documentation and examples to get a minimal installation. The minimum set of files for webMathematica is shown below (the normal file layouts are described in Appendix: File Layout).
Note that you can remove all the J/Link native libraries from webMathematica/WEB-INF/lib/SystemFiles/Libraries except for the library required for your system, which is located in a directory named by $SystemID.