We have newly introduced the principle of protecting webapp by Jar2Exe: 

http://www.jar2exe.com/solutions/webapp , you can understand what we are going to do when converting webapp into exe files.

And then we introdeced a simple way to pre-compile and wrap webapp:

1. Pre-compile: we use a maven plugin to pre-compile, it is more simple than using ant.
2. Wrap webapp: we use a packer tool which will split pre-compiled webapp and launch j2ewiz automatically.