I did the following test with jython.jar:
- I expended the archive I added a script a the root level.
- I packaged again as an .jar with the script.
- I started the archive with java -jar jython
- I tested if I could import the script that I added.
This was working fine. Than I did the same thing but I moved the script from the root to the Lib folder. It both cases, Jython was able to find my script.
This is really strange. It is a problem with pygments only? Can you do a little test?