Use symbolic links
Why dont u use a symbolic link to setup a "normal" directory structure jk2 is awaiting.
providing there exists: /usr/local/games/jk2.104/base as a empty directory, do a
ln -s /usr/local/games/jk2_base/base /usr/local/games/jk2.104/base/
and install (as mentioned in posting from DoA) in /usr/local/games/jk2.104/jedimod your mod. (unzip should create the directory jedimod)
PVC (running his own linux server :-)