If you have tried to install any WeiDU mod on linux, you may already know the hassle it is to deal with a case-agnostic system on a case-aware filesystem.
I wrote a small script that works pretty well to remedy this problem. I was at least able to install bg2_tweaks, and it should work for other mods (barring problems inherent to the mods themselves, ie if they are not compatible with the EE version).
The script can be found at this address: http://pastebin.com/raw/nmkSGj0L
Save it anywhere and make it executable (chmod +x ./path/to/script)
Go to your game folder (the one with chitin.key in it) and run it. It does not need to be in the same folder. Remember to make a backup beforehand.
To uninstall it, execute the command:
find . type -l | xargs rm
Your game folder should now be compatible with the WeidU executables. The symbolic links are make with a relative path so moving around your game folder should not cause any problem.
One last thing that is not present in the script, but that will be necessary to launch a weinstall:
ln -s ./lang/en_us/dialog.tlk
From the same game folder (the one with chitin.key).