Thanks Ken,
For Linux users, the file:\\\ line needs to be file://
Example:
<jnlp spec="1.0+"
codebase="file:///home/<username>/MegaDrum Config Tool">
Obviously replacing <username> with your username.
I didn't need to change permissions. I don't think you should have to if it is in your home folder.
Also, I just copied the files from /tmp/cache/http/www.megadrum.info/configtool