Disassembling Java classes is easy, so perhaps I’d need to encrypt all my classes? And when the main program (which is not encrypted) starts, it decrypts all the classes and uses them, and when the program ends a cleanup-thread will place the files back into their original state.
Through then the main program needs to know the code. Which can be disassembled again.
So is there a proper way to protect your code?
No. And don’t bother, it’s really a waste of your time. If you don’t want people to see the code… leave it on your server and connect to it remotely 
Cas
I agree you can’t completely secure your code.
However I disagree it’s a waste of time to
[i]raise the bar[/i].
Sometimes your want to wear off the scriptkiddie by
adding a layer of protection, like obfuscating, which is
about the best and easiest you can do.