Remove trailing whitespace
Account for proto files that set their own Java package

This gets auto-inflated by proc and resulted in the wrong target being
returned by this module.
Remove commented out code
Remove debug lines
Merge pull request #1 from JamesLaverack/master

Via the power of horrifyingly expensive phoneternet I deem this fix to to be "probably correct". It contains exactly what I knew would have to happen (scanning the whole proto file for one specific line) but I'm not sure if we need/want to support people specifying /com/example/subdomain as their target folder AND specifying /com/example/subdomain as their package name option in the .proto as well. I'll add that later.

Thanks James.

PS: All commented out code was probably debug lines, I just left them in at this stage because this doesn't have a bunch of tests yet. Not that it matters, they're not exactly hard to put back.