[Biojava-dev] Broad reformatting commit

[Spencer Bliven]

I'd like to do a few basic formatting commits either tomorrow or
immediately after the release. I'm thinking:

- Convert all files to unix line endings
- Run addlicense.sh
- Convert the last few files using 3-space indenting to use tabs like
everything else
- Remove whitespace at the end of lines
- Add missing @Override
- remove unneeded imports

I do not plan to run the formatter or checkstyle unless other people think
it would be a good idea.

BTW, I hope that everyone who uses eclipse is aware that we have formatting
templates in the development directory. (Confession: I haven't been using
them since at least the last eclipse update.) It would be good if we could
use those more consistently and translate them for other IDEs (filling out
the wiki <http://biojava.org/wiki/BioJava3:Coding_Conventions> page might
be a good start).

I know that this type of large commit can be controversial, so let me know
if anyone is strongly opposed to this.

-Spencer
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