[Biojava-dev] Renaming BioJava3 packages & modules

[Spencer Bliven]

Jose mentioned this a bit in the BioJava 4 release thread, but I think it
deserves independent discussion.

Due to historical reasons, the 'biojava3' identifier is used in several
places in the project:
- Most module names (except integration and protein-comparison-tool)
- Some maven groupids (integration and biojava3-survival)
- Most package names (except for parts of biojava3-structure and
biojava3-structure-gui

Aesthetically it would be nice to remove the 3 from all of these places
given the plan for frequent major releases. It is simpler to be consistent
and will prevent future confusion about why biojava v4+ still refers to
biojava3. That said, there are downsides to the changes:

- Changing groupids will require downstream projects to update their maven
dependencies (although they have to update version numbers anyways)
- Changing module names will be a major code rearrangement. It would
probably require some moderately advanced git wrangling to merge branches
and uncommitted code to the new master. Eclipse users would probably have
to update their projects as well.
- Removing the 3 from package names would require changing imports on all
downstream projects. It might also cause conflicts with legacy packages
which would break any projects that tried to include both biojava3 and
biojava1 (a bad idea to start with, but I know of one case).
- Changing package names requires carefully updating the Cookbook and
tutorial by hand
- All of this requires work from developers which could be better spent
writing code

My personal opinion: Changing all groupids to 'org.biojava' is a
no-brainer. Changing module names is fair amount of work for us, but
doesn't effect downstream projects much and now is the best time to do it.
Changing package names completely breaks all downstream projects (even if
it's easy to fix), which isn't worth it. If anyone asks we can just explain
it's a historical thing.

-Spencer
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