Remove references to organism abbreviations in the organisms file

[mattb112885]

James and I talked about this... the organism abbreviations are the only manual part about the organisms file that is left, and they are hard \ buggy to maintain. They aren't really used for anything within ITEP... we have thus decided to get rid of it.

The following will have to adapt to this:

• Any functions that use the organisms file and expect the ID to be in the third column (and not the second)...
• The SQLite schema

I should probably make a standard organism file parser function to prevent any issues if we need to change this around again.

[mattb112885]

This is fixed with everything I could find that references this file. I really should get rid of all references to this file in the scripts and just reference the database instead.

Let me know if any of the scripts break that I missed...