cleanup for review

[wdwvt1]

we need to remove the code that is not being used in the final version of the paper.

things to remove:

• unused
• paper_analysis_code
• .DS_store's found in a host of places
• remove unused generators
• remove tests for unused generators (i.e. test_rules.py)

its been several versions since we checked that the tests are fully covering for the correlations.test modules. in that vein:

• verify that generator tests are operating properly. note that since they were written with older version of almost every other dependent package we may encounter unpleasant numpy errors.

we need to write some new test code for the parsers:

• write new code for testing parsers to deal with the hacks put in to work with various versions of tool result files, biom, etc.