Io dev 3

Please test and merge atop master.
( I just merged master atop this, so merge should be trivial).

I have moved query into current database modality (case, case_tube_idx).

Query db info:
See tests: ./testone -v test_database.Test_query_database.test_query_getfiles
See subcommands:     add_FCSstats_db, query_db, template-query_do, viz-cases-2d

Note that my end-to-end test solution is scripted:
dev/test_run.sh <dir> 5

In terms of architecture of HDF5, I would prefer to have it mirror database organization (see /home/local/AMC/hermands/repos/flow_anal/FlowAnal/database/FCS_declarative.py). This has the downside of making interpreting HDF5 require db, but the upside of making it easier for HDF5 and db to interact. I prefer the latter, because the point is to store different sorts of information that is linked together.