Modifying exclude_seqs_by_blast.py in order to store the output in a folder.
reorganizing workflow library files

this partially addresses #698. the previous workflow.py is now workflow/util.py, and the separate workflow library files (core_diversity_analyses.py and pick_subsampled_reference_otus_through_otu_table.py) also now live in the new workflow/ directory. all unit tests and script interface appear to be passing, but i wouldn't be surprised if i still uncover some imports that need to be updated.
Changing hard-coded tmp by qiime.util.get_qiime_temp_dir
ported otu picking worflow functions to upstream.py

these are bloated with a lot of extra import statements and test data. next step will be to clean that up.
fixed class name

also git rm'ed files that should have been git rm'ed a few commits back. in hindsight i should have git mv'ed some files, but it's too late now.
updated to ignore files created by compiling denoiser code
ported downstream workflow functions to downstream.py

this is really bloated right now with extra test data and imports. will be cleaned up from here.
modified to split workflow function to new script

still needs some clean-up
fixed missing import
updated to use new test data
removed unused imports
removed extra import
updated all tests to use qiime.test.get_test_data_fps()
updated imports and credits
cleaned up comments and credits
removed outdated comment
added taxonomy data for test refseqs
2/5 of the tests are updated to use qiime.test.get_test_data_fps()
updated all tests to use qiime.test.get_test_data_fps()
added aligned seqs and lanemask

these can be used as the pynast template and lanemask in tests to speed them up and not rely on external data.