Update rtax to 0.984
fixing issue 1089 principal_cordinates.py failing if the input folder contains other folders
fix #1076 stderr not loaded, using option_parse.error instead
changes based on @jrrideout comments
Update test expectation to match correct rtax 0.984 output
remove obsolete comment re test failures
Merge pull request #1176 from teravest/issue1089

fixing issue 1089 principal_cordinates.py failing if the input folder co...
Merge pull request #1175 from davidsoergel/master

Update rtax to 0.984
fix #1076 making stylistic change requested
fix #1110 changed to say files are whitespace separated not tab separated
Merge pull request #1177 from teravest/issue1076

fix #1076 stderr not loaded, using option_parse.error instead
fix #1142 added documentation for the default case.  Output seen from sourt_otu_table.py -h
Merge pull request #1182 from teravest/issue1142

fix #1142 added documentation for the default case.  Output seen from so...

I feel compelled to make a style comment... :grin:
fix #1150 updated -h documentation
changes recommeded by @gregcaporasso
Ignore extra samples when performing sanity checks

Fixes #1120.
Fix filename extensions in alpha_diversity.py

When invoked in batch-processing mode, the output filenames will now have a .txt extension instead of .biom. Fixes #1147.
Erroneous error message in split_libraries_fastq

The option mentioned in the error message should be
  --barcode_read_fps
instead of
  --barcode_fps
Slight modification to text in log file, added percent of total seqs demultiplexed, added unit test for demultiplex_fasta.py
uclust picker handles filenames with multiple dots

Intermediate .uc files are now correctly named based on the input sequences filename, including the case where there are multiple dots in the filename.

Also updated QIIME codebase to use uclust.py in pycogent_backports/ (was previously only being used in assign_taxonomy.py).

Fixes #191.