fix #1110 changed to say files are whitespace separated not tab separated
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.
Added explicit test for zero length output sequence when truncating reverse primer and modified unit tests
update add_alpha_to_mapping_file.py to address #969
update virtual box docs to address #969
update otu_category_significance.rst to address #969
update core_diversity_analysis.rst to address #969
provided api-level control over line color, and added dashed line for median pre to median post
added control over line color to command line interface, also improved first usage example as the previous ymin/ymax range wasn't good for these data
updated usage example results
made plot background transparent. this addresses #1174
Merge pull request #1196 from gregcaporaso/issue-1174

Issue 1174: enhancements to identify_paired_difference plots
Merge pull request #1185 from jrrideout/issue-1120

Fixes #1120
Merge pull request #1184 from teravest/issue1150

fix #1150 updated -h documentation