Updated documentation, includes input / output file descriptions
s/cogent.util.misc.app_path/bipy.app.util.which/g

Replace usage of ```cogent.util.misc.app_path``` with ```bipy.app.util.which```. Remove ```qiime.util.which```.

Related to #1369.
fix import spacing
Merge pull request #1379 from jrrideout/issue-1369-which

s/cogent.util.misc.app_path/bipy.app.util.which/g
Fix FastTree version check when non-interactive

Fixes the FastTree version check when running in non-interactive mode. Based on @spikebike's suggested regex.

Fixes #1371.
fix issue with "version" having different case

grep command has to be case-insensitive
added ability to change color choice - fixes #258
Merge branch 'master' of github.com:qiime/qiime into issue-258

Conflicts:
	qiime/make_otu_heatmap.py
	scripts/make_otu_heatmap.py
pep8'ing
added myself to credits, noted in changelog
Remove qiime.util.DistanceMatrix and unit tests
Merge pull request #1386 from gregcaporaso/issue-258

fixes issue 258
Remove DistanceMatrix usage from test_format.py

Also cleaned up related test code so that it uses mock stats results dictionaries. This makes the test code much simpler and decouples it from qiime.stats.
Merge branch 'master' into issue-829
added new parameters for more control over row labels
Merge branch 'master' of github.com:qiime/qiime into issue-751
updated changelog
modified handling of level to make more consistent with other scripts
replaced try/except with if/else
addressing comments from @wasade