Add scipy, bipy, and pyqi as dependencies

Fixes #1330.
Change required pyqi version to 0.3.1

Deps were impossible to satisfy because biom-format 1.3.1 requires pyqi 0.3.1, but we were installing 0.3.1-dev.
update to address @gregcaporaso's comments
add optional pycogent deps to extra_requires
Updated documentation, includes input / output file descriptions
Merge branch 'master' into issue-1330

Conflicts:
	ChangeLog.md
Removed deprecated 'commands' import
Merge pull request #1373 from lkursell/issue_1352

Removed deprecated 'commands' import
Merge pull request #1331 from jrrideout/issue-1330

Add scipy, bipy, and pyqi as dependencies
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