Add __str__ and __add__ to qiime.util.MetadataMap

This will facilitate printing and merging of MetadataMap objects.
Modify merge_mapping_files library code

Removed write_mapping_data (one can now call print or str() on
MetadataMap objects)

Changed merge_mapping_files to make use of the newly added __add__ function
of the MetadataMap class.
Replace tests for new merge_mapping_file code
Fix script to work with new library code
Merge branch 'master' of https://github.com/qiime/qiime into improve_metadata_map

Conflicts:
	qiime/merge_mapping_files.py
	scripts/merge_mapping_files.py
	tests/test_merge_mapping_files.py
Accidentally deleted this file!
Update script interface
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.