Alternative hypothesis is now explicitly stated.

Alternative hypothesis is now stated in the output stats file. Affects make_distance_boxplots.py and make_distance_comparison_plots.py. Also updated script usage example output.

Verified this using the overview tutorial dataset, as well as with smaller examples in R and using PyCogent's t_two_sample.

Fixes #657.
Merge branch 'master' into issue-657

Conflicts:
	ChangeLog.md
Merge pull request #910 from jrrideout/issue-657

Alternative hypothesis is now explicitly stated.