Move conversion code to stand-alone lib
Fix import statement
Fix code guidelines
Correct Sample ids to be MIENS compliant
Fix #1092 and Fix #979
Merge branch 'master' of https://github.com/qiime/qiime into issue-1092
Removing Unifrac file conversion code as it has been ported to the FastUnfrac repo
Merge branch 'master' of git://github.com/qiime/qiime into MIENS
Ooops, forgot to delete the qiime_test_data folder for the convert_unifrac_sample_mapping_to_otu_table script
Merge branch 'master' of git://github.com/qiime/qiime into MIENS

Conflicts:
	qiime/parse.py
	tests/test_parse.py
Update code for mpl 1.3.1 upgrade

Test in tests/test_stats.py was checking the x ticks of an empty plot, which apparently are different between mpl 1.1.0 and 1.3.1.

In this case, the fix is to remove the test since it is version-specific and isn't all that useful.

I manually ran through the tutorials for make_distance_boxplots.py, make_distance_comparison_plots.py, and compare_distance_matrices.py and the generated figures look good.

Any other scripts you'd like me to manually test? Switching mpl versions is always a little scary...
Update print_qiime_config.py and ChangeLog for mpl
Merge branch 'master' of git://github.com/qiime/qiime into MIENS
Changes added to ChangeLog
Removing documentation
Moving convert_otu_table_to_unifrac_sample_mapping.py functionality to the FastUnifrac repo
Update install docs for mpl 1.3.1
print_qiime_config.py uses max_acceptable_version
Remove checks for mpl 1.1.0 version
Re-adding format_unifrac_sample_mapping as it is used in beta_significance.py