typo fixes and formatting fix for contributing.md

git commands weren't being rendered correctly
update script usage testing docs

now that we don't have output files/dirs included under qiime_test_data/
Removed text referring to script that currently isn't merged into qiime
Converting to PEP8
Fixing qiime/plot_rank_abundance_graph.py = pep8 changed several lines to a single one, that make a numpy array became a list, the solution is to use sorted vs. sort
Fixing tests/test_make_distance_histograms.py = pep8 removed some empty lines from the HMTL and now the count does not match, decided to inspect output and looks fine but @gregcaporaso and I think that in the long run is better to remove this test
Fixing tests/test_denoiser/test_denoiser.py = pep8 removed some spaces from multiline strings in tests.py so test were failing. The solution was to change the multiline string to single lines
Fixing tests/test_pycogent_backports/test_alpha_diversity.py = pep8 changed some function lines that made evident (1) the misuse of sorted and (2) collapsing lines that changed an array to alist. The fixes: (1) renamed the variable to sorted_counts, and (2) cast to array
Fixing tests/test_validate_mapping_file.py = pep8 removed some empty spaces so test failed, fixed this from the expected strings
Changes with 11 -a
Changes with 22 -a
Changes with 42 -a
Merge pull request #1294 from walterst/fix_rst_text_for_script_not_present

Removed text referring to script that currently isn't merged into qiime
Merge pull request #1293 from jrrideout/doc-fixes-post-1.8.0-release

Misc. documentation fixes
Fix if errors
Merge pull request #1295 from antgonza/autopep8

Converting to PEP8