Adding more information to open reference log
Addressing Greg's comments
Merge branch 'master' of git://github.com/qiime/qiime into upstream_log
Resolves issue #1065

Changes the 'simpson_e' calculation to be increase as evenness increases. Reference thread:
https://groups.google.com/forum/#!searchin/qiime-forum/simpsons%2420e/qiime-forum/F7GvTT2Elgw/rU8fnNfLoNMJ
Added another example

Added another test calculation from another ecology lab. Given that the literature definition of this function is unclear, I wanted to have another resource which validates our interpretation.
Changed permissions to 644.
Removed commented line
updated changelog
ported run_script_usage_tests from qcli
added text on the source of this code
Remove "versions" from the QIIME overview tutorial

The document was pointing to an FTP site that read "QIIME-1.5.0" and in
turn was confusing users. I've changed this such that there's now a
folder named qiime-files in thebeast.colorado.edu where I've copied the
current contents of qiime/examples/qiime_tutorial/ and updated the
documentation of tutorial.rst.

Fixes #1137
Merge pull request #1242 from gregcaporaso/issue-1019

updated default rdp_max_memory
Merge pull request #1250 from gregcaporaso/issue-950

updated so script usage test output from all_tests.py is more informative
Rename folder to be qiime_overview_tutorial.zip
Fixing formatting on several lines
Making API logs callable
Fixes #1258
Merge pull request #1259 from jrrideout/issue-1258

Fixes #1258
updated to latest version of pycogent's uclust.py
updated to latest version of pycogent's uclust.py