Moved lonely 4-SoftwareEngineering and 5-Debugging contents deeper into tree
Replaced non-POSIX wc example with ls examples
Added biopython module from 2013-06-tufts
Merge remote-tracking branch 'wltrimbl/branch2'

* wltrimbl/branch2:
  Replaced non-POSIX wc example with ls examples
Merge pull request #175 from wltrimbl/toplevelcleanup

Moved lonely 4-SoftwareEngineering and 5-Debugging contents deeper
Merge pull request #172 from wltrimbl/master

Spelling fixes
Merge pull request #177 from wltrimbl/biopython-tufts

Added biopython module from 2013-06-tufts
Update shell_cheatsheet.md

Clarified use of varname in loops.
Would like to see the mention of Windows clarified, since most of this doesn't apply there anyway (not just the two noted exceptions)
fixed missing space in #121