initial notes
updates...
removed section on bug reporting as that was integrated earlier in the doc
removed info that is now covered in CONTRIBUTING.md
removed info that is better covered in http://pycogent.org/scripting_guidelines.html
various updates through-out
changes to address comments from @teravest
addressing comments from @antgonza
updating based on @wasade's feedback
fixing typos
more typo fixes; fixes #1207
one more change requested by @ElDeveloper
added link to QIIME webpage
Merge pull request #1279 from gregcaporaso/issue-1207

addition of developer documentation