Completed/removed most code TODO items
Completed most incomplete tests
Added user- and project name validation
Significant relocation of several directories

The goal is to put directories that should be served outside the server document root
Updated code to match relocated directories
Server doesn't print share too much internal info
Added license and copyright notice in source files
Refined future features list in README
Updated README's to match directory relocation
Added (incomplete) first draft of INSTALL.md
Merge branch 'stabilization'
Added tests that QIIME scripts exist

Also modified test to pass with more strict server config
Improved draft of INSTALL.md

Still needs to be tested by someone other than the author