Edited Makefile to produce api documentation for MG-RAST and KBase on every make.
Some edits to api.cgi so that url's appear correctly in return structures.
Edited documentation generator script to accept a site name as a command line option.
Merge pull request #408 from jaredbischof/develop

Edits to make API url's show up correctly in return structures and some fixes to API documentation.
Merge branch 'develop' of github.com:MG-RAST/MG-RAST into develop