tests for cli and clmain
added comments to point to where things are tested
fixes 100
shit from #100
command_handler test
cli write_string output handler test
tests for make_bash_completion
docstrings
tests for make_cli
Additional input handlers
comments and docs for driver
input handlers handle None
Merge pull request #101 from jrrideout/death-march

Additional input handlers
Merge pull request #102 from gregcaporaso/death-march

fixed bug in creation of our BelovedFunctionality
Merge pull request #98 from wasade/death-march

tests for cli and clmain
fixes to make web code run again, looks a little prettier.
removing path from qiime-server
removing path from qiime-server
Merge pull request #103 from douginator2000/death-march

Just fixing a few things preventing the web interface from running.
reorganized directory structure; fixes #105