Fixes #8
fixes #9
Merge pull request #10 from gregcaporaso/issue-8

Fixes #8 and #9
Merge branch 'master' into add-doc
some edits to clean this code up

it is not currently working to generate rst from qcli/scripts, but it wasn't before these edits either. so, trying to figure out how to proceed here - this script needs to be completely re-written anyway, so i'm considering just leaving it broken for the short-term (at least for this commit).
ported scripting guidelines from PyCogent