DOC: Fixed sphinx documentation and .gitignore

sphinx documentation: in packages.html, the ModuleSettings
named tuple was still showing up in camel case, which is now incorrect

.gitignore: added pycharm and other misc file extensions and folders
Removes some ignore patterns for now

We really should use these, however we currently have a dist/ directory
which we should rename first.
Merge pull request 17 from ericdill

https://github.com/VisTrails/VisTrails/pull/17