Documentation Update

[joezuntz]

This adds partial or full documentation, mainly on files and file types.

It also updates various docstrings to make the sphinx-friendly.

Finally, it updates the list of stages.

[empEvil]

I think we also need to update the file running.rst since it references running on nersc on cori.

[joezuntz]

Removed the mentions of "cori" too!

[empEvil]

Great!, but I think we accidentally broke the link to the CC-IN2P3 installation details

[joezuntz]

Thanks - I fixed that broken link.