Merge pull request #45 from rakhimov/source

Cyclus is added as a dependency.
added first draft of module spec cep
added cep21 to cep0 index
address anthony's comments. module spec -> agent spec. no default path
Merge pull request #46 from rwcarlsen/module-spec

added first draft of module spec cep
accepted->draft for cep21
accepted cep21
Updated amalgamate.
Added nuclear data update section
some updates
more style fixes
more updates
color pallette fixes and clock move
further layout updates
add new images
cafe closing.
fixed directive and added agent files
Some ignore updates
have basic pivot table layout
some raw types