removing simplicial complex class

[ccurto]

Everything is now a "collection" rather than a "simplicial complex." The latter class no longer exists, but some of the code in @code and @codestream might still be assuming the existence of this class. We need to check this and make sure everything is only using collections and graphs.

Also, documentation in the "Graph" class (and in other places as well, probably) needs to be updated to reflect the current set of functions, and remove references to the simplicial complex class.

[zjroth]

The CodeStream class has not been fully updated to reflect the removal of SimplicialComplex. Weighted collections need to be supported for this to be finished.