Don't update the same path source multiple times

Don't update the same path source multiple times

Updating a path source can be a possibly expensive operation (lots of
directories that need to be traversed), and currently the root path source is
updated three times:

* Once when the root package is initially loaded.
* Again when the first resolution pass happens over a graph.
* Finally a third when the second resolution pass happens over the graph.

This commit pushes through the original `Source` trait object into the
`PackageRegistry` and removes the implicit call to `add_sources`, pushing that
call up to the stack a bit.