Removing refresh features and documents refrences

It seems I've had to totally rethink how I handel flushing the
resources. I wanted to originally defer flushing for one document until
all the resources that require it had flushed or otherwise indicated
they were in sync, however, this is not possible. Even though a document
will have multiple resources referencing it, I'll have to flush once per
resource that is brought into sync. I am at least deferring the flushing
of single resources using the 'flush' hook.

This commit removes the refresh ability and the document referencing
ability. Now changed resources will directly affect the document.