Don't store an aggregate's uri as a URI object.

Just use a string. Knew this would bite me eventually.
Add Manifest#remove_aggregate.

Also forward this method from ROBundle::File.
Don't store an agent's uri or orcid as URI objects.
Remove the Util.parse_uri() method.

No longer used anywhere as we no longer use URI objects anywhere.
Consolidate all require directives into one place.

All done in lib/ro-bundle.rb now.