Replicas are still missing for HCA

[nadove-ucsc]

Follow-up from #6582

The linked issue adds replicas that were previously missing for many HCA entities, such as donors and some protocols. However, there are still HCA entities that are not being replicated. There are two distinct cases:

1. Entities that are linked to a file, but are not replicated because they are not tracked while traversing the links. An example is the dissociation_protocol in canned bundle for test_indexing.
2. Entities that are not linked to any file in their bundle.

The solution for case 1 is to modify the TransformerVisitor class to track all linked entities it encounters, potentially consolidating all currently untracked entities in a single data structure. These entities will then be emitted as replicas by the FileTransformer.

The solution for case 2 is to modify the ProjectTransformer to emit a replica for every entity in its bundle. The hub IDs for these replicas will not include any file IDs. Duplicate replicas will be merged by the index service before any replicas are written to ElasticSearch.

This design depends on the current implementation of the linked ticket, as in #6584