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Allow deleting manifest by repo ID and manifest ID

João Pereira requested to merge manifest-delete-by-repo-and-id into master

So far we only have one option to delete manifests, which is through the repository store, scoped by repo, and identified by digest (which is what we need for the API). For online GC we now need to be able to delete a manifest by (repository_id, id) (spec).

This MR adds such a method and in exchange removes two that are not needed at all.

Related to #256 (closed).

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