Update manifests entity and its dependent entities

Related to #206 (closed).

Manifest records are no longer deduplicated and shared across repositories but rather scoped by repository. This means that each manifests row will now have a repository_id FK for repositories. As a consequence, the link between manifests and its dependent entities, namely manifest_references, layers, and tags becomes broken and needs to be un-deduplicated as well. For this reason, we had to perform all these changes in this single MR, otherwise, all tests would be broken.

Note: With this change (and #206 (closed) in general) several utility methods and integration test cases for the stores in the datastore package become meaningless. For example, the AssociateManifest and DissociateManifest methods in the repository store are no longer applicable. A more detailed analysis and cleanup will be performed as a followup and in separate MRs, as part of #206 (closed). This MR only contains the minimum required changes to make the pipeline green, but instead of refactoring meaningless methods, they are removed in this MR as well.