Use manifest provenance (local/index) for finer diagnostics (#485)

Use manifest provenance (local/index) for finer diagnostics (#485)

* Use manifest source (local, index) for finer errors

* Generate `metadata-version` during release saving

* Script to prepend manifest metadata versions

Not really necessary since we don't expect index manifests to include such
metadata version. Still, it makes clear the change.

* Testsuite adjustments for extra error output

Since we now take advantage of the manifest provenance (index/local), some
error messages require tweaking.

* Review: remove `metadata-version` field