When creating annotations in the manifest, say from a Path, URIs of "content" are set relative to the "/.ro/" directory, e.g. "annotations/foo.ttl". However when parsing back a manifest these appear as "/.ro/annotations/foo.ttl".
The URIs should remain relative to /.ro/ for consistency and predictable JSON-LD output on a load-save roundtrip. This should also be true if the manifest is loaded back with /.ro/.