Fix Repository#newDocumentAdapter(String, Function) signature

In the context of NXP-27465, we needed to instantiate CommentAdapter in order to handle comments or annotations replies.

But it's not possible as it is currently, because the function expect to have Adapter as returned type which is not a super type of CommentAdapter or AnnotationAdapter.

We want to fix this signature and replace Document.Adapter by Document.AbstractAdapter.