Information available in the pull request comments:
See ticket #4456 which includes a possible solution. Can you review that and, if it is something you want to move on with, close this issue? Thanks!
I've created a branch that allows for the disabling of the base rewrite as a first step toward the broader solution of allowing the linked documents to define their own base.
Testing is required.
@johnbender - Is this still on your radar for 1.3?
The branch has been updated, and it's ready to merge. I think we need to just pull it in and live with the change for a bit before 1.4
I want to get this in before starting in on the container refactor.
I set milestone 1.3.2. If feel it's safe we can cherry-pick it for that release, otherwise wait until 1.4.
The branch has been merged in master. This will land in 1.4. Closing as fixed.