As Git moves to SHA-256 object ids by default, OpenGrok does not yet support it. Attempting to load such a repository fails like:

Caused by: org.eclipse.jgit.errors.InvalidObjectIdException: Invalid id: ff3bd48b0ed2f325e1b52e5538cdc66e48a8e1fab20397f8bf0ad709ee38ddc2
	at org.eclipse.jgit.lib.ObjectId.fromString(ObjectId.java:220)

First, JGit needs to support the new object id format: eclipse-jgit/jgit#73
After this support lands upstream, OpenGrok should test and support the new SHA-256 format, ideally before it becomes the Git default.