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I found that JGit creates the file .git/packed-refs with format peeled by default.
However, usual Git CLI creates the file with format peeled fully-peeled sorted. This format seems to be more up to date and should thus be preferred.
Running the JGit command packRefs switches to fully-peeled format, similar to running git pack-refs.
So why not use this as default when cloning a repo with JGit?
Motivation
Not all Git clients support legacy "peeled" format, e.g., Fork Git Client: fork-dev/TrackerWin#2265
Alternatives considered
Run packRefs changes to fully-peeled format.
But would be nice to have this as default for a new clone.