sync: Pass --allow-unrelated-histories to git merge when used with git git 2.9.0...

sync: Pass --allow-unrelated-histories to git merge when used with git git 2.9.0 or newer.

This makes merging a remote into a freshly created direct mode repository
work the same as it works in indirect mode.

The git-annex branches would get merged in any case by a sync,
since that doesn't use git merge.

This might need to be revisited later to better mirror git's behavior.