setup: correctly reinitialize repository version

setup: correctly reinitialize repository version

When reinitializing a repository, Git does not account for extensions
other than `objectformat` and `refstorage` when determining the
repository version. This can lead to a repository being downgraded to
version 0 if extensions are set, causing Git future operations to fail.

This patch teaches Git to check if other extensions are defined in the
config to ensure that the repository version is set correctly.

Signed-off-by: Caleb White <cdwhite3@pm.me>
Signed-off-by: Junio C Hamano <gitster@pobox.com>