Start with doing "submodule absorbgitdirs" as otherwise "submodule
deinit" will fail if a module has been cloned first and later added as
a submodule (as it will then contain the .git dir instead of it being
under the superprojects .git dir).
Then try to deinit the submodules before moving the repo and abort the
upgrade if it fails for any submodule. Then do the move and finally
initialize the submodules that were initialized before the upgrade.
See #285
