Cleanup the VCS commands configuration

It's not really necessary to differenciate the commands for checking out
or updating a repository. Only the path to the binary and eventual
top-level flags are useful to configure.

Signed-off-by: Maxime Petazzoni <maxime.petazzoni@bulix.org>
Signed-off-by: Thomas Petazzoni <thomas.petazzoni@free-electrons.com>