Honor the repository permssions set with the umask or
core.sharedRepository when creating directories by using tools.MkdirAll.
Pass an appropriate configuration or filesystem object through as needed
to ensure that we can query the proper permissions. Add a test that
these code paths work by cloning a new repository and then performing
some operations on it.
Note that in the test, we match patterns with either the setgid bit
clear or set, since it may be set or not depending on whether the system
has SysV or BSD group semantics.
