checkout: Ensure copies of unreadable usermode checkouts are readable

checkout: Ensure copies of unreadable usermode checkouts are readable

The extreme special case of "zero mode" files like `/etc/shadow`
comes up again.  What we want is for "user mode" checkouts to
override it to make the file readable; otherwise when operating
as non-root without `CAP_DAC_OVERRIDE` it becomes very difficult
to work with.

Previously, we were hardlinking these files, but then it intersects
with *another* special case around zero sized files, which is
*also* true for `/etc/shadow`.

Trying to avoid hardlinking there unveiled this bug - when
we go to do a copy checkout, we need to override the mode.