Also run prepare-tree before download phase.

Previously, we were just running `prepare-tree` before a build.
Unfortunately, that means it doesn't get run if you do a `make download`
and then immediately tar up the whole tree, which leads to `sudo` not
having the setuid bit set, which leads to a concierge failure.
Reset system time before preparing tree.

This should avoid warnings from tar about ctime/atime/mtime values that
are in the future. These tend to occur on VMs or systems without a
real-time clock.
Merge branch 'dev' of https://github.com/browndav/medic-os into concierge-refactor