checkout: also chmod in the user checkout case

checkout: also chmod in the user checkout case

When falling back to copying, we previously would only chmod checked out
files in the non-user-checkout mode. Fix this by always doing chmod.
The file_mode was being prepared but never actually applied.

Add a basic test in the archive-z2 --> usermode checkout case in which
we're guaranteed to always fall back to copy mode.

Closes: #633
Closes: #903
Approved by: cgwalters