Makefile: make skeleton rsync options consistent

Initially, a "cp" was used for the one-time target skeleton
installation, and an "rsync" was used for the every-time overlay
skeleton installations.  Then, the target skeleton install was
changed to also use rsync (1cd3f992).
Now there are two rsyncs, but with different filter specs, which
seems odd.

This patch adds --excludes to both invocations of rsync to make them
consistent, and removes the -u option from the initial target skeleton
installation.

Signed-off-by: Danomi Manchego <danomimanchego123@gmail.com>
Signed-off-by: Peter Korsgaard <jacmet@sunsite.dk>