Fixes spurious overwrite of a standard config, but also doesn't
update the standards anymore in a running installation. Install
media is unaffected from this change. Users that have had their
standard config overwritten need to rewrite the file accordingly:
/usr/local/etc/config.xml
It also enables users to use their own sample configs on a running
installation from now on. Might add a knob in the GUI to do e.g.
`use this config as the factory reset configuration'. :)
While there, move the pkg-related Makefile glue into its own
file in the subdirectory for clarity.
