boards native: Deprecate CONFIG_NATIVE_APPLICATION

This option is used in tree only by native_posix, which is deprecated
and being replaced by native_sim. But may be used also in out of tree
targets.
As part of the native_posix deprecation, and therefore the lack of
testing this feature would have in the future, we are also deprecating
this option.

Signed-off-by: Alberto Escolar Piedras <alberto.escolar.piedras@nordicsemi.no>