doc: :zephyr-app: should point to existing in-tree folders

As there is no check (yet!) in the directive, many
.. zephyr-app-commands:: in the documentation are pointing to
non-existing sample applications, which is problematic for users who
typically expect to just copy-paste the commands and have them work.

This commit fixes all offending references to point to existing samples,
or converts them to simple ":app:" instead of ":zephyr-app:" when the
intent wasn't to refer to in-tree samples.

Signed-off-by: Benjamin Cabé <benjamin@zephyrproject.org>