For a few commands the options aren't fully documented. This commit
makes the manpage documentation (almost) match the options shown
when you run "<command> --help" on the command line.
Even without -d this shows the whole ref, as well
as the source of the app (user/system) and if it
is a runtime.
This is important now as the default is to show
both user and system and both apps and runtime.
- Fix typos in doc/flatpak-install and doc/flatpak-update.
- The commands ending in -app were deprecated in commit f7a1fdaa,
so update a few remaining references to them.
- flatpak-update is used for runtimes and applications, so fix its short
description.