Change how automatic pinning is implemented

This commit re-works how we automatically "pin" runtimes that are
explicitly installed, to prevent them from being removed automatically.
In this implementation we do the update to the config as part of the
deploy, which has the following advantages:
(1) It ensures that there's never a confusing polkit prompt about
configuring the software installation when the user asked for a runtime
to be installed (https://github.com/flatpak/flatpak/issues/4200)
(2) It means we don't have to rely on the code on the error path of
flatpak_transaction_real_run() to un-pin the runtime in case something
went wrong with the installation, since we pin it almost atomically with
the deploy.

Fixes #4200

(cherry picked from commit 6f5bb3597e14a28be5953d5d773c225a86039254)