Missing pinentry and pinentry-qt
Pinentry is basically a part of GnuPG, as a safe way to let user input their passphase safely. Kleopatra and KMail talks to gpg-agent, and gpg-agent will use pinentry for every place that needs a passphase. The problem here is we don't have pinentry in the Runtime, and build and bundle it with the application won't solve this. Because gpg-agent don't find pinentry executable in $PATH, instead, it use a hard-coded path /usr/bin/pinentry
(only runtime can add this, but Freedesktop SDK and KDE sdk both not have this thing).
Gnome have pinentry and pinentry-gtk3 shipped with runtime to make their Evolution and Seahorse work, maybe KDE can do this to fix Kleopatra and KMail. This two app suffers from missing pinentry
when working with gpg.
There're some discussion about this topic in github: https://github.com/flathub/flathub/pull/3182