However, ignoring the aspect of software distribution, wouldn't you agree that the approach taken by the Linux desktop today is deficient security-wise? For example, I would like to be able to give mbsync (or Thunderbird or whatever) my IMAP password without giving it to any other program. So I don't want to store it in mbsync's config file in plain text. Neither will I use gnome-keyring (or any other keyring) because it doesn't have any kind of "program authorisation". Any program can just spawn a new "secret-tool" process and get my credentials from gnome-keyring.
I've been thinking for a while about implementing a keyring which runs as a daemon with SUID of a dedicated user and checks which program sends requests to it, using /proc/pid/exe, but I'm not sure if it's a secure source of truth: how e.g. namespaces affect what's visible in /proc/pid/exe. I know you've been developing himitsu[1]. Have you thought about this problem in that context?