I'm hopeful about efforts like bubblewrap, but widespread adoption is very tough. As long as policies are delegated (like AppArmor), I don't see that improving.

TPMs and Passkeys are also a good refuge - Just keep private material off the device.

What I'd like to see is a boundary between system installed packages (which I implicitly trust, but worried about malicious commits upstream, as others have noted) and other code, such as installed via pip, npm, cargo etc.

While it's feasible for me to audit a single shell script, or a PKGBUILD from AUR, it's pretty impossible for modern lanaguage package managers.