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The heat death of the universe?

No, that'd be like closing all outstanding bug reports with a WONTFIX.

Heat death of the universe is just nature's stalebot.

Possibly the only maybe valid answer.

Containerization built in to the OS, with strict privacy controls on what containers can access inside of other containers.

All applications run in its own container, unless they are granted granular permissions to do otherwise.

The code and assets for a program belong in its own quarantined section, not spread out over the filesystem or littered around /etc/, /var/

Built in networking for these containers.

Couldn’t you essentially make a Linux distribution that has these by default?

That's exactly how ChromeOS works.

Silver bullets

Only if you have physical access to the server.

Well you are onto something.

Even if it is a joke, people want to have silver bullets. Those are killing the hairy problems which can be named werewolves.

Downside is hairy problems just like werewolves come from people. So it in the end it is people problems not some container tech or other stack problem. There are no werewolves without people :)