I just want to separate Skype, because I don't trust it. We are using it only to call/chat with people, no file transfers!
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Firejail is a Linux namespaces sandbox program that can jail Skype, Firefox or any other GUI software. It should work on any Linux computer.
There're builtin application restriction approaches, you don't have to run it within a container.
Take a look at apparmor, it should fit all your needs. e.g what file it can read / write, what binaries it can execute