The difference with system shell scripts is that you can't accidentally clobber libraries that the system tools require to work - shell scripts don't really have any notion of installable libraries.
Would you mind elaborating on this? Maybe I'm using Linux wrong, but Nix seems like a huge step forward fixing a lot of my frustrations. Admittedly, I haven't used it in production.
One huge benefit of language-specific package managers is having multiple versions of packages on the same system and you can choose which you'd like for the project (without changing the OS). I feel like 10 years ago I heard a lot of grumbling about languages like Ruby or Python should just use apt/rpm, but I haven't see any OS package manager put much effort into this use-case (this is ignoring mac/win support). The closest I've seen is something like Red Hat's Software Collections.
Personally, I feel strongly that any software that's critical to your company should be decoupled from the OS. This is borne through painful and much delayed OS updates and following it makes things much easier long term.
My personal use-case is that different projects (working on multiple in tandem) need different stacks of versions. Also giving the ability to swap versions on the fly. Here's one package manager specifically designed for it https://github.com/nerdvegas/rez
Swapping versions in Linux is pretty heavy out of the box (with rpm/apt); download, remove old versions files, write new versions files. Only one installed at a time. a/b comparing libraries is a pain. For the things I need, I build things into folders like libjpeg-turbo/2.0.2 and nasm/2.14.02 and set the ./configure flags to point to these...basically a more ad hoc approach to what Nix does.
