> symlinks are indexed anD the move or deletion of the target would trigger a "would you like to change/delete the symlink as well?"

Patch your coreutils. Difficulty: easy.

Most of your other needs can be addressed by making a specialized Linux distro (difficulty: hard), rather than writing a kernel that does all of this (difficulty: max). Build your packages to be containerized by default. I suggest using chroot containers and writing some kind of FUSE filesystem to mount in the container and provide controlled access to user files. You'll also want to write or modify a Wayland compositor to suit your needs. You can have this provide the permission prompts and similar things. Difficulty: hard, but very much doable.

Skills to learn: Linux, thoroughly. You should be comfortable making packages, running things in containers, and writing C before you embark on this.

You should definitely build this. I'm working on something similar but my design appeals to fewer people. Feel free to reach out to me if you have questions with anything, email is in my profile.