Your IDE comment made me think of this. IDEs store each project completely self contained in its own directory. How about allowing some directories to be marked as development dirs. A blacklist of commands when run inside that directory will be prohibited from accessing anything outside that directory, except for read-only access to /usr etc. and RW access to whitelisted dirs.

For example: I mark ~/school/operating-systems as a development directory. I place git, vim, wget, curl, and make on the blacklist (potentially globally-configured). Additionally I whitelist ~/.config/git for git and ~/.vim for vim. This allows core commands that we consider 'safe' like cd, mv to be run without restrictions - presumably they are only being used manually or from sandboxes tools like Make. But when I execute git from anywhere inside ~/school/operating-systems, it will only be able to R/W inside that directory and within the ~/.config/git directories. Meanwhile read access to system folders lets Make etc. work properly.

With a single global configuration + directory-specific overrides, it remains pretty straightforward and doesn't require a huge time investment like AppArmor/SeLinux do. Meanwhile all non-dev work remains unaffected. If you need to download and build a random program, just mark it as a dev directory and you're pretty safe. It's not perfect, but better than nothing