Did you install EasyEffects and other apps with flatpak? If so you need to add some override flag, can't remember what it is but it should be easy to find, maybe arch wiki etc.
You can imagine how many node projects there are running in production with npm run. I have encountered js/ts/node devs that don't even know that you should like, build your project, with npm build and then ship and serve the bundle.
Not really afaik, you can make file immutable with chattr +i /path/to/something but that means you cannot write to it either, which will probably cause problems.
Anything but actually doing what needs to be done to solve the problem