We can make operating systems where the islands can interact. Its just needs to be opt in instead of opt out. A bad Notepad++ update shouldn't be able to invisibly read all of thunderbird's stored emails, or add backdoors to projects I'm working on or cryptolocker my documents. At least not without my say so.

I get that permission prompts are annoying. There are some ways to do the UI aspect in a better way - like have the open file dialogue box automatically pass along permissions to the opened file. But these are the minority of cases. Most programs only need to access to their own stuff. Having an OS confirmation for the few applications that need to escape their island would be a much better default. Still allow all the software we use today, but block a great many of these attacks.

In such a scenario, you can launch your IDE from your application manager and then only give write access to specific folders for a project. The IDE's configuration files can also be stored in isolated directories. You can still access them with your file manager software or your terminal app which are "special" and need to be approved by you once (or for each update) as special. You may think "How do I even share my secrets like Git SSH keys?". Well that's why we need services like the SSH Agent or Freedesktop secret-storage-spec. Windows already has this btw as the secret vaults. They are there since at least Windows 7 maybe even Vista.

naturally even flatpak on Linux suffers from this as legacy software simply doesn’t have a concept of permission models and this cannot be bolted on after the fact