This problem has been around for decades. An application installer doesn't just copy some files to a few directories. It may put them in hundreds of different places. In addition, it adds entries to the registry or other system files. Even the best uninstallers or cleaners miss something when deleting the app.

This is one of the many issues my side project is designed to address. Imagine if installing every application meant just dropping it on the computer. The software 'package' was just a list of data objects the comprised all the files, config settings, etc. Needed to run the app. All these objects would be copied to the storage drive(s).

Imagine further, that the operating system did not have a central registry. Instead, all configuration was managed via a set of configuration objects, spread all over (preferably in the app folders). The configuration manager was just a program that could find every configuration object and make them appear to the user (and the OS) like they were in a unified file.

If a configuration object was copied anywhere in the system, it looked like its contents were just appended to the configuration store. If you deleted an object, all its settings just disappeared.

Uninstalling an application would mean just deleting all the objects in its package. The files would be gone and any configuration settings with them.

This is just one of the features my 'file system replacement' project is designed to handle.