Extend `upgrade` command with lib cleaning

[jaschdoc]

I don't see the difficulty, at least for a naive solution. When I change TOML, I go from one dependency graph to another. Add the new stuff and remove the difference.

Originally posted by @mlutze in https://github.com/flix/flix/issues/10227#issuecomment-2796179582

[magnus-madsen]

What if you change it while the compiler is not running? I.e. between two separate invocations?

[jaschdoc]

What if you change it while the compiler is not running? I.e. between two separate invocations?

Remove the libraries that are not in the dependency graph (after dependency resolution)