Fix logic in generate.rb to make all the generated code private

[pepicrft]

We have a generate script that uses swift-bridge to generate the Swift package from the Rust code. This package makes everything public by default leaking internal Rust-specific types. Since we don't want that, we extended the workflow to make everything private after the generation, but that's too strict because Swift expects some conformances to be public.

The goal of this task is to adjust that logic to only make private what needs to be private.