Rework linter API to remove a `Clone` implementation on `LinterSettings`

[snowsignal]

In https://github.com/astral-sh/ruff/pull/10652, we had to implement Clone for LinterSettings and all sub-settings so that the source.organizeImports resolver could clone the settings from a reference and then modify rules to [I001, I002]. Since this cloning operation is wasteful (we only need to update one field), we should find a way to temporarily override values in LinterSettings without needing to clone the entire struct.