chore: make a copy in setCatalogue and setOptions

[timakro]

Prevents:

• us from removing stuff from the apps object
• the app from internally mutating the options after setOptions

[patrickskowronekdkfz]

I see why this would make sense, but we would override the current options/catalogue regardless of the correctness.

[timakro]

Already before this PR the validation was only showing a warning and not stopping the options/catalogue from being loaded. At some point in the past we made this change from error to warning because it was annoying during development to not be able to test stuff just because the schema doesn't 100% match.