Update build files and fix incompatibility with other extensions

[MarelliF]

Hello,

This pull request addresses the two following points:

1. update the build files to the latest standards to avoid a deprecation warning (and potential failure to install in the future)
2. add the logic to ignore unknown classes instead of crashing when combining this extension with some others (e.g. nbsphinx)

[asmeurer]

Thanks, although it looks like some other fixes might be necessary to get the CI working here.