Clean up debris in pkgdown deployment

[gaborcsardi]

Right now we need to use clean: false for the deployment, to avoid removing the other version of the site. But this also keeps old files that are not needed.

The solution to this might require changes in pkgdown (as well?).

[gaborcsardi]

This is currently blocked because there is no way to partially update GH pages currently.

[gaborcsardi]

A workaround would be to use our own pkgdown deployment action, which could decide what files to keep and what files to delete.