It can't really, or at least not using its knowledge. Jam goes to a lot of trouble to build exactly what it is told, and that is all it knows how to clean.

Usually, when I do a deep clean, I use the "rm -rf" tool and then repopulate from source control.

A deep clean, under jam's control, could possibly come about by building a list of all source files, and then handing it to an action that deletes everything _except_ those files.

Christopher