Follow-up from #28925.

We modify clean_stale_files so that the incremental install logic of sagelib can work even if we want to install namespace packages in addition to sagelib, such as:

• sage.numerical.backends.coin_backend. The package sage.numerical.backends is turned into a namespace package. It serves as an example of a module in a namespace package that is maintained outside of the sage source tree (here: https://github.com/mkoeppe/sage-numerical-backends-namespace)

Depends on #32874

Component: refactoring

Branch/Commit: u/mkoeppe/out_of_tree_namespace @ d825e55

Reviewer: Kwankyu Lee

Issue created by migration from https://trac.sagemath.org/ticket/30152