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This page demonstrates how to clean up a build tree using toc2's built-in support.
package.clean_files += file1 ... fileN
package.distclean_files += fileA .. fileZ
(Note the use of the += operator!)

That's all there is to it. The files (or directories) listed in package.clean_files will be removed when make clean is run, and those listed in package.distclean_files will be cleaned up by make distclean.

By adding the cleanup lists in the file, all makefiles in all subdirs can implicitly use them. For example, that file commonly contains:
package.clean_files += *~ *.o
The manual explains how to create custom cleanup sets independent of the package.clean_files variable, but those are not terribly useful except for unusual cases.