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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 toc2.PACKAGE_NAME.make.at, 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.