For the record: The problem was that the Makefiles not managed by autotools were missing the "distclean" target.
Therefore, dh_auto_clean was falling back to `make clean` (when it actually wanted to run `make distclean`), which skipped the removal of a bunch of files generated by `configure`: - Makefile - config.log - config.status - libtool - src/common/Makefile - src/usr/Makefile - src/usr/argp/Makefile - src/usr/joold/Makefile - src/usr/nat64/Makefile - src/usr/nl/Makefile - src/usr/siit/Makefile - src/usr/util/Makefile And this made dpkg-source think the workspace was damaged. I'm explaining this because Kbuild Makefile samples aren't terribly keen on referencing GNU targets [1] they don't immediately need, so I suspect lots of novice kernel module coders will run into this problem eventually. [1] https://www.gnu.org/prep/standards/html_node/Standard-Targets.html#Standard-Targets
