pkg_repos.h is generated at configure time, not build time (which is, in itself, a bug, but is non-trivial to fix).  Listing it in CLEANFILES means you have to re-run the configure script after "gmake clean".
Reinstate CLEANFILES as DISTCLEANFILES, so a simple clean still works but distclean and maintainer-clean remove pkg_repos.h as expected.
Merge pull request #852 from dag-erling/cleanfiles

Remove CLEANFILES from Makefile.am