I don't use a MANIFEST.SKIP. Using Module::Build 0.35_09 (from the Perl 5.11.2 distribution), "./Build distclean" generates a MANIFEST.SKIP (1197 bytes) and MANIFEST.SKIP.bak (251 bytes), and then complains about the former not being in MANIFEST. This seems to run contrary to the "clean" part of what I asked it to do. The problem does not occur with M:B 0.35.
-zefram