I noticed this commit: commit aecbf6b95a028f43a09ffe058cea8f09e7eb4de9 Author: Mike Pagano <mpagano@gentoo.org> Date: Mon Aug 10 18:48:35 2015 -0400 Linux version 3.14.50. Remove old. Package-Manager: portage-2.2.20 sys-kernel/vanilla-sources/Manifest | 4 ---- sys-kernel/vanilla-sources/vanilla-sources-3.14.49.ebuild | 19 ------------------- sys-kernel/vanilla-sources/vanilla-sources-3.14.50 | 19 +++++++++++++++++++ 3 files changed, 19 insertions(+), 23 deletions(-) I don't see --force so repoman didn't complain about random file with no extension. In the package directory we expect Manifest metadata.xml and *.ebuild. Other file should generate a warning.
Note that https://dev.gentoo.org/~ulm/pms/head/pms.html#x1-340004.3 seems to indicate that other files and directories in the "Package Directories" may be present, which are not covered by the specification and which should be ignored by the PM. So I'd say this should only be fixed on repoman level with a non-fatal warning.
repoman support has been removed per bug 835013. Please file a new bug (or, I suppose, reopen this one) if you feel this check is still applicable to pkgcheck and doesn't already exist.
pkgcheck has UnknownPkgDirEntry.