Okay I admit I'm not 100% sure that this is the case but it seems to me that repoman is currently not checking for size of files in sub-directories of $FILESDIR. So this is a request to check this out mostly :)
When checking this out, it works and thus gives a fatal error:
$ mkdir files/test
$ dd if=/dev/urandom of=files/test/test bs=1M count=2
2+0 records in
2+0 records out
2097152 bytes (2.1 MB) copied, 0.258748 s, 8.1 MB/s
$ repoman full
RepoMan scours the neighborhood...
!!! A file is not listed in the Manifest: 'dev-java/jnr-ffi/files/test/test'
(2048 KiB) dev-java/jnr-ffi/files/test/test
Note: use --include-dev (-d) to check dependencies for 'dev' profiles
Please fix these important QA issues first.
RepoMan sez: "Make your QA payment on time and you'll never see the likes of
Furthermore, looking at http://packages.gentooexperimental.org/repoman-current-issues.txt we get to see two such files that confirm this for cvs added files:
(24 KiB) dev-libs/mpfr/files/3.1.0/patch07
(22 KiB) x11-misc/xorg-cf-files/files/xorg-cf-files-1.0.2-solaris-prefix.patch