Trying to clean packages in the package folder where a repo was created with $ pkg repo /var/ports/packages portmaster fails with the following message ===>>> Empty origin in /var/ports/packages/digests.txz ===>>> Aborting update Apparently, it treats the file 'digests.txz' like a compiled package (and maybe it would have also done so with 'meta.txz' and 'packagesite.txz', had it not failed on the first one). If these file names are hard-coded into the repo system, perhaps they should be known to portmaster too? These files are even stored in 'packages' root folder rather than in 'packages/All' where portmaster normally saves them. It seems that portmaster should not look in the root folder, because no packages should be found there.
Look at poudriere The "normal" packages are in the directory "All" pkg repo -o output-dir, --output-dir output-dir Create the repository in the specified directory instead of the package directory.