[fix] Cmd now passes an absolute manifest path in its run message to upstream.

This is not as good as passing part of the manifest options forward,
but it still fixes some of the practical problems when using the
components together. The code makes sure that the manifests exists,
3 jobs for 8-bad-relative-path-handling-between-command-line-client-and-daemon in 2 minutes and 32 seconds (queued for 2 seconds)