Handle the case where version of an indirect dependency is missing

parent #255 

For now, if an indirect dependency's version is missing (e.g. the `Ninject` dependency of `Nancy.Bootstrappers.Ninject` mentioned in #255 ), we won't download nupkg for it. @davidfowl , do we want to warn users in this case? They won't be able to do `k run` because of missing indirect dependencies.