The packager is fine, its packaging all the things you give it to package.
Its doing exactly what you told it to do, is all. Although it sometimes gets confused when it has so many tags to process at once.
Once its done, just push another new tag on top, and at your own discretion delete the files you never wanted to have in the first place.
Just be careful what you push, the packager just works through whatever list you give it. Git isn't for everyone, apparently!
If its Git, just push two both repos at the same time, its trivial to setup with most Git clients.
External repos have never worked flawless with the current packager, so I wouldn't hold my breath for a quick fix, considering they are working on a new platform which should embrace external repositories and promote them to full functionality.