@jsuereth 

About your note number 1, yes, I know that it fixes only stage element and it does not have any action on the generation of the zip file. I thought it was better than nothing for the moment. I need to dive a little bit more in sbt and sbt-native-packager comprehesion in order to propose something relevant for all the scopes you mentionned MSI/DEB/RPM ...

About note 2 , I am ok with your proposal:
```Scala    
mappings in Universal ++= allFilesRelativeTo(file("/foo/bar")
```
I will give it a try.