After having discussed with the sbt-native-manager team and a first "rejected" pull request, here is the way to do this directory mapping in the build.sbt file (see pull request https://github.com/sbt/sbt-native-packager/pull/160 which provides mode detailed documentation) :
mappings in Universal <++= (packageBin in Compile, target ) map { (_, target) =>
val dir = target / "scala-2.10" / "api"
(dir.***) pair relativeTo(dir.getParentFile)
}
To reduce verbosity of the above snippet, there is an issue (https://github.com/sbt/sbt-native-packager/issues/161) to propose a more human readable way to express this directory mapping:
mappings in Universal ++= allFilesRelativeTo(file(target / "scala-2.10" / "api"))