I think one of the issues you are battling is that the second pattern covers files that are already included in the first pattern. The easiest way to deal with that is to move everything that is under /js but not in /js/navigation into a separate folder like /js/app. Then rewrite the configuration as:
joinTo: {
'app.js': /^js\/app/,
'nav.js': /^js\/navigation/
According to documentation that should give you two separate files.
