I'm pretty happy with my current system where my framework uses different paths in the templates to the source javascript files. Then at startup, through a combination of checking os.environ and get_application_id() I automatically detect whether I'm running locally on dev_appserver, or under my test appid or production appid on GAE.
And on to the next step, you most likely want to cache your minified JS aggressively, in which case you'd be unable to force clients to update a new version. The typical workaround is to append a hash or date string to the minified js filename whenever it's updated. This is something you'll also need to do in your framework/templating layer instead of app.yaml.