This is a problem I face often when dealing with js vs php. As my JS applications become more complex there is more and more a desire to keep all my JS in library files and keep my php as clean as possible. One solution I have started using is to do the following:
js file:
myNamespace.bootstrap = function( payload ){
...
// internally boot up all the modules that need
// the data, passing it where relavent
module.load( payload );
}
php file:
...