I am currently maintaining a large number of JS files and the dependency issue is growing over my head. Right now I have each function in a separate file and I manually main
Have you tried using a dependency manager like RequireJS or LabJS? I noticed no one's mentioned them in this thread.
From http://requirejs.org/docs/start.html:
Inside of main.js, you can use require() to load any other scripts you need to run:
require(["helper/util"], function(util) {
//This function is called when scripts/helper/util.js is loaded.
//If util.js calls define(), then this function is not fired until
//util's dependencies have loaded, and the util argument will hold
//the module value for "helper/util".
});
You can nest those dependencies as well, so helper/util can require some other files within itself.