Add modules config

[dbashford]

As proven out by the work done here and discussed in dbashford/mimosa#274, the following is necessary when using the modules r.js config.

runConfig.dir = "./public/javascripts"
runConfig.keepBuildDir = true
delete runConfig.insertRequire
delete runConfig.include
delete runConfig.out
delete runConfig.name

• Add a modules config to the optimize config. Add that to the runConfig.
• When modules exist, perform all the above changes to the runConfig, such that if overrides is called, the object is as the above code would suggest it needs to be.