require.extensions should not be modified in the top level. For example, variable require.extensions of a script file that loads coffee script by using var coffee = require('coffee-script') is modified unexpectedly. require.extensions should remains as-is until 'run' is explicitly called.
var coffee = require('coffee-script')
By implementing this, I created another script file named compile-helper.coffee and moved some functions from coffee-script.coffee to it. In 'compile-helper.coffee' the new function is named registerRequire, which replaced the code in the top level before. registerRequire is called in function run of coffee-script.coffee.
Stop modifying require.extensions in the top level.
Done. You now have to require coffee-script/extensions to enable 'em.
@jashkenas: Not true. You may want to check out michaelficarra/CoffeeScriptRedux@23a597e to see how I did this in CSR. Let's try to get this fixed up before 1.7.0.