Generate documentation

Hello all, maybe is not the best place to write, but I've a problem to generate the documentation from my code.
I've seen that your plugin do that:
ensure(ids: string[], WebpackRequireEnsureCallback) => any;
that permit to compile in ts when you write something like that:
var Controller = require("entry.Controller");

but how I can permit to compile the other things?
For example if you use http://typedoc.io/ it fail when it found:
var Controller = require("entry.Controller");
because it's not a valid ts code.
Same things for the other tools.