@bcoe: (In order):

We'll discuss the name
Yes, it very much is. I defiantly plan to use that as a starting point, I just want to make it support more than one hook.
It's already been done: https://github.com/istanbuljs.
I'm happy to let you contribute, although I'm not quite sure what you mean by "pull it in to nyc". (I also think that it might be out of scope for the istanbul org, but I'm happy to put it there if people want) Here's what I'm hoping the API will be like:

var pirates = require('pirates'); // This auto-calls `pirates/register`, see below.

// ...

pirates.addCompiler('.js', function (module, filename) {
    return this.addFile(module, filename).content; // Just return the new source for the module.
});

Pirates will take care of the rest, including support for auto-fixing modules that directly modify require._extensions. People who's projects include one or more require hooks that don't support pirates can do something like this:

require('pirates/register');
// For some weird reason, part of my app is in coffee script, and some is in ES6.
require('coffee-script/register');
require('babel-core/regsister');
require('some-bad-module/register');

Uh oh!

extract require hook logic into an external module #70

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