Fixes issue #3349, prints deprecation warning

This patch fixes issue #3349, by prints deprecation warning for
users who depends on old(<1.7.0) implicit module registration.

I've done local tests, but I have no idea where to put my test cases because existing tests are executed after registering coffee extension.

My tests are pasted below. Let me know where to put(or not) these tests then I'll do.

```javascript
// test.js
require('./lib/coffee-script');
require('./test/importing/import.coffee'); // expects throwing
```

```javascript
require('./register');
require('./lib/coffee-script');
require('./test/importing/import.coffee'); // expects nothing
```

```javascript
require('./lib/coffee-script');
require('./register');
require('./test/importing/import.coffee'); // expects nothing
```

Thanks @epidemian for this idea.