Do not emit `/// <reference types=".." />` for augmented declarations in dependencies

``` ts
/// <reference types="node" />
interface I {
    e: Error;
}
```

``` sh
> npm install @types/node

> tsc --d a.ts

> type a.ts

/// <reference types="node" />
interface I {
    e: Error;
}
```

`Error` should not be cause a type dependency as it partially came from `lib.d.ts`
