<reference types="" /> is not emitted when dependency is in a namespace

[azz]

TypeScript Version: 2.3.2

Code

// deps/dep/dep.d.ts
declare namespace NS {
    interface Dep {
    }
}

// deps/dep/package.json
{
  "typings": "dep.d.ts"
}

---

// src/index.ts
class Src implements NS.Dep {}

Compile with

// src/tsconfig.json
{
    "compilerOptions": {
        "declaration": true,
        "types": [
            "dep"
        ],
        "typeRoots": [
            "../deps"
        ]
    }
}

Expected behavior:

// src/index.d.ts
/// <reference types="dep" />
declare class Src implements NS.Dep {
}

Actual behavior:

// index.d.ts
declare class Src implements NS.Dep {
}

If the namespace is removed from dep.d.ts (with an interface at the top-level), the <reference> is (correctly) emitted.

[azz]

Full repro available here:
https://github.com/azz/typescript-issue-15487