<reference types="" /> is not emitted when the dependency is indirect

[azz]

TypeScript Version: 2.3.2

This is similar to #15487.

Code

// deps/dep/dep.d.ts
/// <reference path="indirect.d.ts" />

// deps/dep/indirect.d.ts
interface Dep {
}

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

---

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

Compile with

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

Expected behavior:

/// <reference types="dep" />
declare class Src implements Dep {
}

Actual behavior:

declare class Src implements Dep {
}

### Tasks

[azz]

Full repro here:
https://github.com/azz/typescript-issue-15488

[azz]

Wrote up a test case, commit referenced above this comment.

[mhegazy]

PRs welcomed.