Inferred base path is wrong when there is a `.ts` file in `node_modules`

TypeScript Version: 2.1.0-dev.20161101

Code

node_modules/foo/index.ts: (note the .ts)

export const x = 0;

app/index.ts:

import * as foo from "foo"; foo.x + 1;

app/tsconfig.json:

{
    "compilerOptions": {
        "outDir": "bin"
    }
}

Expected behavior:

Writes to bin/index.js.

Actual behavior:

Writes to bin/app/index.js.

The problem is that getCommonSourceDirectory considers all files, not just the ones that will actually be emitted.