Subfolder structure is lost without file at lowest level.

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For broccoli-timepiece dist,
with the following folder structure
src
| - index.ts
| - subfolder
| | - sub.ts

Depending on brocfile:

var files = new Funnel('src', {
 include: ['subfolder/**/*']
});

vs

var files = new Funnel('src', {
 include: ['index.ts', 'subfolder/**/*']
});

The following may be gotten:
dist
| - index.js
| - subfolder
| | - sub.js
(Correct)

OR

dist
| - sub.js
(Wrong)

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Related to microsoft/TypeScript#812

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Solved using microsoft/TypeScript#2772.