Windows platform template stores it's package structure (bin and template folders, package.json, etc.) inside of "windows" subfolder, and this is just a heritage of windows8 platform.
Such a structure of platform template makes for example impossible to get package using npm install directly from git repo, and adds unnecessary complexity to tooling scripts.
Since wp8 platform is already moved to proposed structure (package.json is in the root of repo), windows - is the last one of major platforms.
For simplicity and consistency, let's flatten repo structure and remove unnecessary windows folder in repo root.