Created Issue: File changes made through a NuGet package don't get the file checked out from the TFS [3129]

__Repro Steps:__
1. Create an empty Web application project
1. Check in the project into TFS
1. Add a folder "Scripts" into the project
1. Add a .js file "_references" into the "Scripts" folder
1. Open "Manage NuGet Package" dialog against the project
1. Search "AppForSharePointWebToolkit" and install the package onto the project

__Expected:__
_references.js file is checked out from TFS because the file is modified by the NuGet package.

__Actual:__
_references.js file is not checked out from TFS but the file is still modified by the NuGet package.