Fast Koala breaks transformations in "One-Click Publish" of web projects

[urig]

First of all, thanks for creating and maintaining Fast Koala. It's very useful and elegantly implemented.

I would like to report the below issue.

Steps to reproduce:

1. Given a C# web project in Visual Studio 2015 that has a publishing profile called "Release" and a matching Web.Release.config transform file.
2. Apply Fast Koala to the project.
3. Observe that the transform file has correctly been moved to App_Config\Web.Release.config
4. Set the project's build configuration to "Release" and build it.
5. Observe that transformations have correctly been applied to the root Web.config.
6. Publish the project to its target using the "Release" profile.

Expected behavior:

The target should contain a root Web.config file with "Release" transforms applied to it.

Actual behavior:

The target contains a root Web.config file and its content are the same as the contents of App_Config\Web.Base.config

This is rather dangerous as no error is displayed to the user and the wrong contents are published to target machines, possibly in production environments.