I have a app which is under source control (TFS 2012 also) on c:\\Dev\\MyApp\\Main.
Because im developing a new feature I decided to open a branch on c:\\Dev\\MyApp\
I had a similar situation, and was looking for an answer, when I found this article. I thought about applying this fixed, but felt it was a lot of effort every time you need to branch or merge again.
I did a little more digging, and I believe I found an easier fix. I found that in Visual Studio 2013 if you open the Properties of the project, and click on the Web option, you will see a Servers section with a button 'Create Virtual Directory' in it.
If you click this button it will prompt you with a question about it pointing to a different directory then the project is in, would like to fix it. When you click yes it makes the fix for you, and when you debug now it will pull from the correct location.