How to setup my environment so my continuous integration applied web.confg transformations and does not ovewrite the original web.config file?

Question

Currently I have in my project my local computer, in which I develop the system and a Dev server, in which the continuous integration is meant to happen. My dev server also has a visual studio in which I would like to be able to open my solution sometimes, so, to be able to do so, I have a folder to which I download my source code and open the solution from it. My IIS also points to this folder.

This brings me to a problem: when the continuous integration runs, I need it to run the webconfig transformation. If I do so and overwrite my versioned web.config, GIT will point it out as a changed file.

I think I am doing something wrong with my architecture here. Something smells bad. What am I doing wrong? What are the best practices to set my environment to be able to

1. Have continuous integration
2. Use web.config transformations
3. Be able to open the source code in visual studio on my dev machine

?

Thanks!