During development, especially debugging, Unity's interaction with MonoDevelop (apparently by rewriting the project files) is being quite bothersome. When it rewrites them, it resets the Target framework to "Mono / .NET 3.5". (I've targeted .NET 4.0 to evaluate some software that uses default values, and the code builds and runs fine.) But, every time that Unity perceives a script change (or any asset change, perhaps), it rebuilds the project files, resetting that to 3.5. So, I have to click through the dialogs to change the settings back. It's time consuming!
Can anyone share how to prevent (or slow down) this behavior?