Disable MonoDevelop project refresh

Unity will sometimes make MonoDevelop do something that looks like its reloading the entire project. This can happen if you change a file in the Unity editor or if you click on a stack trace in the log.

The reload can easily take over a minute in our project and it hurts productivity.

Is there any way to disable this reloading? I would be happy to manually add script files and update the project settings from MonoDevelop.

We’re using Mac OS X.

Does anyone else have the same issue and how do you deal with it?