I think I should have been clearer. I do believe that EGM can be used for what I want. Basically, while you are using the IDE, you can access the files inside the game (like object files, room files, etc.) outside of the IDE, modify them in some way (a text editor, a pull through git, etc.), and you can then refresh the IDE (or similar) to get the changes, without having to restart the IDE. Likewise, if you change something inside the IDE, it will be reflected in the file system, and the VCS can see the changes.
An example of what I am talking about is gedit. You change a file inside gedit, save it, and it is reflected in the file system. If you then change a file you have open in gedit outside of gedit (for instance through another text editor or pulling some updates) and you switch to the view of the file in gedit in which the changes have been made, gedit informs you that the file has changed, and offers to either reload the file or cancel reloading. Basically, gedit checks the status of the files on the file system and reacts on it. I know that other editors like Eclipse and NetBeans have similar handling of files changing on the system.
Currently in LateralGM, if you save as an EGM, the game is stored compressed in EGM. If you go into the EGM file without unpacking it and make changes in it, LateralGM is unaffected. If you restart LateralGM, it will see the changes you made to the EGM. Basically, what I want the editor to do is to detect any changes in the EGM file, and handle it in some way, without having to restart the editor.
So I guess what I actually want is for the editor to detect changes on the file system (for instance coming from some VCS) and handle it, such that the editor does not need to be restarted. That would enable it to work well together with different VCSes.