Jase00 Good point, if this happened at a different point in time (e.g. while I was in the middle of the last game jam where we were using folder save and git for the project), it could have been pretty difficult! I know it's experimental, so we are signing up for bleeding edge items, but it would be nice for us folks on the edge...
Also I think it could have been to discuss a work around (e.g. to open a project folder, zip the project folder, change extension to *.c3p and load the *.c3p, you can do the reverse to get back to a project folder (e.g. to check into git.) Something to think about for next time something like this occurs.
How about an in editor alert/notifications that can be cleared, with important messages like this (and you can sign up for: stable, beta, experimental feed?)