I think your first possibility is most likely (which implies that the fourth is too, de facto). When I started coding professionally I used IBM's VisualAge for

I think your first possibility is most likely (which implies that the fourth is too, de facto). When I started coding professionally I used IBM's VisualAge for Java (which was actually a multi-language tool based on Smalltalk) and it did exactly that: all Java classes were managed as code artefacts held in the IDE's internal repository. You had to export from the IDE if you wanted your standard files-in-directores source/objects. It worked very naturally and when IBM moved to Eclipse instead I found it to be quite a step backwards in terms of working with my code. But the drawback was was you could do exactly what the VisualAge IDE supported and not much more. The file-based model gives a level of low-cost interoperability that's pretty hard to beat.