Right now there are two big sets of scripting, the HEAD branch and the stable branch. The stable branch is basically completely different from the HEAD branch. The HEAD branch is much better, and has all of the scripting improvements that've been done in the last year or two. It's been a long time.
I thought the pilot file corruption bug was fixed but I don't know. That's an ask-taylor thing.
Basically, the stable branch scripting is not forwards compatible, and the HEAD branch is not used for official releases (nor is it necessarily stable). I don't really like cutting off potential mod opportunities like that, but it's already going to be one hell of a job ever getting the stable branch stuff working with the updated scripting system stuff. Changes to the stable branch are supposed to be committed to HEAD as well, but that's not the reality of things at all, so there's an unknown number of scripting functions that may have to be updated to work with code that was never committed to the unstable branch.
What it means is that whenever scripting does become a part of an official release, scripts will have to be updated by changing things like mn.getShipByName("Alpha 1")
to mn.Ships['Alpha 1']