Yeah, this is a Windows thing – running
julia init.jl locks the
init.jl file so it can't be overwritten by the plugin manager.
Both your suggestions should be fairly feasible in principle, but I haven't done anything with LT's plugin manager yet so it would take some time to dig into that code.
A nice (and fairly easy to implement) option would be to copy the
init.jl file over to a temporary location and run it without locking the original. That would mean you don't have to shut down the client at all. I'll take a look at doing that if I have a moment.