I don't really like the idea of using #I to access the lines and such.

Sounds good. But incidentally, the 210c limit's been gone for a while.

Still, RC can manipulated server strings very easily. There needs to be a way for data to be stored securly.

Limiting special scripting functions to only restricted people will probably hard to do :)

Yes a way of accessing files might be good, although it can be quite slow if you want to use it for big files since Graal will need to cache the file (so that accessing the lines is fast and don't mean to save the entire file immediately when you change the lines).