For 1, yes, there will be a way to specify generating into a project folder. In the name field, if you start typing a relative path (i.e. \), you'll get IntelliSense enumerating all the available folders and can create a new file there.
For 2, awesome feedback -- those are both things that we'd love to do and have on our list of really-want-to-see. You won't see us open custom functions in the next release since we're thinking architecturally how we want to enable this kind of extensibility, but we'll keep these on the radar.