Thanks for the feedback, I haven't been working on this as much recently, as I've been gearing up for a possible Google Summer of Code(and another mystery project), but I have partial relative folder support. I believe if you put in your own relative folder path(relative to the exe) it will work fine, but I haven't yet changed the file selector to behave like such.
An undo function is something from the start I had wanted to implement, but since it requires a hook into an item changes, and some changes have no good hook for(dragging objects on the left, the only way to detect what happened is actually to look for "selection changed", I believe)so it's a little tricky, hence why it isn't there yet.
One cool thing is that these "distraction projects" I mentioned above(GSoC and mystery project), no matter which one succeeds(or both) the code will most likely be reused into Pey, which will yield some awesome features, so keep an eye out, as I have plans for Pey's future.