Here's a TAS (on Dolphin) of what Jr. Troopa skip looks like when put into motion:
http://www.youtube.com/watch?v=z5ZkJhyD3Fw
I heard something about him not starting the TAS over. Though it'd be nice to have a finished TAS of this game, when you have major 'tas-only' sequence-breaks like this I think I wouldn't be able to resist restarting if I were doing it :p. Also I think that this sort of trick could be used as a minor optimization in rooms where you just go in, get an item, and then leave the way you came. An example might be, IDK, when getting the 2nd letter for Parakarry. You'd just walk in, store the loading zone, get the letter, and then immediately get warped back to the previous screen.
EDIT: I think we will be able to skip all the berries in chapter 6. This doesn't actually skip anything in the chapter lol. But I think yellow berry would save time and bubble berry probably has a good chance to as well. The Blue and Red berries... you would have to skip the gates 4 times each to skip those, so I kinda doubt they will be faster. Though... bonecrusher tried it now and it didn't work, but it worked when hacked so now we're trying to figure out why...
An interesting thing of the yellow berry skip is that it could also skip one of the 4 required uses of Parakarry. Could be interesting to skip him someday.
