Hey, awesome to see you read these comments! I've been enjoying spending a lot of time just reading/rewriting/mucking around with the code and seeing ways this project could be taken further. In this case, it seems to be due to the merging of states. As you know, states nodes are created, and then compared to existing states, to see if it's actually an already existing one. In the case of 2 players (other than when they can't reach each other), every state (other than when they are in the same node), involve an exact replica, in which the two players are switched. This visual bug is caused due to the state in which the players are where you'd expect, having been replaced with the state in which they are switched. The ideal solution in my mind is not so tightly linking specific 'movables' to each state, but instead merely linking the concept (or definition) of that movable to the state, and then evaluating which particular movable is most appropriate to animate to the new location.
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I saw this a couple years ago, and was so glad to see source come out to muck around. Was reading through it and came across something funky though. Sure enough:
Just thought I'd drop that here in case you are after (visual) bug reports.
Regardless. Incredible project.