Good news! Windup does not run for 16 hours anymore... when refactoring, we omitted to sync one constant between addons... and it was a name of indexed graph DB property. As a result, windup ran 3 times slower on SSD disk and 10 times slower on HDD.
Now I fixed that and voila - you don't have to wait 20 hours for Windup to finish your 300 MB app
Additionally, I've increased Titan database cache size to 9 % of available heap, which I experimentally ascertained to give best results with our current default heap size.
But my notion is we take wrong approach for some modeling cases and we should use edges rather than indexed properties. That could give some more performance gain, and not insignificant.
Enjoy the recovered performance and stay tuned for more