How easy is it going to be modify the JS for themes in 4.0?

[Dylan Riggs]

I haven't looked at the JS side of things yet and only the templating of 4.0. That said, my new website is going to be very animated and I don't like the stock 4.0 animations on modal windows (for example when you click "Mark site as read" and I want to change that around. Is this going to be a piece of cake, or will I have to dig through tons of hoops just to make some simple changes like in 3.4.x?

Just a curious if anyone knew off the top of their head, I haven't had time to do the research or investigation my self.

Thanks!