Detect and resolve collission between capsule-shaped objects

Heya,

I have been working on collision detection because I want to simulate growing bacteria. I actually got quite far (link and image below), but my code is a mess and I feel like Dan would do a much better job. Especially calculating the rotation of the overlapping capsules is a bit of a mess, and I think I'm not doing everything correct. I thought it would be a super cool coding challenge :)

https://jsfiddle.net/bramvandijk88/goad4m5v/