@can – I was half-right. The issue was concatenation-related, but not how I initially thought.
The concatenation order matters, so you need to list jQuery first, since your other JS libraries depend on it.
So change this:
{{ $jsCombined := slice $transition $zoom $jQuery $bootstrap | resources.Concat "js/main.js" }}
To this:
{{ $jsCombined := slice $jQuery $transition $zoom $bootstrap | resources.Concat "js/main.js" }}
And your errors should go away.