If have a file in a a directory that I want to reference in a sibling directory can I use

../dir1/file.js

where my file is in

dir2

on the same level?

Yes you can use

..

to go up tp the parent directory and then back down into dir1

Quick Reference

/   = Root directory
   .   = This location
   ..  = Up a directory
   ./  = Current directory
   ../ = Parent of current directory
   ../../ = Two directories backwards

https://stackoverflow.com/questions/7591240/what-does-dot-slash-refer-to-in-terms-of-an-html-file-path-location

I wasn't sure if suitescript followed the spec.