Autoptimize by default excludes inline JS and jquery.js from optimization. Inline JS is excluded because it is a typical cache-buster (due to changing variables in it) and as inline JS often requires jQuery being available as a consequence that needs to be excluded as well. The result of this “safe default” however is that jquery.js is a render-blocking resource. So even if you’re doing “inline & defer CSS” your Start-Render time (or one of the variations thereof) will be sub-optimal.
Jonas, the smart guy behind criticalcss.com, proposed to embed inline JS that requires jQuery in a function that executes after the DomContentLoaded event. And so I created a small code snippet as a proof of concept which hooks into Autoptimize’s API and that seems to work just fine; The next step is having some cutting-edge Autoptimize users test this in the wild. You can view/ download the code from this gist and add it as a code snippet (or if you insist in your theme’s functions.php). Your feedback is more then welcome, I’m sure you know where to find me!
The notification might be less welcome for some users; YUI compression and the CDN options are marked as deprecated in this release. YUI compression was pretty exotic and required the installation of JAVA and the YUI compression jar, so I doubt anyone was actually using this. CDN options are deprecated as well; some people reported issue that I could not reproduce or fix. As I consider CDN not to be core functionality and as it can better be accomplished using e.g. WP Super Cache (which is a must-have companion of Autoptimize anyhow), CDN will indeed also be removed from Autoptimize. Expect the deprecated parts to be removed in 1.7.0 (which isn’t planned yet).
At work we were stumped by a simple link that upon clicking didn’t have the browser request the target page. Our supplier investigated using VisualEvent, a bookmarklet-initiated javasript-tool that goes through a page and visualizes all events on DOM nodes. The developer released VisualEvent 2 a couple of days ago (also on GitHub), which I played around with for a bit and it really is great for debugging purposes!