My Clojure app originally written to run on EB worked with no issues. The problem was with an old, sprawling "monorail" Rails app that needed a very specific system configuration, including running a daemon or two in addition to the web app itself. I can't remember all the individual issues, but the .ebextensions directory was getting pretty big and complicated.

I finally gave up when I ran into bugs in the Rails provisioning scripts that only appeared on initial deploy (or re-deploy; I forget). I had to patch and overwrite them, which was very brittle, and it was just easier to use Chef to spin custom AMIs exactly as I wanted them.

Having Docker be the common "configure a system to your app's needs" mechanism shields me from all these details about how EB works, and that's exactly what was needed.