I'm using this to run the Hypothesis annotations without having to always press the bookmarklet. I prefer this method over using the via.hypothes.is proxy, and I was able to get it working by putting "https://cdn.hypothes.is/hypothesis" in the JS link field. This has the benefit of maintaining the URL so as to keep bookmarks/history simple.

However, Hypothesis seems rather slow on some sites (e.g. google homepage), so I don't want it to be active everywhere. With this plugin, I'm able to turn on Hypothesis for all of www.ncbi.nlm.nih.gov (PubMed), but that doesn't turn it on for www.nih.gov. Ultimately, I would like to annotate entire website extensions (i.e. .gov and .edu). Alternatively, enabling it on sites and blacklisting a few sites. Am I missing a feature that would make this possible currently?