Use Firefox SDK
Current versions of HTTPSE (4.0.2) don't seem to use the add-on SDK. The SDK provides modules for toolbar buttons (soon with a text overlay option too, for hit counters), non-restartability, preference/data storage, etc. Using the SDK makes add-ons uniform and more familiar to users, as well as more compatible with new releases of Firefox and easier to develop/maintain.
Site-specific preferences like user-disabled rules are currently stored in about:config under a new key for each rule: extensions.https_everywhere.rule_toggle.9gag (partial) boolean false This in particular creates a big mess of little entries in about:config that probably don't get removed and just create bloat in prefs.js. One improvement would be to store these site-specific entries in a single JSON object string in a single key. An even better improvement would be use the SDK's storage module, avoiding about:config altogether.
Trac:
Username: Marnes