Trying to figure out how to reset $script at this point.  I believe what happens is, based on this. when initReady is called for init.js, $script is still the last script in memory which is topCommand.js for me.  There is a Java API call though to set $script, so figuring out how to solve this now.

[02-05-2016 @ 19:48:19] Loaded module: commands/streamCommand.js (Enabled)
[02-05-2016 @ 19:48:19] >> addHook: ./commands/topCommand.js[-1]
function () {
    if ($.bot.isModuleEnabled("./commands/topCommand.js")) {
        $.registerChatCommand("./commands/topCommand.js", "top5", 7);
        $.registerChatCommand("./commands/topCommand.js", "top5time", 7);
    }
}

[02-05-2016 @ 19:48:19] Loaded module: commands/topCommand.js (Enabled)
[02-05-2016 @ 19:48:19] Bot locked & loaded!
[02-05-2016 @ 19:48:19] >> addHook: ./commands/topCommand.js[101]
function () {
    $.registerChatCommand("./init.js", "chat", 1);
    $.registerChatCommand("./init.js", "module", 1);
    $.registerChatCommand("./init.js", "reconnect", 2);
}

Notice that topCommand.js is reloaded.. because of $script in addHook:

  function addHook(hook, handler) {
    var scriptFile = $script.getPath().replace('\\', '/').replace('./scripts/', ''),
        i = getHookIndex(scriptFile, hook);
if (hook == 'initReady') $.consoleLn(">> addHook: " + scriptFile + "[" + i + "] " + handler);
    if (i > -1) {
      hooks[i].handler = handler;
    } else {
      hooks.push(new Hook(scriptFile, hook, handler));
    }
  };