Some larger plugins take a while to shut down. We should be able to "watch" the plugin directory more as a plugin is shut down and make sure it's really shut down before we install the updated plugin. I'm envisioning something where you plop down a new .jar, it goes to erase the plugin's directory and sits there and watches until it's really removed. Ie, install new gateway.jar. Remove gateway. Is it gone? No? Wait a second. Remove gateway. Is it gone? No? Wait a second. Remove gateway. Is it gone? It is? good, install new gateway. With some sort of timeout of course.. maybe try 5 times or something and if it fails throw some sort of error back to the user (especially if done via the admin console).