The above question refers to using ScriptCraft for CraftBukkit so I'll answer that first:
You can get the permissionsEx (or any other plugin) like this...
```javascript
var pex = server.pluginManager.getPlugin('PermissionsEx');
if (pex.getUser(player).inGroup('moderator') ) {
...
}
```
Generally if you want to use another plugin's API, then get the plugin object by name and then call its methods. In the above example the `pex` variable refers to the aforementioned `PermissionsEx` Plugin. Once you have that reference you can call any of the plugin's methods just as you would in Java. The tricky part is getting the reference and that's where `server.pluginManager.getPlugin()` comes in.