Not entirely sure I understand the question. To address the first part, from a very high level, from Java, to access the Twitch API you need to create a class that queries the various Twitch API calls via HTTPS. The data comes back in JSON format, you will need to use a class like org.json to parse that data and get the data out that you need.
Not sure I follow an ArrayList for mods? Do you mean you are trying to setup commands that the bot allows like !title and !game versus !users ?