In addition to enabling/disabling modules (datapacks) via the modules.yml file, you can also use in-game commands. /vt enable <module> and /vt disable <module> give you control of enabling and disabling any module. I recommend using the in game commands as they save you some effort finding which module you are looking for in the modules.yml file (NOTE: if you do edit the modules.yml file, you will need to reload the plugin for any saved changes to take effect. /vt reload can help you there).
In addition to the modules.yml file, there is a config.yml. This contains an option to disable tracking metrics for your server. The metrics are anonymous and useful for me to see how my plugin is used so I can improve the experience for everyone using it.
Next, there is the modules folder. This contains the configuration files for each of the modules (NOTE: some modules do not have any configuration options, and therefore are not present in this folder). Once again, if you make a change to one of this configuration files, you must either reload the whole plugin or just the module that you changed the config file for. Use /vt reload module <module> to reload a specific module.
Lastly, there is the i18n folder. i18n is short for "internationalization" which means translations. Most messages shown to the player can be changed in the various language files. Currently, only English is supported, but I hope as the plugin grows, more people contributing translations will expand that list. See i18n for more information on this.