The plugin.yml and Extending JavaPlugin

Long story short, don't make anything extend JavaPlugin and don't create a plugin.yml.

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Extending JavaPlugin

You don't need a main class nor do you need to extend JavaPlugin. I know what you're thinking, "what about onEnable/onDisable?" We have you covered. Instead of using the onEnable and onDisable methods use the @PostConstract and @PreDestroy annotations on any method anywhere in the project. You can make as many of these methods as you like. I suggest you create one on every Spring bean that needs something setup (e.g.: connecting to Mongo/MySQL).

The plugin.yml

Don't bother with creating plugin.yml either, mcspring will take care of that.

If you need to add a dependency to the plugin.yml instead use the @PluginDepends annotation somewhere in your project and it will be automatically added for you.

If you need to set the plugin version, name, or description add the @SpringPlugin annotation to a class somewhere inside your plugin.