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AbstractPublishApplicationOperation has two separate methods to return a module: getModule() getModules() They both return the same module, except one is an array. Since publish operations only work on the root module in an array of modules, consider removing one of these two methods and just using one to avoid confusion which one to use.
This has already been "fixed". There are still two methods to fetch modules in the operation: all the modules, or the first module. The API change now reflects this.