Module uses project content root as its content root
已回答

I have set the modules content root but it still requires me to prefix the modules name in the paths like following:
inputPath = "MyModule/res/input.txt"
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Not sure I understand. Please elaborate.
What Run Configuration do you use to run the app? Where the file is located?
You can check the file's path in the module's output directory (or artifact if you deploy to an application server).