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That's one of the reasons why file access is generally discouraged in J2EE applications: it's not easily standardized.
What many applications do instead is to access a central database and store all necessary information in there.
Alternatively you can easily make your file system path configurable in your application.
You can use application.getRealPath("/") for saving the file in your application.
This will save the file on the application directory of your web application.