Short answer:
Put data files outside of the binary and ship together with JAR in a separate folder.
Long one:
It seems like you are approaching the problem from the wrong direction. JAR file is something like an executable (.exe) on Windows platform - a read only binary containing code.
You can (although it is a bad practice) put some resources like data files, multimedia, etc. inside JAR (like you can inside .exe). But a better solution would be to place these resources outside of the binary so you can switch them without recompiling/rebuilding.
If you need to modify the resources on-the-fly while the application is running, you basically have no choice. The data files have to be outside the binary. Once again, you'll never see a Windows .exe file modifying itself while running.
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