question about program execution

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I have a strange problem that I'm not quite sure what the issue is or how to fix it.

I have a USB drive with a jar file and 2 text files on it.

If I have the drive mounted as /media/USB and I do the following:

cd /media/USB
java -jar myfile.jar

The program runs fine, and when I enter the name of the data file it finds it in the local directory and all works well. 

When I use the file browser and click my way to the same place and double click on the jar file and enter the file name I get a file not found exception from java.

Note I have setup nautilus so that when I open a jar file it runs java -jar on that file.  This works and the program does execute.  However, rather than looking for the file in the local directory which I would expect to be /media/USB, since that is where I went to to run the program, it is looking for the files in my home directory.  The only way I have managed to get things to work is to copy the data files to my home directory before running the program.  This seems strange to me.  Is this normal behavior or is this some sort of security policy?

Any help is appreciated.

Thanks,
Paolo

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