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Created a Simple JUnit Test Case. Edited it but did not save it before deciding that I didn't want it. I then deleted the file by highlighting the file in the FileSystems panel and pressing the delete key. The error dialog then appeared with the exception in this title. Repeating the steps to test reproducability produced a NullPointerException instead.
Created attachment 13041 [details] ide log with both original error and repeat test
The problem actually appears to be a matter of closing files rather than removal per-se. My system is SuSE Linux 9.0 running against J2SDK1.5.0.
*** This issue has been marked as a duplicate of 39015 ***
v/c