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This isn't a bug in Eclipse but in Java 6: If a Zip file changes while Eclipse reads it, chances are that the native code behind ZipFile.getEntry() crashes the VM. The workaround is to disable automatic refresh while building with Maven (i.e. Run -> Maven install or running "mvn install" from the command line). This bug is tracked at Oracle: http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=7074879
Closing since it's not an Eclipse bug.
Moved to https://github.com/eclipse-m2e/m2e-core/issues/