I am using ClearCase in my application which generates a whole load of ".copyarea.db" files (one in every folder).
These cause conflicts when publishing to Tomcat as Eclipse will bundle the "classes" and "test-classes" folders into one JAR (not sure why it does this - as there is no need to have test classes available on the application server).
Any folders with the same names will have a separate .copyarea.db in the classes and test-classes branches.

I managed to get around this problem in general by adding ".copyarea.db" to the Filtered resources on the Java->Compiler->Building->Output Folder preference page. This stops the file appearing in source output (package/class folders), the vast majority of cases.

However there remains the problem of the root folder, i.e. "target/classes/.copyarea.db" and "target/test-classes/.copyarea.db".
These files are not filtered as they are not part of the compile task.
Just deleting the files manually doesn't help either, as Eclipse expects to find them and doesn't.

How can I exclude these ".copyarea.db" files from the root "classes" and "test-classes" folders?