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There is no way to select the location of where .project, .classpath and .settings are located. Currently they are stored where ever the project is created. By default they should be stored in the users home directory, which is similiar to other IDE's. The problem that these files are too easily deleted when working in CVS, clear case type enviroments. Also, multiple users in the same location or in clear case , VOB, will overwrite each other settings.
*** This bug has been marked as a duplicate of 78438 ***