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As discussed on m2e-dev mailing list http://dev.eclipse.org/mhonarc/lists/m2e-dev/msg00377.html.
Did this earlier: http://git.eclipse.org/c/m2e/m2e-core.git/commit/?id=a9bde94d569a1c93b267ab7e16609680198429fa From a suggestion by Pascal I've left the Open POM action for dependencies, etc. and removed it for workspace files.
Moved to https://github.com/eclipse-m2e/m2e-core/issues/