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Creating a an empty workspace using Java EPP package M6 triggers the download of the index. From a quick look, it seems that this is caused by the activation of our UDC bundle.
The early startup used to configure projects was touching m2e.core, to avoid this I've moved the calls to m2e core out of that method, and added a check to see if there are projects to configure. http://git.eclipse.org/c/m2e/m2e-core.git/commit/?id=20adda52abe844ebd1acae94ade1984c86262acc
*** Bug 341551 has been marked as a duplicate of this bug. ***
Moved to https://github.com/eclipse-m2e/m2e-core/issues/