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Currently the 'Fix Copyright' tool does not work for XML files and has been disabled (see bug 276257 comment 12).
Note that the functionality is disabled in the code i.e. changing the preference to not skip the XML files, won't do anything.
Implemented fixes. Please see: https://bugs.eclipse.org/bugs/show_bug.cgi?id=276257 Gerrit commit awaiting review. Will post update once approved.
Leo, correct me if I'm wrong, but believe you Gerrit patch re-enabled as well. So builds > 201407-2000 should have reenabled, and be fixed. Community "real life" verification would be appreciated.