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I deleted a file outside of Eclipse and told Eclipse to "refresh" that project. Later, on "synchronize", Eclipse thinks the file is an "incoming addition" from the repository, thus trying to undo the local change. Of course, I think it should be an outgoing deletion to the repository. This is 2.1 RC3b.
Workaround: "Mark as merged" turns the incoming addition to an outgoing deletion.
*** This bug has been marked as a duplicate of 31914 ***