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If I create a sync project to a remote directory, say xxx, then delete the project from my workspace and create another that uses the same remote directory, I get merge conflicts. I think this is because you are synchronizing the .project and .cproject files. Do you think this is wise, or should only the source be synchronized?
Yes, this was the problem. It has been fixed by the new file filtering code. The .project and .cproject files are no longer synchronized.