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It would be good if the file with the text/bin and ignore tables was external to .metadata. That way, a team or company could share a more comprehensive list. Since the defaults are generated from the plugins, the simpler answer may be that these external files contain *additional* entries. There would be a Team preference for locating these files (or one pref. for the directory where both live). Default would be .metadata?
Of course, it would be better if eclipse on the whole had a consistent story for preference sharing, but I we shouldn't avoid trying to solve the specific one just because we'ld prefer a more general one.
*** This bug has been marked as a duplicate of 19691 ***