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If a vcs filesystem is selected, then the Versioning menu is given a "Customize Filesystem" item. We're trying to remove the use of the word "customize" from the IDE. Check with Jano to find out what the best alternate phrasing for this item would be.
This was fixed in 4.0 builds, no "Customize Filesystem" is now under Versioning Menu. Though it was handy IMO, now you have to find the appropriate item in Versioning Manager.