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When tagging with existing a project, the files that have been deleted should be "untagged". Otherwise people that check out using that tag might end up getting files that should not be there and that can be completely out of date with the other files. Using the rtag -a command should do it. A simple check box for the existing "Tag with existing" functionnality would be good enough.
Unfortunately, in some situations, it is more complicated than that. It is possible to configure local projects such that there directory structure does not mirror that of the server. So, although it would be possible to add another checkbox to the Tag>As Versions dialog that indicates that rtag should be used, it would need to be made clear to the user what the risks were. The work around is to perform a Tag with Existing in the repo view which does do an rtag with the proper parameters. Given that there is a workaround, there is no plan to address this in 3.1.
*** Bug 88723 has been marked as a duplicate of this bug. ***
This bug hasn't had any activity in quite some time. Maybe the problem got resolved, was a duplicate of something else, or became less pressing for some reason - or maybe it's still relevant but just hasn't been looked at yet. If you have further information on the current state of the bug, please add it. The information can be, for example, that the problem still occurs, that you still want the feature, that more information is needed, or that the bug is (for whatever reason) no longer relevant.