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See issue #62863. If you *cut* a CVS-controlled folder and paste it somewhere, currently the actual folder is deleted. This is wrong (from the perspective of CVS operations); you want it to cvs rm -f every file in the folder and its subfolders, but leave the folders themselves intact so that **/CVS/Entries will record the deletions.
Probably waivable but should at least be in release notes IMHO.
It works for me. Maybe the confusion comes from the fact that these files and folders actually dissappear. We agreed in early stages of development that files should be deleted on Delete and Cut operations. So now everything is deleted and CVS module interally remembers Entries for deleted files. Try opening a Versioning view or invoke Commit and see that deleted files will be actually removed from CVS.
OK, I don't have time to set up a testing repo so I will trust you that it works... It won't help someone who expects to commit from another tool, though. Neither does adding a file/dir, but at least in that case it is clear from the '?' warnings during update that you need to "cvs add" the new file/dir. If you did a cut&paste of a folder (not file) in the IDE and then did a "cvs update" from the command line, CVS would just quietly restore the deleted dir, effectively reverting half your change before you could commit it. I guess that's the tradeoff you make - interoperability with other CVS tools will not be great.