Actually this did not quite solve my problems because TortoiseCVS automatically adds the -d flag when updating, so that the directories are back immediately. Tortoise CVS does have a "Update special .." command which allows me to turn off the -d option. But that has the disadvantage that I will also not get any new directories that may get added to Moodle.
What I want is to only get rid of the language directories that I do not use but keep all other functionality in place.
General developer forum
removing directories in TortoiseCVS
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