Hi, it removes the annotations of all plugins in the folder, if your terms state that users cannot do that for your plugins it would most likely break your terms if someone used it on your plugins.
Any plugin someone does not want to use the tool on could be moved outside of the plugins folder temporarily, then moved back after the tool is done running.
If you have mandatory text that must be included in the file but still want your users to be able to use this tool, you could put it in a non-annotation comment.