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I am currently rewriting this in javascript for a Node project I am working on, and I just discovered a bug in the lua script for tag cleaning I committed 8 years ago(!):
since we are pre-processing the tags before passing them to the script, the last line of the script that removes the affected tags from the global tags list effectively does nothing (the tags in this list are not prefixed).
I have updated the script, so that the prefix addition happens inside it and is used for all operations except for the last one.
Better late than never, I suppose :-)