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Yeah, overwriting the existing parser is probably not typically what the user intended.
However, I could see someone doing this if, say, they had a parser designed by another module writer, and they wanted to use it but just change one of the sub-parsers or something like that. But a "set_parser" method would probably make more sense for this use case than "add_parser".
I guess my recommendation is to add a "set_parser" method that replaces the old parser (like "add_parser" does now), and then issue deprecation warnings in "add_parser" if a parser with the given name is present (like the patch does, but with deprecation warnings instead of exceptions).
We could then turn the warnings into errors in a few releases.