This has been a longstanding issue. For some reason there is a great love of adding things to the Diagnostic Shell Tool (CLI) rather than the actual SQLite product. I cannot fathom why one would do this, as it is fraught with all sorts of peril. However, it is a rather trivial matter to remove all the "crappola" from the Diagnostic Shell Tool (CLI) and add it to the SQLite3 library where it belongs -- I have to do this every single time yet more dreck that belongs not in the CLI is added there instead of to the core.