At one point people talked on the nesdev forums about a serial bootloader that used the second controller port, and I don't think anyone actually put one into a game? I found code for an implementation at https://web.archive.org/web/20120401200051/http://blargg.parodius.com/nes-code/bootloader/usage.html and made it so you can launch it by putting a code in at the title screen of Nova 1.
I also put put in a hex editor, also accessible via code, and put a bunch of useful routines in a fixed place, Commodore KERNAL style.
I doubt anyone will use any of this but it's neat
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