CLI is short for command line interface. It is the command prompt under Windows or Terminal under MacOS.
Instructions for using the KFX Input plugin CLI are found under the heading "Command Line Interface" in the first post in the
KFX Input plugin thread. I suggest posting in that thread if you need further help with this.
The KFX Input plugin will convert your KPF to an EPUB that contains proprietary markup for fixed layout that is Kindle-specific. You will probably need to edit it to make into something acceptable to Apple. You may be better off starting from scratch with whatever source files you used to produce the KPF.