I think this was a typo, or perhaps an older way to handle it.
Within the folder `keyboards` and its subfolder `handwired` is a directory for each keyboard project, for example `qmk_firmware/keyboards/clueboard`. Within it you'll find the following structure:
* `keymaps/`: Different keymaps that can be built
-* `rules.mk`: The file that sets the default "make" options. Do not edit this file directly, instead use a keymap specific `Makefile`
+* `rules.mk`: The file that sets the default "make" options. Do not edit this file directly, instead use a keymap specific `rules.mk`.
* `config.h`: The file that sets the default compile time options. Do not edit this file directly, instead use a keymap specific `config.h`.
### Keymap Structure