Yes you need the Lufa folder inside the lufa folder.

Fork it to your Github, and use the git clone command
i used git clone. now when i opened the directory in terminal and used the "make" command i get this error
Microsoft Windows [Version 10.0.18362.592]
(c) 2019 Microsoft Corporation. All rights reserved.
C:\Users\senic\pkmn-swsh-automation-tools> make
make -f wattsfarmer.mk
make[1]: Entering directory `C:/Users/senic/pkmn-swsh-automation-tools'
wattsfarmer.mk:32: lufa/LUFA/Build/lufa_core.mk: No such file or directory
wattsfarmer.mk:33: lufa/LUFA/Build/lufa_sources.mk: No such file or directory
wattsfarmer.mk:34: lufa/LUFA/Build/lufa_build.mk: No such file or directory
wattsfarmer.mk:35: lufa/LUFA/Build/lufa_cppcheck.mk: No such file or directory
wattsfarmer.mk:36: lufa/LUFA/Build/lufa_doxygen.mk: No such file or directory
wattsfarmer.mk:37: lufa/LUFA/Build/lufa_dfu.mk: No such file or directory
wattsfarmer.mk:38: lufa/LUFA/Build/lufa_hid.mk: No such file or directory
wattsfarmer.mk:39: lufa/LUFA/Build/lufa_avrdude.mk: No such file or directory
wattsfarmer.mk:40: lufa/LUFA/Build/lufa_atprogram.mk: No such file or directory
make[1]: *** No rule to make target `lufa/LUFA/Build/lufa_atprogram.mk'. Stop.
make[1]: Leaving directory `C:/Users/senic/pkmn-swsh-automation-tools'
make: *** [all] Error 2
C:\Users\senic\pkmn-swsh-automation-tools>