If you add or remove code files in the source-code folder, you need to update the file list in CMakeLists.txt and SerialPrograms.pro.
If you know a bit about Python, we have a Python script add_new_file.py to help you to add a new file to those file lists. For example:
python3 Arduino-Source/SerialPrograms/Scripts/add_new_file.py Source/<some_middle_path>/Pokemon_NewFile.h
This adds the path of Pokemon_NewFile.h to both CMakeLists.txt and SerialPrograms.pro.
If you are adding a new program and want the program to show up in the side panel in the UI, you also need to add your program to <GameName>_Panels.cpp. e.g. For a Pokemon Scarlet/Violet game, add the program to PokemonSV_Panels.cpp.