The project structure really shouldn't be flat anymore, as things are too complex at this point. I should modularize things into some subfolders that make sense. For example:
gui folder for gui-related stuff
animations folder for animation-related stuff
dungeon/room folder for dungeon/room-related stuff
engine/utils folder for stuff like the TextureMap, Engine, etc
GameObjects folder for Items, Player, and other GameObjects (and ofc GameObject base class)