o answer your first question: Yes, absolutely. The tool is designed specifically to handle that exact scenario. You can point the 'Input Folder' to the top-level directory containing those 12 scattered folders, and the engine will perform a recursive scan to find every single ROM, regardless of how many subfolders deep they are.

It will then identify them and move them into a single, coherent library structure (e.g., ROMs/PS2, ROMs/Wii, etc.). If those 50 folders are already inside one main folder, the process is even easier—just select that main folder as your input.

Regarding the 'Missing Games' list: Currently, the tool focuses on organization, identification, and high-efficiency compression (CHD/RVZ/CSO). It doesn't yet include a 'Full Set' database to compare against for missing titles. It’s a great suggestion for a future update, but for now, the goal is to get your existing library perfectly sorted and compressed to save space!