That's layeredFS; you only need the modified files and a clean ROM to play instead of having to unpack the ROM, replace files, and rebuild it. Saves a lot of headaches!
The "a" folder can't possibly be causing it, that's just data (think of it as a bunch of spreadsheets - nothing that actually "does" anything, it just gets read). If anything it'll be the code.bin, which is a mix of code and small data tables like mart inventories, or maybe a .cro file.