The entire ALU and Control Unit of the CPU are programmed in EEPROMs. The ALU uses 7 ROMs [1], the Control Unit uses 3 ROMs [2], the program counter uses 5 ROMs [3], the bit shifter uses another ROM [4], so I see 16 EEPROMs in total. Thus, hundreds if not thousands of logic gates are replaced by bitstreams in EEPROMs. This CPU certainly is based on the design philosophy of "EEPROMs as poor-man's FPGA" (not meant to be interpreted in a discouraging way, I found this design is still rather interesting).
[1] https://github.com/pineapple-one/hardware-eagle/blob/main/al...
[2] https://github.com/pineapple-one/hardware-eagle/blob/main/co...
[3] https://github.com/pineapple-one/hardware-eagle/blob/main/pr...
[4] https://github.com/pineapple-one/hardware-eagle/blob/main/sh...