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I still have some important hints to you regarding this.

minsoc_top.v: on line 817 you should also include:
assign wb_gpio_err_o = 1'b0; (otherwise simulation might drive crazy and prob real life if it doesn't "automatically" be set to 0.

You probably missed it since these are gathered together around line 358 for uart, spi and start_up. And I forgot myself to add it for Ethernet.

On gpio_defines.v, the GPIO_IOS definition I'd set directly to 32. Instantiation would be instead of GPIO_IOS + 1, GPIO_IOS only. Is there any problem regarding this? The definitions generally are more human friendly than coding, so the register definitions of reg [GPIOS_IOS-1:0] which considers 0 to be something is let for the implementation. That's more or less standard I'd say. It is the same as when you define the address width on minsoc_defines.v you define it and I implement it considering the necessary -1s.

GPIO_LINES32 instead of GPIO_LINES31.

I'd substitute the whole minsoc_spartan_3a_starter_kit_ios.v. Instead of it, place a bidirectional port on minsoc_top if GPIO is enabled.
`ifdef GPIO
, gpio_io
`endif

//
// GPIO
//
inout [GPIO_IOS-1:0] gpio_io;

//
// GPIO tri-state
//
// I hope this works without generate, otherwise it is also easy but I'd first try this way
integer iterate;
for (iterate = 0; iterate < GPIO_IOS; iterate = iterate + 1)
    assign gpio_io[iterate] = ext_pad_oe_o[iterate] ? ext_pad_o[iterate] : 1'bZ;

assign ext_pad_i = gpio_io;

And then only define the pins for the inout port on the ucf file. Like this:
NET "gpio_io(31)" LOC = "a1(pin number)" | DRIVE = 12 | SLEW = SLOW;
NET "gpio_io(30)" LOC = "a1(pin number)" | DRIVE = 12 | SLEW = SLOW;
...
NET "gpio_io(0)" LOC = "a1(pin number)" | DRIVE = 12 | SLEW = SLOW;

After that you only need the definition GPIO on minsoc_defines.v. Of course, interrupt and address you also still need. 

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