Heyhey,
First of all, thank you for your awesome work of making and maintaining this!
I didn't immediately found the InputAutoCfg.ini (Linux Mint), but I had already found mupen64plus.cfg in ~/.config/mupen64plus
I've played around a bit with 'button', 'axis' and 'hat' and got it working. The article told me to share this with you, so that it might get into new releases as well.
This is the changed section I have in mupen64plus.cfg:
[Input-SDL-Control1]
# Mupen64Plus SDL Input Plugin config parameter version number. Please don't change this version number.
version = 2
# Controller configuration mode: 0=Fully Manual, 1=Auto with named SDL Device, 2=Fully automatic
mode = 0
# Specifies which joystick is bound to this controller: -1=No joystick, 0 or more= SDL Joystick number
device = 0
# SDL joystick name (or Keyboard)
name = "Guillemot Corporation DA Leader"
# Specifies whether this controller is 'plugged in' to the simulated N64
plugged = True
# Specifies which type of expansion pak is in the controller: 1=None, 2=Mem pak, 5=Rumble pak
plugin = 2
# If True, then mouse buttons may be used with this controller
mouse = False
# Scaling factor for mouse movements. For X, Y axes.
MouseSensitivity = "2.00,2.00"
# The minimum absolute value of the SDL analog joystick axis to move the N64 controller axis value from 0. For X, Y axes.
AnalogDeadzone = "4096,4096"
# An absolute value of the SDL joystick axis >= AnalogPeak will saturate the N64 controller axis value (at 80). For X, Y axes. For each axis, this must be greater than the corresponding AnalogDeadzone value
AnalogPeak = "32768,32768"
# Digital button configuration mappings
DPad R = "hat(0 Right)"
DPad L = "hat(0 Left)"
DPad D = "hat(0 Down)"
DPad U = "hat(0 Up)"
Start = "button(12)"
Z Trig = "button(11)"
B Button = "button(1)"
A Button = "button(3)"
C Button R = "button(6)"
C Button L = "button(4)"
C Button D = "button(7)"
C Button U = "button(5)"
R Trig = "button(2)"
L Trig = "button(0)"
Mempak switch = "key(44)"
Rumblepak switch = "key(46)"
# Analog axis configuration mappings
X Axis = "axis(0-,0+)"
Y Axis = "axis(1-,1+)"
Hope this helps :)
I also thought it could be a good idea to document in the default mupen64plus.cfg file that you can use 'button', 'axis' and 'hat' to play around with. It at least would've saved me some trouble :p