In 2.6, my controller file located in /opt/retropie/emulators/retroarch/configs had the following lines which were used:

input_device = “Microchip Technology Inc. Ultimate 2”
input_driver = “udev”
input_up_axis = -1
input_down_axis = +1
input_left_axis = -0
input_right_axis = +0

In 3.0 Beta 2, this file is no longer read..

For the Atari 2600 (lr-stella) emulator, I added the lines below.

#include “/opt/retropie/configs/all/retroarch.cfg”
config_save_on_exit = “false”
input_player1_joypad_index = 0
input_player1_left_axis = “-0”
input_player1_right_axis = “+0”
input_player1_up_axis = “-1”
input_player1_down_axis = “+1”

The file will get rebuilt after running the emulator if I remove the config_save_on_exit. It will add many lines and reformat it. It will keep many, if most/all, of my settings but the config file does get updated.

Since I wanted it to keep my formatting, I added the config_save_on_exit. This behavior of updating the config file is not in 2.6.