I deleted the prboom.cfg in ~/RetroPie/roms/ports/doom folder and relaunched doom from emulationstation. This puts it back to the config that comes “out of the box” when you install emulationstation. This puts it in a “playable” state but the controls will be whatever you configured in emulation station. Trying to change the controls from within the game will likely result in disaster since only the keys mapped in emulation station will be recognized. So basically the libretro doom is only good if you want to use a controller. I wasn’t able to get the mouse working with this.
I’ve decided to remove libretro prboom and stick with the regular prboom since it has full use of the keyboard/mouse.