I don't see any .conf files. I could try to uninstall and reinstall but I am not sure which step the .conf file would have been created.
sudo apt-get update -y
sudo apt-get install build-essential autoconf automake libtool pkg-config libcurl4-openssl-dev libudev-dev \
libjansson-dev libncurses5-dev libusb-1.0-0-dev zlib1g-dev -y
git clone https://github.com/wareck/cgminer-gekko.git
cd cgminer-gekko
sudo usermod -a -G dialout,plugdev $USER
sudo cp 01-cgminer.rules /etc/udev/rules.d/
CFLAGS="-O2 -march=native" ./autogen.sh
./configure --enable-gekko
make
sudo make install
Would it have been in the ./configure --enable-gekko step you think?