@ikkeT you can build the Raspberry Pi mysGateway as either Serial, Ethernet or MQTT by using appropriate commandline parameters with the configure script. Just do ./configure --help and you'll get a list of all the options available. Once you've chosen your options and run configure then you 'make'. An example of a set of options that will generate an MQTT Gateway is:
./configure --my-debug=enable --my-gateway=mqtt --my-rf24-channel=100 --my-rf24-pa-level=RF24_PA_LOW --my-controller-ip-address=127,0,0,1 --my-port=1883
--my-mqtt-client-id=MyGW2 --my-mqtt-publish-topic-prefix="MyGW2out" --my-mqtt-subscribe-topic-prefix="MyGW2in"

In this case my MQTT Broker is Mosquitto and is on the same Raspberry Pi hence the use of 127,0,0,1 for the specified --my-controller-ip-address. Change that as appropriate to your intended setup.

Hope that helps.