I finally managed to upload the FPGA bitstream via MQTT.

At the moment I use a protocol in which I publish the bitstream split up into messages of 128 byte each into a different topic and let mosquitto (the MQTT Broker) ensure that they all arive. At the moment the bottleneck is the Serial Port between the ARM board and the configuration Controller but in the next days I am going to work on sppeding that up.

Now I will start working on the bitstream that will go into the FPGA that configures all the other boards on the bus.