Ok, got it working. I found hint at the "Is the cloudBit™ open source?" (https://support.littlebits.cc/hc/en-us/articles/200785649-Is-the-cloudBit-open-source-), which points to the schematic on Github (https://github.com/littlebitselectronics/eagle-files/blob/master/WIRE/LB_BIT_w20_CLOUD/LB_BIT_w20_cloudV1-(3_3)OHW/w20-cloudV1-(3_3)OHW.pdf).
I'm not an electronics expert but connecting ground to ground, input to output and vice versa was easy (after pind were soldered to the pads). Then Putty with serial terminal did the rest. The Cloudbit logs as root on the serial console, so the system is entirely open for hacking.