Factories of the future must be agile to adapt to rapidly changing customer needs, market volatility and shortened product life cycles. This requires flexibility in hardware and software at distinct levels of the factory and manufacturing process: multipurpose machines with fast change-overs, easy to use reconfigurable software and distributed decision-making are key. This paper leverages the new Industry 4.0 design principles to cope with these new manufacturing requirements: (i) distributed auction-based coordination allows local decision-making and task allocation, (ii) distributed model predictive control-based transportation enables free space collision avoidance of automated guided vehicles (AGVs), and (iii) distributed vision-based localisation provides scalable and dynamic position information of key resources on the factory floor. Furthermore, these contributions are brought together in a lab-scale reconfigurable manufacturing system to showcase modularity and distributed decision-making at several levels of a manufacturing process' logistics.