The design and operation of manufacturing systems is evolving to adapt to different challenges. One of the most important is the reconfiguration of the manufacturing process in response to context changes (e.g., faulty equipment or urgent orders, among others). In this sense, the Autonomous Transport Vehicle (ATV) plays a key role in building more flexible and decentralized manufacturing systems. Nowadays, robotic frameworks (RFs) are used for developing robotic systems such as ATVs, but they focus on the control of the robotic system itself. However, social abilities are required for performing intelligent interaction (peer-to-peer negotiation and decision-making) among the different and heterogeneous Cyber Physical Production Systems (such as machines, transport systems and other equipment present in the factory) to achieve manufacturing reconfiguration. This work contributes a generic multi-layer architecture that integrates a RF with a Multi-Agent System (MAS) to provide social abilities to ATVs. This architecture has been implemented on ROS and JADE, the most widespread RF and MAS framework, respectively. We believe this to be the first work that addresses the intelligent interaction of transportation systems for flexible manufacturing environments in a holistic form.