This paper presents a platform-agnostic distributed navigation architecture for autonomous mobile robots operating in intra-factory logistics. Communication, control, navigation, diagnosis and hardware are layered in a hierarchical approach increasing robustness, modularity and flexibility. This architecture promotes several key features, such as dynamic selection of navigation profiles, semantic mapping and human-aware navigation. The approach allowed multiple autonomous mobile robots, cooperating through a fleet management system, to adapt to a wide range of situations, alternating their path planning between high-speed free-space strategies, and high precision low-speed for tight passageways and docking to assembly stations. The benefits of the proposed architecture were validated through a set of experiments in a mockup shopfloor environment. During these tests 3 robots operated continuously for several hours, self-charging without any human intervention.