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In the context of automated manufacturing systems (AMS), Petri nets are widely adopted to solve the modeling, analysis, and control problems. So far, nearly all known approaches to liveness enforcing supervisory control investigate AMS with either flexible routes or assembly operations, whereas little work investigates them with both. In this paper, we propose a novel class of systems, which can well deal with both features so as to facilitate the control of more complex AMS. Using structural analysis, we show that liveness of their Petri net model can be attributed to the absence of undermarked siphons, which is realizable by synthesizing a proper supervisory controller. Moreover, an efficient method is developed and verified via AMS examples.