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This paper presents the ongoing development of a modeling methodology and a tool (the so-called simulation integrated system with modeling and optimization (SISMO) solver) that permits manufacturing systems to be both simulated and optimized according to several improvement strategies. We point out that the different steps of modeling, simulating, and optimizing uses the same integrated formalism and environment. A major point of this methodology and tool is the original decision-making mechanism over a hierarchy of complex discrete systems that model the real world. For the SISMO platform to be validated, we applied it to an actual highly constrained discrete-continuous scheduling problem. This study on a real-life problem has systematically led to improvements.