This paper is devoted to the behavior, evaluation and management of non-cyclic discrete systems in general and manufacturing systems in particular. We introduce a special type of Petri nets called CFIOs (Conflict-Free nets with Input and Output transitions). It is shown that CFIOs are live, reversible if consistent, and can be kept bounded under certain conditions. We also develop reduction rules which facilitate the computation of the t-invariants of CFIOs. We then take advantage of the qualitative properties of CFIOs to perform planning in manufacturing systems. Numerical examples illustrate these approaches