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Refactor older ODE analyses to use PolynomialSystem #919

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The mass-action dynamics analysis for e.g. Petri nets uses PolynomialSystem; older ODE semantics analyses, such as Lotka–Volterra and linear ODE, do not.

To make @kasbah 's work on #766 easily applicable to these older analyses, we should refactor them so that they too use PolynomialSystem.

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    coreRust core for categorical logic and general computation

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