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fix: outputs and metabolite merging in replaceMets - #756
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edkerk
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Same changes as #755, which was merged into main instead of develop.
replaceMets:removedRxnsandidxDuplRxnswere declared as outputs but never assigned, so requesting them raised an error.replaceMets:idxDuplRxnsdid not indexremovedRxnsin the input model.replaceMets: a reaction containing both the replaced and the replacement metabolite did not have its stoichiometries summed.replaceMets: replacement indices were not remapped after metabolite deletion, and the replacement metabolite could be deleted when merging by name.Each fix has a regression test.