Fix issues with some models failing to find steady state. - #1356
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Made some changes, but need to make sure they don't break things elsewhere.
We were dropping all rule-defined species from the conserved moiety test, but those with rate rules needed to not be dropped, and instead not look for conserved moieties.
Tracked down the problem to conflicted AssignmentRules when we suddenly allowed species with assignment rules to participate in conserved moiety analysis runs.
luciansmith
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Fix for #1350, roadrunner failing to find the steady state for BioModel 64. Turned out to have two parts: some species were 'constant' but not 'boundary', and ended up in the 'floating species' section, making parts of the stoichiometry matrix all zeroes. Also, since there were assignment rules, roadrunner didn't want to find conserved moieties, so the NAD+NADH conserved cycle created other problems in the Jacobian. Once we relaxed that restriction, it turned out that assignment rules affecting species levels wasn't being propagated. Fixing that finally made everything work!