Dot plot is not evaluated with pknots when pknots are enabled

[LunarFawn]

The pfunc call in the GetDotPlot function in FullFold.cpp has teh complexity hardcoded to 3, sodium hardcoded to 1, magnesium hardcoded to 0, and use_long_salt hardcoded to 0. The big issue is complexity 3 being hardcoded as to find pairs for pknots you need to pass complexity as 5 or 8. A complexity of 3 is for non-pknot structures. The pfunc code uses complexity to determine whether to perform pknot routines and a complexity 3 means only run simple non-pknot routines. It is worth noting that we do set the global C variable for sodium, magnesium and long salt, and complexity adn they are the same but the complexity is a big issue

[luxaritas]

While I will mark this as a bug, we have intentionally not fixed this due to the long compute time when enabling pknots for the dot plot (especially since you are still liable to see latent evidence of pseudoknotted structures without this anyways)

Also fwiw, while we should probably use the globals for the other values for consistency, as mentioned they are identical and we never touch them anyways, so I don't consider that a significant issue