Update peakdetector to support isotopic extraction - and fix related bugs

[PMSeitzer]

Specifically, just need to add

group.pullIsotopes(isotopeParameters,
                   samples,
                   false //debug
                   );

and corresponding parameters to enable this (e.g., --extractIsotopes) and encoded isotopeParameters string. (--isotopeParameters)

In the main groups block. This can then fit nicely in a single R script pipeline for diff iso rescoring, e.g. via mzkitcpp.

There is no need to implement diff iso scoring, since this will just be rescored anyway via mzkitcpp and metisotopes.

[PMSeitzer]

Potentially implemented as of acc0a24, needs testing per https://github.com/calico/mass_spec/issues/1489

[PMSeitzer]

In order for this to work properly, need to read in ADDUCTS.csv, and associate the appropriate adduct with peak groups - otherwise, the isotopic extraction code will fall back to assuming the compound is unknown, and pull out slightly different isotopes (unknown compounds use the observed m/z directly, and compute mass shifts from there, while known compounds use the theoretical m/z from formula + adduct).

The resulting information should also be properly saved in the mzrollDB files:

from GUI:

from peakdetector:

[PMSeitzer]

The search parameters in the GUI should always use the parameters specified in the dialog - not the global parameters.
the isotope parameters has a peakPickingAndGroupingParameters field, which is currently pulling from the main window - instead, should be from the dialog!

[PMSeitzer]

Another little bug in the GUI - the adduct should not be associated with unknown isotopes

[PMSeitzer]

Upon further investigation, there appears to be a bug in the isotope extraction code - it appears to be giving different results between two identical runs generated in the GUI, as well as two identical runs generated via peakdetector.