Fix Kendrick base consistency between MSPeak and MolecularFormula

Two related fixes for Kendrick base handling:

1. MolecularFormulaBase.__init__ fallback used hardcoded {"C":1,"H":2}
   instead of MSParameters.ms_peak.kendrick_base, so molecular formulas
   without a parent peak ignored user-configured Kendrick base.

2. MSPeak.change_kendrick_base() now recalculates KMD on all associated
   molecular formulas, so they stay consistent when
   change_kendrick_base_all_mspeaks() is called after formula assignment.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: robertyoung3

corems/molecular_formula/factory/MolecularFormulaFactory.py

@@ -136,7 +136,9 @@ def __init__(
                 self._mspeak_parent._ms_parent.mspeaks_settings.kendrick_base
             )
         else:
-            kendrick_dict_base = {"C": 1, "H": 2}
+            from corems.encapsulation.factory.parameters import MSParameters
+
+            kendrick_dict_base = MSParameters.ms_peak.kendrick_base
         self._kmd, self._kendrick_mass, self._nominal_km = self._calc_kmd(
             kendrick_dict_base
         )

corems/ms_peak/factory/MSPeakClasses.py

@@ -139,6 +139,10 @@ def change_kendrick_base(self, kendrick_dict_base):
             kendrick_dict_base
         )
 
+        # Also update all associated molecular formulas
+        for mf in self.molecular_formulas:
+            mf._kmd, mf._kendrick_mass, mf._nominal_km = mf._calc_kmd(kendrick_dict_base)
+
     def add_molecular_formula(self, molecular_formula_obj):
         """Adds a molecular formula to the peak.