fix-remove the duplicate met MAM00077x and corresponding rxns

[feiranl]

• Fix one naming issuse identified in the process Duplicate IDs for same mets #519 :
  remove the metabolite MAM00077x, as it only relate to 2 rxns, while the duplicate MAM02766x is associated with 13 rxns from all compartments
  remove reaction MAR03489 and merge the GPR to its duplicate rxn MAR03387 as discussed
  remove reaction MAR03488 as discussed

I hereby confirm that I have:

• Tested my code on my own computer for running the model
• Selected develop as a target branch
• Any removed reactions and metabolites have been moved to the corresponding deprecated identifier lists