fix: consolidate subsystem of coenzyme A metabolism

[haowang-bioinfo]

Main improvements in this PR:

This PR improves subsystem organisation by merging Pantothenate and CoA biosynthesis, CoA synthesis, and CoA catabolism into one Pantothenate and CoA metabolism, as proposed in #487

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

[feiranl]

Looks good to me!