Fix duplicate metabolites identified by EHMN IDs

[JHL-452b]

Main improvements in this PR:

As discussed in #616

• remove mets MAM03354c, MAM03332c, MAM03332e for being duplicates
• remove rxns MAR03441, MAR02588, MAR10164, MAR10433 for being affected by duplicate mets
• change EHMN ID annotations for MAM01123c, MAM01123m, MAM01123x
• replace mets

old ID	new ID
MAM03354r	MAM00131r
MAM00029c	MAM00028c
MAM03368m	MAM00748m
MAM03368x	MAM00748x
MAM00902c	MAM00853c

Also fix bugs of import and export cycle caused by the missing lines introduced in #662

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]

LGTM!