Fix Stereochemistry of Phytanic Acid Oxidation

[Devlin-Moyer]

Main improvements in this PR:

As proposed in #773:

• Renamed MAM02746e, MAM02746c and MAM02746x to "(3R)-phytanic acid"
• Brought back previously-deprecated MAM03884e, MAM03884c and MAM03884x and renamed them to "(3S)-phytanic acid"
• Brought back previously-deprecated MAR00659 and MAR01617 (exchange and [e] <-> [c] transport reactions for MAM03884)
• Renamed MAM02747c and MAM02747x to "(3R)-phytanoyl-CoA"
• Replaced MAM02746c with MAM03884c in MAR03388
• Edited MAR03481 to be MAM02747c + MAM01371c + 2 MAM02040c -> MAM02746x + MAM01597c + MAM02039c + MAM01285c + MAM02751c, GPR: ENSG00000117528, references: PMID:24333844;PMID:33500543
• Edited MAR06779 to be MAM03362c + MAM01371c + 2 MAM02040c -> MAM03384x + MAM01597c + MAM02039c + MAM01285c + MAM02751c, GPR: ENSG00000117528, references: PMID:24333844;PMID:33500543
• Replaced MAM02746x with MAM03884x in MAR03389
• Renamed MAM00655x to "(3R)-2-hydroxyphytanoyl-CoA"
• Created MAM20083x to represent peroxisomal (2R)-pristanal
• Replaced (2S)-pristanal (MAM00564x) with MAM20083x in MAR03486
• Renamed MAM02766e, MAM02766c, and MAM02766x to "(2S)-pristanic acid"
• Brought back previously-deprecated MAR03488 and MAM00077x
• Replaced MAM00564x with MAM20083x in MAR03488
• Replaced MAM02766x with MAM00077x in MAR03493
• Created MAM00077c and MAM00077e to represent cytosolic and extracellular (2R)-pristanic acid
• Replaced MAM02766c with MAM00077c in MAR03390
• Created MAR20179 to represent ATP-dependent export of (2R)-pristanic acid from the cytosol to the extracellular environment
• Created MAR20180 to represent exchange of (2R)-pristanic acid

While I was creating MAM00077c and MAM00077e, I noticed that the MAM02766 metabolites were associated with both MNXM3342 and MNXM7698 in metabolites.tsv, but MNXM7698 has apparently been deprecated in favor of MNXM3422, so I edited those rows so that they're only associated with MNXM3342.

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!