fix: correct 4-hydroxy-13-cis-retinoate (misnamed 4-oxo) and merge duplicate

[edkerk]

Main improvements in this PR:

Resolves #375. MAM01026 and MAM00348 were near-duplicate metabolites named as the 4-oxo-13-cis form, but an adversarial review against PubChem/DrugBank and the reactions shows they are actually 4-hydroxy-13-cis-retinoate:

• Their formula (C20H27O3) is the 4-hydroxy anion (matching 4-hydroxy-all-trans-retinoate MAM00993), while the true 4-oxo forms (all-trans MAM01031, 9-cis MAM01029) are C20H25O3.
• Every reaction producing them (MAR06681/06682/08703/08706) is a hydroxylation (adds one O, removes no H). Changing the formula to 4-oxo would unbalance all four, so the fix is to correct the name.

Changes:

• Merge MAM00348 into MAM01026 and rename to 4-hydroxy-13-cis-retinoate (formula C20H27O3 kept).
• Remove the incorrect 4-oxo MetaNetX cross-references (MNXM37697, MNXM6902, MNXM146866).
• Fix MAR08703 so all-trans-retinoate is hydroxylated to the all-trans product (MAM00993), not the 13-cis form.
• Remove MAR08704 (interconversion of the two duplicates, trivial after the merge) and MAR01564 (duplicate nuclear transport of MAR01563).

MAM00348 and the removed reactions are in the deprecated lists. All modified reactions remain mass and charge balanced; no genes orphaned. The true 4-oxo-13-cis-retinoate (major isotretinoin metabolite) is not represented and could be added with the 4-hydroxy -> 4-oxo step as a follow-up.

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

[github-actions]

This PR has been automatically tested with GH Actions. Here are the results of the quality-control tests:

MACAW: dead-end and duplicate tests

Starting dead-end test...
 - Found 1382 dead-end metabolites.
 - Found 1138 reactions incapable of sustaining steady-state fluxes in either direction due to these dead-ends.
 - Found 1369 reversible reactions that can only carry steady-state fluxes in a single direction due to dead-ends.
Starting duplicate test...
 - Skipping redox duplicates because no redox_pairs and/or proton_ids were provided.
 - Found 377 reactions that were some type of duplicate:
   - 0 were completely identical to at least one other reaction.
   - 13 involve the same metabolites but go in the opposite direction or have the opposite reversibility as at least one other reaction.
   - 377 involve the same metabolites but with different coefficients as at least one other reaction.

Mass and charge balance

Unbalanced reactions (excluding boundary and biomass): 277 (87 mass, 240 charge)

More detailed output is committed to data/testResults/ (macaw_results.csv and balance_results.csv).

Note: In the case of multiple test runs, this post will be edited.