fix: remove charge-imbalanced duplicate lipoxygenase reactions (#348)

[edkerk]

Main improvements in this PR:

As reported in #348, five arachidonate/DHA peroxidation reactions are 1:1 duplicates of balanced multi-stoichiometry reactions that produce the same hydroperoxide (same substrate and product, no GPR), but with charge-imbalanced stoichiometry.

• Remove the charge-imbalanced 1:1 versions, keeping the balanced counterparts (removed reactions moved to deprecatedReactions.tsv):

Removed	Kept (balanced)	Product
MAR01364	MAR03880	12-peroxy-eicosatetraenoate
MAR01355	MAR03882	8-peroxy-eicosatetraenoate
MAR01358	MAR03878	9-peroxy-eicosatetraenoate
MAR01361	MAR03884	11-peroxy-eicosatetraenoate
MAR01405	MAR03261	10-peroxy-docosahexaenoate

Each product is still produced by its balanced counterpart, so the model stays balanced.

The deeper cause (hydroperoxide and hydroxy fatty-acid metabolites that are one H short, affecting ~105 reactions) is tracked separately in #1042.

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 is the output of the MACAW test:

Starting dead-end test...
 - Found 1384 dead-end metabolites.
 - Found 1141 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.

This and a more detailed output from MACAW are also committed to data/testResults/.

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