fix-GPR curation for PPP, TCA and Pyruvate metabolism

[JHL-452b]

Main improvements in this PR:

As proposed in #865

• Remove ENSG00000152556 from MAR04567;
• Remove ENSG00000165140, ENSG00000130957 from MAR20070;
• Remove ENSG00000138030 from MAR09800;
• Remove ENSG00000130313 from MAR08653;
• Remove ENSG00000182224 from MAR03859;
• Remove ENSG00000196616 from MAR08502;
• Remove ENSG00000184254 from MAR08503;
• Remove ENSG00000196616 from MAR08508;
• Remove ENSG00000166816 from MAR08514;
• Remove ENSG00000148090 from MAR08516;
• Remove ENSG00000116882 from MAR07704;
• Remove ENSG00000116882 from MAR07706;
• Remove ENSG00000184254 from MAR08775;
• Remove ENSG00000072210 from MAR08778;
• Remove ENSG00000196616 from MAR08507;
• Remove ENSG00000072210 from MAR08506;
• Add PMID: 25709564 to the references of MAR08516;

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 1514 dead-end metabolites.
 - Found 1319 reactions incapable of sustaining steady-state fluxes in either direction due to these dead-ends.
 - Found 1977 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 447 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.
   - 447 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/macawResults/.

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