chore: update Actions dependencies for all workflows

[mihai-sysbio]

Main improvements in this PR:

This PR bumps up all workflow dependencies.

I hereby confirm that I have:

• Any removed reactions and metabolites have been moved to the corresponding deprecated identifier lists in data/deprecatedIdentifiers/.

• This PR has develop as target branch, and will be resolved with a squash-merge.
• This PR has main as target branch, and will be resolved with a merge commit.

[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.