chore: iYali 4.1.2 additional file changes

doc: update readme.md

- updated model statistics
- remove version number from model identifier (iYali)
- more detailed information on how to contribute

Significant update to version 4.1.0 by new reconstruction

* Model is completely reconstructed from scratch, using Yeast 7.6 as template.
* Standardized reaction IDs are introduced, referencing where the reaction came from (y0 is derived from yeast concensus network, y1 is modified from yeast concensus network, y2 is from other Yarrowia lipolytica reconstructions, y3 is manual curation).
* Gap-filling during model reconstruction was automated via MENECO. Some reactions from the previous model that were identified through gap-filling are omitted in this version.

Correct grRules, metFormula, additional annotation (InChi, ChEBI, KEGG)

* Removed incorrect annotation of FAD:ubiquinone oxidoreductse (yli0053), while allowing flux through NADH:ubiquinone oxidoreductse (773).
* Some complex grRules were incorrect. Some metFormula gave error message when loaded as SBML.
* Cytosolic and mitochondrial branched-chain amino-acid transaminases are encoded by different genes (BAT2 and BAT1, respectively).
* Metabolite annotation (InChi, ChEBI, KEGG) that were previously lost during conversion from RAVEN to COBRA format are now included by exporting the file in RAVEN format. This format is now fully COBRA compatible.

Correct energetics, SBML L3V1 FBCv2

Changed equations of complex III, IV and V of oxidative phosphorylation to correct the transport of protons over the mitochondrial membrane (reactions 226, 438, 439). This was incorrectly represented in the template model.

Made asparate transport over the mitochondrial membrane irreversible (reaction 1117), otherwise this would transport protons for 'free' over the mitochondrial membrane. This was already identified in the Yeast consensus network.

Updated SBML to L3V1 with FBCv2, also using updated RAVEN functions. This changed the compartment IDs slightly (removed C_). Amended README.md to reflect the changes.

Fixed metabolite names

Due to an error in model generation, some of the metabolite names were
appended with "_ActiveX VT_ERROR:". This is now removed.

Update LICENSE and README files