Promote main to stable: model and ontology restructure

[ctn]

Summary

• promote the current main branch into stable
• switch the repository license to MIT
• restructure the repository around model and ontology subtrees
• import the ontology subtree into the repository
• add model and ontology Makefiles for the main runnable commands
• refresh the root, model, and ontology READMEs
• add SemiKong paper citations and project history context
• update the PyTorch dependency pins to address the current GitHub security alerts on develop/main

Stable Promotion Notes

• this promotion carries the MIT license onto stable, which should allow GitHub license detection to update
• this promotion also carries the integrated ontology subtree so semikong remains the single public repository
• validate-flow remains in place as the required promotion check