cleanup: Remove all V1 legacy, add CognitiveAgent V3 (#5)

Add .gitignore and UPGRADE.md; update run.py and runner.py for persistent state management

Enhance README and scripts for cognitive architecture testing

Refactor README and add new scripts for cognitive architecture testing

Add initial project configuration and dependencies

v2: precision-modulated learning, needle-in-lies 3/3, FHRR Hopfield scoring

v2 complete: NGC graft, causal energy, auto-expanding codebook, benchmark integration

v2 architecture: FHRR-RNS encoding, hierarchical predictive coding (NGC), unified energy landscape

Add logit-bias graft: beliefs → token biases + convergence gating + hybrid pipeline

Initial implementation of Tensegrity architecture