chore: update dependencies and streamline docs

[Bug-Finderr]

Summary

• update direct dependencies and align Node, Nub, Biome, and CI versions
• replace hybrid nubx calls with explicit local nub exec calls
• condense the README, architecture, and learning notes around project-specific invariants and decisions
• remove two learning notes whose unique rationale now lives in the architecture document

Verification

• nub run test - 84 unit, 19 Node compatibility, and 4 Python compatibility tests passed
• nub exec tsc --noEmit
• nub exec biome check .
• nub audit --production
• nub exec wrangler deploy --dry-run