[0.2.6] - Substrate Consolidation & Contextual Governance

[Badoot]

Added
Intent Classification: Revived intent classification to be a first-class citizen in the architecture.
SPIFFE URI SAN: Refactored SPIFFE URI SAN logic to strengthen mTLS and workload identity.

Changed
CLI & UX Improvements: Improved login UX, operator-side UX, and trust script stability. Enhanced build output for Mac and Linux.
Protocol Refinement: Ripped out legacy protobuf definitions, refined boundary structures, and decoupled operator auth from the app layer.
Session Isolation: Improved session typing and untangled CLI chat sessions to better separate the substrate and app layer.
Code Quality & Linting: Comprehensive code quality passes including Go critic/lint fixes, Ruff, and Pyright typing improvements.
Eval & Testing: Refactored the eval harness and bench tests. Improved chaos testing with better audit summaries, L1 reporting, and correct DB location.
Documentation: Reorganized and updated documentation including improved diagrams and README updates.