refactor(core): remove modes

[cniska]

Summary

• remove mode-specific lifecycle contracts, state, and evaluator and guard gating to run a single execution flow
• remove mode-based config and protocol surfaces including modeModels, verifyScope, and per-mode keys
• simplify tool registry and tool contracts by dropping permission grants and exposing one runtime tool set
• rewrite core, soul, and tool instructions to be shorter and friendlier while preserving execution and signal contracts
• delete obsolete mode docs and update architecture, lifecycle, tooling, and feature docs for the single-flow model
• update tests and behavior and perf scenarios to validate intent and single-flow behavior after mode removal