fix: honor configured framework runtime settings

[codeforester]

Summary

• Apply every validated framework log level to native and attached user-facing streams while keeping persistent diagnostic logs at DEBUG.
• Preserve Click parameter-source information so explicitly supplied positive or negative lifecycle values override file config, while validated config overrides declared and callable defaults.
• Document precedence and add native, Typer, JSON, retention, and direct logger API regressions.

Validation

• Focused runtime/config/logging/lifecycle/Typer tests passed.
• Ruff check and format, focused strict mypy, generated API-reference check, and git diff --check passed.

Fixes #357
Fixes #358