feat: add governed skills and tool hooks

[linjiaye929]

Summary

• discover and lazily load source-qualified inert SKILL.md instructions with strict YAML, filesystem identity, and SHA-256 drift checks
• add deterministic host-registered pre/post Tool Hooks with monotonic authorization, timeout, failure isolation, and bounded audit records
• document threat boundaries, learning notes, resume evidence, and prepare v0.13.0-alpha.0

Verification

• Python 3.12.13: 867 passed, 8 skipped, 90.86% branch coverage
• Python 3.13.14: 867 passed, 8 skipped, 90.86% branch coverage
• Ruff format/check, strict Pyright, Bandit, locked runtime pip-audit
• wheel and sdist isolated smoke on Python 3.12 and 3.13