[codex] fix: mark graph stale on doc-only hook commits

[aa-matsunari]

Summary

• stop post-commit hooks from silently treating doc-only commits as fresh code rebuilds
• mark graphify-out/needs_update when only non-code files changed

Changed files

• graphify/hooks.py
• tests/test_hooks.py

Impact

• prevents stale document/image/paper knowledge from being left behind without any signal after commits

Tests

• /private/tmp/graphify-review/.venv/bin/python -m pytest /private/tmp/graphify-review-pr7/tests/test_hooks.py