[codex] fix: preserve non-code graph knowledge on watch rebuild

[aa-matsunari]

Summary

• preserve non-code nodes, edges, and hyperedges during code-only watch rebuilds
• keep report file counts aligned with full detect() results

Changed files

• graphify/watch.py
• tests/test_watch.py

Impact

• prevents code edits from disconnecting docs, papers, images, and memory from rebuilt code nodes

Tests

• /tmp/graphify-review/.venv/bin/python -m pytest /tmp/graphify-review-pr2/tests/test_watch.py