Align Linx trace tooling with v0.4 maintenance

[zhoubot]

Summary

• align pyCircuit Linx trace tooling with the expanded commit bundle fields
• update the canonical stage catalog and trace schema id in the runtime writer
• make the QEMU-vs-pyCircuit flow resolve the superproject and LinxCore roots from the in-repo layout

Validation

• bash -n contrib/linx/flows/tools/run_linx_qemu_vs_pyc.sh
• python3 /Users/zhoubot/linx-isa/tools/bringup/check_trace_semver_compat.py --root /Users/zhoubot/linx-isa --strict

skill-evolve: no-update (module PR only; reusable skill guidance already updated in linx-skills)