metrics_compare_base: catch TimeoutExpired; fix code-size skill docs

- run() now catches subprocess.TimeoutExpired (only triggered by `cmake --build`'s
  timeout=600) and returns CompletedProcess(rc=124) so the caller falls through to
  error reporting and worktree cleanup instead of crashing with a traceback.
- code-size SKILL.md: document the actual default filter (per-side absolute
  <checkout>/src/ path, not the old `tinyusb/src` substring) and adjust the
  reporting guidance to match what the report rows actually contain.

Co-Authored-By: Claude Opus 4.7 (1M context) <[email protected]>

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