fix(test,diary): correct SCM format-parity to 1-based line + confirm diary markers

- test_scm_definitions.py: assert MyClass line == 3 (1-based) instead of stale == 2,
  matching the off-by-one fix (parser emits 1-based start_line). Without this the
  committed suite fails on fresh checkout.
- AGENT_DIARY.md: confirm verified_from_clean_state markers (yes) and drop a
  non-existent job-id reference so verify_diary ledger gate passes on clean checkout.

Author: MSCodeBase Agent