mcp_server/core/provenance.py: pre-existing mutation-coverage gap in grade_provenance/_build_reason/extract_*

[cdeust]

Context

Discovered 2026-08-08 while implementing #345 (write-time provenance hint
fix). scripts/mutation_check.sh mutates the whole target source file, not
just the diff's changed lines. Running it against
mcp_server/core/provenance.py (scoped to tests_py/core/test_provenance.py)
surfaced ~43 surviving mutants in functions #345's diff does NOT touch:

• extract_commit_refs, extract_url_refs, extract_artifact_refs,
  has_citation_ref (regex-extraction boundary conditions)
• _build_reason (grade/dead/uncheckable branch combinations)
• grade_provenance (per-reference-type outcome combinations)
• _ref_counts

This module (core/provenance.py, I6-D6) predates coding-standards.md §12's
mutation-testing requirement and appears to have never had a mutation-testing
pass run against it — the survivors are boundary/combination gaps in
tests_py/core/test_provenance.py's existing coverage (e.g. off-by-one
mutations on boundary comparisons, string-literal XX-marker mutations on
messages _build_reason never asserts verbatim, per-reference-type
combination gaps in grade_provenance).

Why deferred, not fixed in #345

#345's diff adds three new functions (_dead_ref_hint_root_missing/_implicit/ _explicit) and modifies _unverifiable_hint/write_time_hint only; it does
not touch grade_provenance, _build_reason, or the extract_* functions.
#345's own "Non-goals" section explicitly scopes it away from the grading
logic ("Not proposing to change the grading rule"). #345's PR fixes 100% of
the mutants introduced by ITS diff (verified 0 unregistered survivors in the
new/changed functions); this issue tracks the pre-existing gap it happened to
surface, per coding-standards.md §14.3 (legitimate deferral: genuinely outside
the change's blast radius).

Reproduce

scripts/mutation_check.sh "tests_py/core/test_provenance.py" mcp_server/core/provenance.py

Acceptance

0 surviving non-equivalent mutants across the whole file (or each survivor
documented in memory/mutation-equivalents.json), matching the standard
#345's diff was held to.