fix(index): preserve persisted coverage summaries

[Enferlain]

What does this PR do?

Fixes #1287.

The index response derived parse_partial_count only from errors produced by the current pipeline run. Incremental no-op and artifact-backed paths could consequently report zero even when persisted coverage rows still recorded parse gaps.

This change loads the authoritative coverage summary from the stored graph when composing the response, with a run-local fallback if that read fails. By-design exclusions remain reported separately. A regression test covers an unchanged incremental run retaining its persisted partial-parse status.

Verification

• make -f Makefile.cbm test-focused TEST_SUITES=index_resilience — 6 passed
• make -f Makefile.cbm test-focused TEST_SUITES='cypher extraction registry pipeline mcp index_resilience' — 884 passed, 2 skipped

Checklist

• Every commit is signed off (git commit -s) and follows the Contributor License Agreement
• Full test suite passes locally (make -f Makefile.cbm test) — focused sanitized suites passed
• Lint passes (make -f Makefile.cbm lint-ci) — not run locally
• New behavior is covered by a regression test that would fail without this fix