fix(all): repair code graph coverage indexing

Context:
========
`graph index` could retain an empty or stale implementation-coverage projection
after forced or incremental indexing, leaving `COVERS_FILE` and `COVERS_SYMBOL` absent.

Changes:
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- Rebuild coverage from persisted implementation state and current logical symbols
- Detect persisted sidecar-only changes and graph-content inconsistencies
- Report coverage summaries and stable diagnostics through the CLI
- Add regression tests, documentation, specs, archive, and patch changesets