Store now indexes every Save into the upload_files table via SetRepo.
DB failures are logged as warnings and do not fail the upload because
.meta.json remains the source of truth and startup backfill recovers.
Add Store.Backfill to walk Root at startup and insert index rows for
any pre-existing .meta.json sidecars, swallowing duplicate-key races.
The upload_file MCP Tool now writes an audit_log entry on success.
Tests cover dual-write args, repo-error non-failure, and backfill
skipping existing rows.
Co-Authored-By: Claude <noreply@anthropic.com>
