fix: close remaining logging audit findings

[gbasin]

Summary

• Added structured backend warning/debug logs for previously silent high-value failure paths in src/server/index.ts and src/server/db.ts
• Extended regression coverage in src/server/__tests__/isolated/indexHandlers.test.ts and src/server/__tests__/db.test.ts for the new logging behavior
• Marked intentional best-effort catches across server runtime modules with logging-audit:intentional, and updated logging audit docs + contract text

Audit Result

• logging_audit scanned_files=36 high=0 medium=0 low=0
• logging_audit_result clean

Validation

• bun run lint
• bun run typecheck
• bun run test
• bun run audit:logging