Feature/fix main bugs post refactor

[emrgnt-cmplxty]

[!IMPORTANT] Rename [kg] configuration section to [database] across documentation and code, with deprecation warning added.

• Configuration Changes:
  • Rename [kg] section to [database] in r2r.toml and other configuration files.
  • Update all related sub-sections like kg_creation_settings, kg_enrichment_settings, etc., to be under [database].
• Code Updates:
  • Add deprecation warning in config.py for the kg section, advising users to move to database.
• Documentation:
  • Update documentation files to reflect the new [database] section for knowledge graph settings.
  • Ensure all examples and references use the updated configuration naming.
• Testing:
  • Add a sleep delay in test_ingest_chunks() in runner_sdk.py to ensure proper test execution timing.

^{This description was created by for 25751d63f5fbc53591e30cb5a29fad13d2064c39. It will automatically update as commits are pushed.}

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