Add ontology-backed semantic layer

[coredipper]

Summary

• add optional vault ontology validation and the scrip ontology command
• allow entity URI/same_as/external_ids metadata while preserving local entity ids
• make harness extract/graph prompts ontology-aware and add graph context to answers
• bump scriptoria to 0.9.0 and scrip-harness to 0.11.0

Testing

• cd scrip && uv run pytest
• cd harness && uv run pytest
• uvx ruff check scrip/src scrip/tests harness/src harness/tests adapters scripts
• cd scrip && uvx pyright@1.1.405
• cd harness && uvx pyright@1.1.405
• git diff --check

Reviews

• fixed and closed roborev jobs 1348 and 1349