[gkennos]

Summary

This release updates Groundworkers to the current OMOP stack and omop-emb 3.0. It improves setup and database checks, clarifies startup errors, and adds guidance for upgrading existing configurations. It also avoids misleading database warnings on SQLite.

• Updated database configuration for the current OMOP stack, including separate primary and vocabulary connections.
• Updated embedding storage and setup for omop-emb 3.0.
• Improved database readiness checks for graph, vocabulary, and embedding stores.
• Added a guide for upgrading from Groundworkers 0.6.
• Clarified startup errors and removed misleading SQLite index warnings.

Checklist

• Applied exactly one label (breaking, feature, fix, dependencies, or chore)
• Tests pass locally (uv run pytest -q)
• Lint passes (uv run ruff check .)