Refactor: remove organism_grouping_key from schema

[emilylm]

📌 Summary

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Remove organism.grouping_key from the database schema and use taxon_id instead, to reflect changes to the data mapper's output. taxon_id is a natural choice for PK on organism table, since it is unique and must exist for all organisms.

🔄 Type of Change

• 🐛 Bug fix (non-breaking change that fixes an issue)
• ✨ New feature (non-breaking change that adds functionality)
• 💥 Breaking change (fix or feature that would cause existing functionality to change)
• 🧹 Refactor (code change that neither fixes a bug nor adds a feature)
• 📚 Documentation update
• ⚙️ CI / build / tooling change

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🧩 Key Changes

• Updates db schema to 1) remove grouping_key from organism table and make taxon_id the PK and 2) update any FK references to the organism table to reference taxon_id
• Update the codebase to reflect these changes

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✅ Checklist

• Tests are passing locally / in CI
• New tests have been added for new or changed functionality
• Self-review completed
• Documentation updated (if needed)
• No sensitive data or secrets included

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🔍 Review Notes

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📎 Related Issues / Tickets

• Closes #AP-394
• Related to #

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