perf(core): batch relation resolution writes

[phernandez]

Summary

• resolve relation targets with one shared session and one set-based repository write
• load and refresh affected source entities as one deterministic batch
• preserve duplicate-edge cleanup across SQLite and PostgreSQL while avoiding per-relation transactions

Testing

• just fast-check
• focused relation/local-index tests: 78 passed
• just fast-test: 163 passed, 1 skipped
• targeted PostgreSQL relation tests: 40 passed
• just package-check
• git diff --check

Part of #1110