fix(): use params entity registry for update_persistent_entities

[benflexcompute]

Summary

• Fix legacy workflow in set_up_params_for_uploading where volume zone modifications (center/axis) made on a separate VolumeMesh object were not reflected in the uploaded simulation.json
• Root cause: entity_info deep copy was discarded after update_persistent_entities, and root_asset.internal_registry missed modifications from different asset references
• Build a deduplicated entity registry from params.used_entity_registry instead, which always contains the user's actual modified entities from stored_entities

Test plan

• Extended test_root_asset_entity_change_reflection to reproduce the bug (separate VolumeMesh object modifying zone center/axis)
• Verified test fails before fix, passes after
• All 6 tests in test_project.py pass
• test_persistent_entity_info_update_volume_mesh and test_persistent_entity_info_update_geometry pass
• Draft context entity update tests pass

🤖 Generated with Claude Code

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Note

Medium Risk
Changes how set_up_params_for_uploading derives the entity registry for update_persistent_entities, which can alter serialized entity metadata (e.g., volume zone center/axis) in uploaded simulation.json for legacy (non-DraftContext) workflows.

Overview
Fixes the legacy (non-DraftContext) upload path so persistent entity updates are driven by entities actually referenced in SimulationParams rather than root_asset.internal_registry.

Adds _build_deduplicated_entity_registry_from_params() to build a de-duplicated EntityRegistry from params.used_entity_registry (keyed by (entity_type, private_attribute_id|name)), and uses it when calling entity_info.update_persistent_entities, ensuring user edits made via a separate asset instance (e.g., VolumeMesh zone center/axis) are reflected in the uploaded params.

Extends test_root_asset_entity_change_reflection and updates VM mock simulation JSON to validate zone IDs and that zone center/axis modifications propagate through set_up_params_for_uploading.

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[chatgpt-codex-connector]

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