Optimize checking for existing ro-crate records

[daniel-thom]

Copilot made this suggestion:

"find_entity_for_file calls list_ro_crate_entities (fetching all entities for the workflow) to find a single record by file_id. In create_ro_crate_entity_for_file this is called once, and in create_ro_crate_entity_for_output_file it is called once more, meaning for each file processed there is a full list fetch. For workflows with many entities this becomes an O(n) per-file lookup. Consider adding a dedicated API endpoint to look up an entity by file_id, or pass in a pre-fetched map of existing entities to these helpers."