Extend preprint-publication dedup from FLoRA to FReD

[LukasWallrich]

Context

FLoRA now has preprint-publication deduplication (added for #105) that:

• Detects when the same paper appears as both preprint and published version (different DOIs)
• Resolves confirmed duplicates, keeping the published version and storing the alternative DOI in doi_o_alt / doi_r_alt columns
• Handles both replication-side (same doi_o, different doi_r) and original-side (different doi_o for the same paper) duplicates

What needs to happen

1. Extend dedup to FReD: The same preprint-publication detection logic (R/preprint_dedup.R) should be applied to the FReD effect-level dataset, not just the paper-level FLoRA dataset.

2. Add alternative DOI columns even without duplicates: Where FReD references a DOI that has a known preprint/published counterpart (from the FLoRA confirmed duplicates or CrossRef metadata), doi_o_alt and doi_r_alt should be populated even if FReD only contains one version. This ensures users can look up papers by either DOI.

References

• Preprint dedup logic: R/preprint_dedup.R
• FLoRA pipeline integration: Step 7c in pipelines/flora/prepare_flora.qmd
• Confirmed duplicates: cache/confirmed_preprint_duplicates.csv
• Original issue: Deduplicate preprints and publications #105