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Repository Shape Rationale

This repository is split by durable owner questions, not by delivery sequence. The split is justified only when a skeptical reader can explain why one package must remain distinct from its neighbors and why one compatibility layer should eventually disappear.

Durable Splits

package durable reason to stay distinct failure if collapsed
bijux-proteomics-foundation shared identifiers, serialization, and migration-safe document rules higher packages would quietly fork payload meaning
bijux-proteomics-core workflow contracts, lifecycle rules, and benchmark-facing scientific law runtime or review layers would become shadow owners of domain truth
bijux-proteomics-runtime execution control, replay, operator entrypoints, and run artifacts scientific owners would inherit transport and provider logic
bijux-proteomics-knowledge cited evidence memory, contradiction handling, and reference-grounded review state intelligence and lab would rebuild private trust models
bijux-proteomics-intelligence recommendation posture, downgrade logic, and refusal behavior ranking policy would blur into evidence storage or lab action
bijux-proteomics-lab assay consequence, readiness, burden, and observed-outcome follow-through recommendation language would overstate downstream executability

Temporary Compatibility Split

agentic-proteins is not a seventh product owner. It remains only as a legacy compatibility bridge for historical runtime imports and entrypoints. New behavior should land in canonical owners first, then forward from compat only when migration continuity still matters.

Candidate Future Merges

  • Merge a seam only when the weaker package stops owning a question that the stronger package cannot answer without duplicating the same proof.
  • Do not merge foundation into core while deterministic serialization, identifiers, and migration discipline still need a low-volatility owner.
  • Do not merge runtime into core or intelligence while execution control and replay proof still need to stay runtime-specific.
  • Do not merge knowledge into intelligence or lab while evidence truth and contradiction state still need to remain distinct from recommendation or consequence policy.

First Checks