Cross-Package Ownership

This matrix answers one question fast: if an artifact, import, or claim crosses package boundaries, who owns it and who is allowed to consume it.

That question matters more now because the repository is no longer thin at the package edges. Core now carries real biology, chemistry, spectra, mzML, quantification, PTM, and benchmark responsibility; runtime carries stronger rerun proof; knowledge and intelligence carry visible grounding and downgrade logic; lab carries real consequence pressure. Once that product depth exists, cross-package ownership has to be readable without maintainers improvising the authority chain.

Package Matrix

Package	Durable role	Allowed outbound imports	Forbidden outbound imports	Owned handoff classes
bijux-proteomics-foundation	shared contracts, identifiers, deterministic serialization	none	core, runtime, intelligence, knowledge, lab, agentic, dev	foundation-contract
bijux-proteomics-core	benchmark assets, durable scientific contracts, workflow requests	foundation, runtime, intelligence, lab	knowledge, agentic, dev	benchmark-asset-bundle
bijux-proteomics-runtime	execution, provider binding, replay, operator entrypoints	foundation, core, intelligence	knowledge, lab, agentic, dev	runtime-run-bundle
bijux-proteomics-knowledge	scientific memory, provenance, contradiction handling, review state	foundation	core, runtime, intelligence, lab, agentic, dev	scientific-review-bundle
bijux-proteomics-intelligence	recommendation posture, ranking sensitivity, refusal behavior	foundation, core, knowledge	runtime, lab, agentic, dev	recommendation-record
bijux-proteomics-lab	assay consequence planning, readiness, observed outcomes	foundation, core, knowledge, intelligence	runtime, agentic, dev	lab-consequence-record
agentic-proteins	legacy compatibility bridge for runtime entrypoints and imports	core, intelligence, runtime	foundation, knowledge, lab, dev	none
bijux-proteomics-dev	maintainer automation, docs checks, release governance	foundation, core, runtime, intelligence, knowledge, lab	agentic	none

Handoff Classes

Handoff class	Owner	Producers	Consumers	Typical examples
foundation-contract	bijux-proteomics-foundation	foundation	core, runtime, knowledge, intelligence, lab	DocumentSchema, JsonModel, ProgramId
benchmark-asset-bundle	bijux-proteomics-core	core	runtime, knowledge, intelligence, lab	flagship benchmark manifest, challenge corpus package, workflow execution request
runtime-run-bundle	bijux-proteomics-runtime	runtime	knowledge, intelligence, lab	run manifest, artifact ledger, review output bundle
scientific-review-bundle	bijux-proteomics-knowledge	knowledge	intelligence, lab	evidence bundle, contradiction ledger, knowledge decision brief
recommendation-record	bijux-proteomics-intelligence	intelligence	lab	ranking brief, recommendation stance, refusal explanation
lab-consequence-record	bijux-proteomics-lab	lab	knowledge, intelligence	assay plan, lab handoff, observed outcome record

Boundary Rules

• When an import direction is not listed as allowed here, treat it as a release-blocking boundary leak.
• When an artifact class is not listed here, the owner has not yet been stated clearly enough for cross-package publication.
• When agentic-proteins needs new logic, move the logic into the canonical owner first and keep the bridge thin.
• When root docs or release language describe behavior stronger than the owning package tests can prove, narrow the wording instead of widening root prose.

What This Matrix Prevents

• core scientific breadth from silently taking over runtime, knowledge, or lab ownership
• runtime rerun realism from being mistaken for scientific truth ownership
• knowledge grounding from drifting into recommendation authority
• recommendation posture from widening into free consequence claims without lab ownership

Strongest Reader Route

• start here when one feature, artifact, or sentence seems to belong to more than one package
• continue to Product Architecture when the dispute becomes end-to-end instead of package-local
• then open the owning package handbook only after the ownership class is clear

First Proof Check

• configs/package-governance/repository-product-shape.toml
• configs/package-governance/package-dependency-policy.toml
• packages/*/README.md
• packages/*/src/*/__init__.py

Design Pressure

The repository gets confusing when dependency direction, artifact ownership, and public wording each tell a slightly different story. This matrix exists so those three surfaces can be reviewed together.