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Package Map

The package map is the shortest route from a cross-package question to the owning handbook. It should help a reviewer classify work before reading deep code.

That route matters more now because the package family is no longer easy to summarize as generic boundaries. The current map has to steer readers through shared meaning, broader core scientific ownership, runtime rerun proof, grounded evidence, recommendation posture, and lab consequence without making neighbors sound interchangeable.

Routing Model

flowchart TB
    question["cross-package question"]
    foundation["shared meaning and serialization"]
    core["durable scientific law"]
    knowledge["evidence truth and contradictions"]
    intelligence["recommendation policy and explanations"]
    lab["assay planning and outcomes"]
    runtime["execution and replay"]
    bridge["compatibility bridge<br/>legacy imports and retirement path"]

    question --> foundation
    question --> core
    question --> knowledge
    question --> intelligence
    question --> lab
    question --> runtime
    runtime --> bridge

This page should let a reader classify work before diffing the whole repository. The table is useful, but it becomes much easier to use once the package choices are visible as a routing model instead of a long lookup list.

Ownership Map

package owns concrete examples use it when
bijux-proteomics-foundation shared payload meaning, identifiers, and serialization canonical JSON, hashes, compatibility profiles, outcome-safe document rules the change affects what packages exchange
bijux-proteomics-core durable scientific contracts and workflow law sequence handling, chemistry, spectra, mzML, identification, quantification, PTM, DIA, benchmark assets the change affects scientific rules, review artifacts, or benchmark-backed workflow contracts
bijux-proteomics-knowledge evidence state, claims, confidence, contradictions, and biological context grounding references, literature audits, pathways, complexes, kinases, disease, drug targets, orthologs the dispute is about belief, support, contradiction, or context
bijux-proteomics-intelligence scoring, ranking, scenarios, challenges, and explanations candidate pressure, review packets, confidence, regret, downgrade, recommendation posture the change affects recommendation policy or analytical judgment
bijux-proteomics-lab assay planning, lab execution, and outcome handling readiness, control demand, handoffs, refusal, requested-versus-observed reconciliation the work concerns experiments, follow-up burden, or outcome promotion
bijux-proteomics-runtime execution, replay, providers, and operator entrypoints rerun kits, replay challenges, state, artifacts, comparability, black-box verification the work concerns running, replaying, or checking the system
agentic-proteins temporary legacy forwarding to runtime compatibility imports, historical CLI paths, migration ledger entries the question starts from an old import or CLI path

What Changed In This Map

  • bijux-proteomics-core now represents a much broader scientific owner than the older workflow-rule framing implied
  • bijux-proteomics-knowledge and bijux-proteomics-intelligence now form a clearer split between scientific truth and analytical judgment
  • bijux-proteomics-lab now matters as a real consequence owner instead of a soft follow-up placeholder
  • agentic-proteins now has to be read strictly as a compatibility bridge, not as a second runtime owner

Shared Non-Product Surfaces

Fast Routing Heuristics

  • if the question is "what does this scientific object mean?", start at foundation
  • if the question is "what scientific workflow law or benchmark packet exists?", start at core
  • if the question is "should I believe this sentence and what contradicts it?", start at knowledge
  • if the question is "how strong may the recommendation sound now?", start at intelligence
  • if the question is "is the next assay worth doing and what will it cost?", start at lab
  • if the question is "can I rerun or replay this publicly right now?", start at runtime

Checked Ownership Proofs

  • configs/package-governance/public-root-symbol-owners.toml for the machine-readable map of canonical package-root exports
  • Repository Shape Rationale for the durable split, temporary compatibility split, and future merge rules
  • docs/09-bijux-proteomics-runtime/migration-ledger/agentic-proteins-compatibility-inventory.md for the wrapper-only compatibility inventory
  • docs/09-bijux-proteomics-runtime/migration-ledger/agentic-proteins-canonical-migration-guide.md for the legacy-import migration path

Strongest Reader Use

  • use this page before deep code reading when two adjacent packages both sound plausible
  • use it with Cross-Package Ownership when the question includes artifact classes or import direction
  • leave this page once the owning handbook becomes obvious; it should shorten hesitation, not duplicate package-local detail

First Proof Check

  • the matching package under packages/
  • the matching handbook branch under docs/
  • package tests that prove the package really owns the claimed behavior

Design Pressure

The easy failure is to make the package map accurate but too flat, so readers still hesitate between neighboring packages that sound plausible.