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Extensibility Model

Extension work should use the package seams that already exist instead of bypassing ownership.

This page is about where variation is welcomed and where it would be a design smell. A package becomes easier to extend when contributors can see which seams are meant to flex and which ones are carrying the core identity of the package.

Treat the architecture pages for bijux-proteomics-intelligence as a reviewer-facing map of structure and flow. They should shorten code reading, not try to replace it.

Visual Summary

flowchart RL
    page["Extensibility Model<br/>clarifies: trace execution | spot dependency pressure | judge structural drift"]
    classDef page fill:#dbeafe,stroke:#1d4ed8,color:#1e3a8a,stroke-width:2px;
    classDef positive fill:#dcfce7,stroke:#16a34a,color:#14532d;
    classDef caution fill:#fee2e2,stroke:#dc2626,color:#7f1d1d;
    classDef anchor fill:#ede9fe,stroke:#7c3aed,color:#4c1d95;
    classDef action fill:#fef3c7,stroke:#d97706,color:#7c2d12;
    module1["orchestration and replay coordination"]
    module1 --> page
    module2["durable runtime models"]
    module2 --> page
    module3["execution engines and lifecycle logic"]
    module3 --> page
    code1["src/bijux_proteomics_intelligence/runtime"]
    page --> code1
    code2["src/bijux_proteomics_intelligence/application"]
    page --> code2
    code3["src/bijux_proteomics_intelligence/model"]
    page --> code3
    pressure1["tests/e2e for governed flow behavior"]
    pressure1 -.tests whether this structure still holds.-> page
    pressure2["tests/regression and tests/smoke for replay and storage protection"]
    pressure2 -.tests whether this structure still holds.-> page
    pressure3["tests/unit for api, contracts, core, interfaces, model, and runtime"]
    pressure3 -.tests whether this structure still holds.-> page
    class page page;
    class module1,module2,module3 positive;
    class code1,code2,code3 anchor;
    class pressure1,pressure2,pressure3 caution;

Likely Extension Areas

  • src/bijux_proteomics_intelligence/model for durable runtime models
  • src/bijux_proteomics_intelligence/runtime for execution engines and lifecycle logic
  • src/bijux_proteomics_intelligence/application for orchestration and replay coordination
  • src/bijux_proteomics_intelligence/verification for runtime-level validation support
  • src/bijux_proteomics_intelligence/interfaces for CLI surfaces and manifest loading
  • src/bijux_proteomics_intelligence/api for HTTP application surfaces

Extension Rule

Add extension points where the package already expects variation, and document them next to the owning boundary.

Concrete Anchors

  • src/bijux_proteomics_intelligence/model for durable runtime models
  • src/bijux_proteomics_intelligence/runtime for execution engines and lifecycle logic
  • src/bijux_proteomics_intelligence/application for orchestration and replay coordination

Use This Page When

  • you are tracing structure, execution flow, or dependency pressure
  • you need to understand how modules fit before refactoring
  • you are reviewing design drift rather than one isolated bug

Decision Rule

Use Extensibility Model to decide whether a structural change makes bijux-proteomics-intelligence easier or harder to explain in terms of modules, dependency direction, and execution flow. If the change works only because the design becomes harder to read, the safer answer is redesign rather than acceptance.

What This Page Answers

  • how bijux-proteomics-intelligence is organized internally in terms a reviewer can follow
  • which modules carry the main execution and dependency story
  • where structural drift would show up before it becomes expensive

Reviewer Lens

  • trace the described execution path through the named modules instead of trusting the diagram alone
  • look for dependency direction or layering that now contradicts the documented seam
  • verify that the structural risks named here still match the current code shape

Honesty Boundary

This page describes the current structural model of bijux-proteomics-intelligence, but it does not guarantee that every import path or runtime path still obeys that model. Readers should treat it as a map that must stay aligned with code and tests, not as an authority above them.

Next Checks

  • move to interfaces when the review reaches a public or operator-facing seam
  • move to operations when the concern becomes repeatable runtime behavior
  • move to quality when you need proof that the documented structure is still protected

Purpose

This page helps maintainers extend the package without smearing responsibilities together.

Stability

Keep it aligned with the package seams that actually support extension today.