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Documentation System

The root handbook should be pleasant to read, not merely regular. The point is clarity, not paperwork.

The root pages are intentionally hand-authored. They are meant for humans who are trying to understand the whole system quickly. Developer-side tooling that helps maintain docs belongs in bijux-proteomics-dev, not in a root scripts/ directory and not in the published reader experience.

Handbook Shape

flowchart TB
    home["home"]
    repo["repository handbook"]
    products["product package handbooks"]
    dev["maintainer handbook"]
    compat["compatibility handbook"]

    home --> repo
    home --> products
    home --> dev
    home --> compat

What We Want From The Root Docs

  • A new reader should be able to skim the root docs and understand the whole idea of bijux-proteomics.
  • Diagrams should explain something real, not exist because a template expects a diagram.
  • The root docs should reduce meeting debt instead of introducing another layer of documentation ceremony.

What We Avoid

  • root docs that read like generated compliance output
  • legacy names leaking into the main handbook after the migration to bijux-proteomics-*
  • developer tooling living at the root when it really belongs in bijux-proteomics-dev

The handbook should feel like part of the wider Bijux docs family without losing the specific shape of this repository.