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Runtime Scope and Ownership

bijux-pollenomics exists to rebuild repository-owned evidence state. Its job is not abstract scientific theory and it is not general-purpose workflow policy. It owns the runtime loop that turns tracked inputs into tracked public outputs.

That ownership boundary matters because this repository has several nearby surfaces that sound similar but serve different audiences. The public runtime, the data handbook, the atlas guide, and the maintainer toolkit should work together without being mistaken for the same thing.

Capability Map

  • collect source families into governed data/ trees
  • normalize pollen, archaeology, boundary, and aDNA evidence into inspectable repository files
  • publish country bundles, atlas layers, and repository truth reviews
  • keep command defaults and output locations stable enough to review in one repository checkout

Surface Map

  • runtime commands
  • tracked source-family and normalized evidence files
  • tracked publication outputs
  • repository truth and claim-audit surfaces

Ownership Boundary

The runtime owns:

  • command entrypoints and command defaults
  • collection and normalization behavior
  • publication behavior for docs/report/
  • file and path contracts needed to rebuild checked-in state

The runtime does not own:

  • repository-health policy that belongs in bijux-pollenomics-dev
  • public provenance interpretation that belongs in public/pollenomics-data
  • atlas interpretation guidance that belongs in public/nordic-atlas
  • broader paper-grade pollenomics analysis that has not been implemented yet

Dependencies And Adjacencies

The runtime sits between repository provenance and repository publication. It depends on source-family inputs and feeds country bundles, atlas layers, and review surfaces, but it should not blur those adjacent responsibilities into one flat story.

Domain Language

  • source family: one governed upstream domain such as LandClim, Neotoma, SEAD, RAÄ, boundaries, AADR, or animal aDNA papers
  • normalized evidence: tracked repository output derived from those sources
  • publication surface: a downstream atlas, country bundle, or report surface
  • partial recovery: a surface that is real and inspectable but still too thin for stronger scientific or release language

Lifecycle

  1. collect or refresh source-family state
  2. normalize it into reviewable repository artifacts
  3. publish downstream surfaces from that state
  4. run validation that can block overclaims or drift

Change Principles

  • preserve provenance differences across source families
  • prefer durable path and artifact contracts over convenience shortcuts
  • keep pollenomics breadth visible while weaker aDNA recovery continues
  • block stronger publication language when evidence depth is not there

Why This Matters

If the ownership line gets blurry, the public guide stops being trustworthy. It becomes harder to tell whether a claim is coming from tracked evidence, presentation logic, or maintainer policy. A clear runtime boundary is what lets the repository say, with some precision, which part of the system produced a given output and which part merely explains it.