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Technical reference map

Use this section for exact behavior: stage order, filenames, interfaces, data formats, validation, algorithms, and internals. If you want a guided task, return to the educational vignettes.

Pipeline contracts

Interfaces

Data and validation

Algorithms and extension

Runtime and internals

Publication evidence

For the historical manuscript evidence and complete SI, use the technical supplement. Current instructions and contracts remain in the workflow/reference pages.

Reviewer and publication paths

Historical audits remain under development history; their counts and blockers describe their recorded revisions, not the current checkout.