Glossary

Page Maps

graph LR
  family["Reproducible Research"]
  program["Deep Dive Snakemake"]
  section["Governance Migration Tool Boundaries"]
  page["Glossary"]
  capstone["Capstone evidence"]

  family --> program --> section --> page
  page -.applies in.-> capstone

flowchart LR
  orient["Orient on the page map"] --> read["Read the main claim and examples"]
  read --> inspect["Inspect the related code, proof, or capstone surface"]
  inspect --> verify["Run or review the verification path"]
  verify --> apply["Apply the idea back to the module and capstone"]

This glossary keeps the language of Module 10 stable.

The goal is practical stewardship clarity: when migration, governance, and tool-boundary terms keep the same meaning, review gets calmer and more precise.

Terms

Term	Meaning in this module
current truth	The repository behavior and contract surfaces that are actually in force today, whether or not they are documented well.
review route	The shortest honest sequence of commands and artifacts that lets a maintainer inspect the repository before changing it.
public contract	The set of files, paths, and meanings that downstream users may safely trust.
internal execution surface	Useful workflow state such as results/, logs, or intermediates that may help maintainers but is not automatically public.
policy boundary	The operating-context surface, such as profiles or executor settings, that should influence how the workflow runs without changing what it means.
proof route	The visible commands and artifacts that let a reviewer compare, verify, or audit workflow behavior.
migration step	One bounded change that moves a single boundary while preserving enough evidence to compare old and new behavior.
preserved proof	The part of the old or current evidence route that remains available while a migration is in progress.
retirement condition	The concrete condition that must be met before an old route, helper, or boundary can safely disappear.
governance rule	A durable review rule that protects contracts, policy boundaries, proof surfaces, or ownership clarity over time.
contract drift	The weakening of the public boundary as consumers, paths, or meanings move outside the reviewed contract.
policy leak	A case where operating policy starts changing workflow meaning instead of only execution behavior.
invisible complexity	Important workflow meaning hiding in helpers, wrappers, or packages that reviewers do not naturally inspect.
evidence suppression	Removing or weakening logs, benchmarks, verification, or comparison surfaces in ways that make the workflow harder to trust.
tool boundary	The ownership line that says which concern Snakemake should keep and which concern another system should own.
hybrid ownership	A design where Snakemake keeps ownership of file-based workflow truth while another system owns service, platform, or lifecycle concerns.

How to use these terms

If a Module 10 discussion starts getting vague, ask which term has become unclear:

• are we describing current truth or a hoped-for redesign?
• is this a policy boundary or a semantic change?
• what proof route is being preserved during this migration step?
• is this concern still within Snakemake's tool boundary?

Those questions usually turn a fuzzy migration argument into a reviewable one.