Course Guide

Page Maps

graph LR
  family["Reproducible Research"]
  program["Deep Dive Snakemake"]
  section["Guides"]
  page["Course Guide"]
  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"]

Read the first diagram as a timing map: this guide is a support hub, not another chapter. Read the second diagram as the loop: identify the kind of help you need, choose the matching surface, then leave with one smaller next move.

Deep Dive Snakemake has four durable surfaces:

1. course home and orientation for entry and reading order
2. modules for the teaching arc itself
3. capstone pages for executable corroboration
4. reference pages for durable review and repair maps

Choose the right surface

If you need...	Start here	Do not start with
first entry into the course	Start Here	the capstone repository
the module sequence explained	Module 00	incident or governance pages
one support page for urgency	Pressure Routes	random browsing through guides/
workflow-versus-policy separation	Topic Boundaries	the strongest available command
module-to-repository routing	Capstone Map	raw repository files
durable review maps	Reference	course-home prose

The teaching arc

Arc	Modules	What becomes legible
file-contract foundations	Modules 01-02	truthful file contracts, deterministic discovery, and explicit checkpoints
policy and scaling boundaries	Modules 03-05	profiles, scaling interfaces, helper-code boundaries, and honest software seams
publish and architecture surfaces	Modules 06-08	downstream contracts, repository file APIs, and operating-context boundaries
incident and governance judgment	Modules 09-10	observability, incident evidence, migration boundaries, and stewardship judgment

The support shelf by job

• Read Boundary Review Prompts when repository splits or module boundaries feel fuzzy.
• Read Module Promise Map when module titles feel too compressed.
• Read Module Checkpoints when you need a visible exit bar.
• Read Pressure Routes when the reading order is shaped by urgency.
• Read Proof Matrix when you already know the claim and need the evidence surface.
• Read Command Guide when you know the route but not the command layer.
• Read Capstone Guide when you need the capstone contract before opening repository files.

Best defaults

Use these as your stable defaults unless the current pressure gives you a stronger reason:

1. enter with Start Here
2. anchor in Module 00
3. read modules in order
4. keep Proof Ladder nearby
5. enter the capstone through Capstone Map

Good stopping point

Stop when you can answer two questions clearly:

• which surface should answer the next question
• why the heavier surfaces would be premature right now