Proof Ladder

Page Maps

graph LR
  family["Reproducible Research"]
  program["Deep Dive Snakemake"]
  section["Guides"]
  page["Proof Ladder"]
  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"]

Use this page when you know the question but not the right amount of evidence. The common failure in this program is not too little effort. It is jumping straight to the strongest bundle, then losing the original claim inside the output.

Rule for using the ladder

Start at the smallest route that could honestly falsify your claim. Move down only when the smaller route leaves an important part of the question unanswered.

That means:

• first contact should not start with proof or capstone-confirm
• a publish-boundary question does not need a full stewardship pass
• a profile question should start with profile evidence, not a generic run log

The ladder

Level	Start here when the question is...	First route
1	what does this repository even claim to do	make PROGRAM=reproducible-research/deep-dive-snakemake capstone-walkthrough
2	how does the repository behave when executed once end to end	make PROGRAM=reproducible-research/deep-dive-snakemake capstone-tour
3	does the workflow still execute and validate its published outputs	make PROGRAM=reproducible-research/deep-dive-snakemake test
4	do I need a saved publish-contract bundle I can review later	make PROGRAM=reproducible-research/deep-dive-snakemake capstone-verify-report
5	do I need to compare local, CI, and scheduler policy surfaces	make PROGRAM=reproducible-research/deep-dive-snakemake capstone-profile-audit
6	do I need the sanctioned multi-bundle stewardship route	make PROGRAM=reproducible-research/deep-dive-snakemake proof
7	am I ready for the strongest clean-room confirmation pass	make PROGRAM=reproducible-research/deep-dive-snakemake capstone-confirm

Start points by claim

Claim	Start here
"I need a bounded first pass through the capstone."	capstone-walkthrough
"I need one executed workflow story with saved evidence."	capstone-tour
"I need to know whether the repository still works normally."	test
"I need durable publish-contract evidence, not terminal scrollback."	capstone-verify-report
"I need to review execution-policy differences across contexts."	capstone-profile-audit
"I need the full review route another maintainer could repeat."	proof
"I need the strongest confirmation before major change."	capstone-confirm

Bad escalation habits

If you are using the ladder badly, it usually looks like one of these:

• choosing capstone-confirm because you feel uncertain, not because the question needs it
• using proof when capstone-verify-report would answer the publish question directly
• reading large saved bundles before you know what claim they are supposed to support
• treating a stronger route as automatically more honest than a narrower one

The stronger route is only better when it answers a different question.

Best companion pages

• Proof Matrix when you know the claim but need the first evidence surface
• Command Guide when the command layer itself is unclear
• Capstone Map when you know the module but not the repository route