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Use the unused substitution example and set aside three duplicates - #102

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Nov 7, 2026
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claude/project-thread-aj2ep4-unused-proof-subfiles

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Closes #88. Part of #60.

Four of the eight files #88 listed are the theorem files _distributive_thm, _conditional-as-or_cor, _negate-conditional_thm and _substitution-logic_thm. chapters/equivalence-negation.qmd already includes all four, so they are in use and stay where they are.

The other four are unused examples:

  • _distributive_exm, _conditional-as-or_exm and _negate-conditional_exm reuse ids that the chapter's own examples in chapters/_subfiles/equivalence-negation/ already carry. Including them would duplicate those ids, so they move to chapters/outtakes/, where their text is kept.
  • _substitution-logic_exm (#exm-substitution-logic) has its own id and covers something the chapter's #exm-substitution does not, namely double negation combined with substitution. The chapter now includes it right after that example.

Checked: I rendered chapters/equivalence-negation.qmd to HTML. Quarto printed no warnings, exm-substitution-logic is on the page, and no reference is left unresolved (no ?@ on the page).


Generated by Claude Code

The four proof-writing theorem files that #88 listed are already
included from the equivalence-and-negation chapter, but four of the
example files are not. Three of them reuse ids that the chapter's own
examples carry (exm-distributive, exm-conditional-as-or,
exm-negate-conditional), so including them would duplicate those ids.
Those three move to chapters/outtakes/, which keeps their text.

The fourth, exm-substitution-logic, has its own id and shows a case the
chapter's example does not (combining double negation with
substitution), so the chapter now includes it right after that example.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_019xfc9pMBq15Hq3DgNBx1ox
Copilot AI balanced review requested due to automatic review settings November 7, 2026 00:28
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Claude finished review — View run


No dangling includes, and the working tree is clean beyond the review-diff artifact. No prior comments exist on the PR, so this is a first review pass.

Review: PR #102 — Use the unused substitution example and set aside three duplicates

Summary: Resolves #88 (part of #60) by disposing of the four previously-unused example subfiles in _subfiles/proof-writing/:

  • _substitution-logic_exm.qmd (unique id #exm-substitution-logic, no clash) is now included in chapters/equivalence-negation.qmd, right after the existing #exm-substitution, surrounded by the standard {{< slidebreak >}} markers.
  • _distributive_exm.qmd, _conditional-as-or_exm.qmd, _negate-conditional_exm.qmd are renamed (pure git renames, 0 content change) into chapters/outtakes/, since each duplicates an id already defined by the chapter's own equivalence-negation-subfolder example of the same name.

Verification performed:

  • Confirmed the four theorem/corollary files Decide what to do with eight unused proof-writing subfiles #88 listed (_distributive_thm, _conditional-as-or_cor, _negate-conditional_thm, _substitution-logic_thm) are indeed already included on chapters/equivalence-negation.qmd, matching the PR description.
  • Confirmed the id-duplication claim: chapters/outtakes/_distributive_exm.qmd (#exm-distributive) duplicates chapters/_subfiles/equivalence-negation/_distributive_exm.qmd; same pattern holds for #exm-conditional-as-or and #exm-negate-conditional. Moving them avoids duplicate-id Quarto warnings.
  • Confirmed cross-reference order: the new include sits after thm-double-negation and thm-substitution-logic are both already defined earlier in the same page, so the [double negation](#thm-double-negation) and [replacing a part by an equivalent part](#thm-substitution-logic) links in the new content resolve on-page.
  • Confirmed chapters/outtakes/ is an established, pre-existing convention in this repo family — .github/workflows/check-exm-figures.yml and .github/workflows/check-avoided-words.yml (plus their mds counterparts) already carry **/outtakes/** in paths-ignore, even though this PR creates the directory's first file here. Filenames keep the _<stem>_<type>.qmd convention through the rename, so this isn't an invented pattern.
  • Checked that the moved files aren't rendered as standalone pages: _quarto-website.yml's render list (chapters/*.qmd, non-recursive) wouldn't pick up chapters/outtakes/*.qmd even without the leading-underscore convention that already excludes them.
  • Checked for any remaining reference to the old _subfiles/proof-writing/_distributive_exm.qmd / _conditional-as-or_exm.qmd / _negate-conditional_exm.qmd paths elsewhere in the repo — none found, so the rename leaves no dangling includes.
  • Checked check-unresolvable-refs.yml's script scope (flags @id in math and @sec- refs) — the moved files use [text](#id) link syntax, not @id, so they won't trip that check even though they're now unreferenced from any rendered page.
  • Verified the math in the newly-included _substitution-logic_exm.qmd is correct: $\neg\neg Q \equiv Q$ by double negation, substituted into $\neg P \lor \neg\neg Q$ to give $\neg P \lor Q$, matching thm-substitution-logic's statement.
  • No R code, no new dependencies, no _site/_freeze artifacts touched, no bibliography changes — out of scope for most of the SERG lab-manual checklist (coding style/practices), which doesn't apply to this prose-only, pure-rename diff.

No issues found.

Verdict

Ready for merge

Structured Review Data (JSON)
{
  "schema_version": "1.1",
  "reviewer": "claude",
  "commit_sha": "2574cbaee14f833ff2683027e80bd98c0c909137",
  "verdict": "CLEAN",
  "findings": [],
  "detailed_assessment": "Checked chapters/equivalence-negation.qmd include ordering and chapters/outtakes renames for dangling references and id collisions; none found.",
  "holistic_assessment": "Scope matches issue #88 exactly, integrates cleanly with the existing outtakes CI exclusion convention, and introduces no rendering or cross-reference regressions."
}

Reviewed commit: 2574cba

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💰 Cost: $0.4354 (review) — run

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🟢 Approval recommended

No active review issues block the substitution-example addition and preservation of duplicate-ID examples as outtakes.

No open issues 🎉

What changed in this PR

Resolves the unused-example decisions in #88 as part of the shared-math consolidation in #60. The chapter gains a distinct substitution example, while three examples with duplicate identifiers are preserved as outtakes.

Changes:

  • Includes the double-negation substitution example after the chapter’s existing substitution example.
  • Moves three duplicate-ID examples to chapters/outtakes/, retaining their text without including them in the chapter.
File Description
chapters/​outtakes/​_negate-conditional_exm.qmd Preserves the unused conditional-negation example.
chapters/​outtakes/​_distributive_exm.qmd Preserves the unused distributive-law example.
chapters/​outtakes/​_conditional-as-or_exm.qmd Preserves the unused conditional-as-disjunction example.
chapters/​equivalence-negation.qmd Includes the distinct substitution example with a slide break.

Review effort: Balanced

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PR Preview Action v1.8.2
🚀 Preview available at: https://Morrison-Lab.github.io/mcs/pr-preview/pr-102/

Built to branch gh-pages at 2026-11-07 00:45 UTC.

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I'm merging this under Ezra's mwc grant and waiving the cross-model review, because no qualifying reviewer could run. OpenCode Go (kimi-k3) returned GoUsageLimitError (monthly limit) at 2026-11-06 16:45 PST, and this session's network proxy blocks ollama.com (CONNECT 403, measured earlier this session). On head 2574cba the Claude review is clean, CI is green, the branch is current with main, and check-pr-fully-clean.py passes.


Posted by Claude Code (AI agent) --- not written by a human.


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@d-morrison
d-morrison merged commit cc1c0f8 into main Nov 7, 2026
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@d-morrison
d-morrison deleted the claude/project-thread-aj2ep4-unused-proof-subfiles branch November 7, 2026 00:46
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Decide what to do with eight unused proof-writing subfiles

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