thesis-consolidate

Thesis consolidate

Overview

One pass over the whole thesis that makes the chapters consistent with each other, with the front and back matter, and with the papers. Scripts go first because they catch what readers miss (spelling and hyphenation variants, repeated acronym definitions, citation commands). Fresh agents then read for what needs judgment. Fixes follow, then a build and a look at the pages.

Core principle: copying errors and mechanical variants are fixed directly. Anything that changes what the thesis claims waits for the student.

REQUIRED SUB-SKILL: load thesis-kit first (<kit> = its base directory). Write <kit> out as an absolute path in every command and every agent prompt.

If the thesis was not built with thesis-theme and thesis-write (no thesis-work/), run paper_text.py papers thesis-work/papers first, ask the student for the research questions and core terms and write them to thesis-work/plan.md together with the chapter-to-paper table, and skip rules_lint.py until a rules file exists.

Process

1. Inventory. From the thesis root, save every output below to thesis-work/consolidate/<YYYY-MM-DD>/inventory.md.
   • Files: python3 <kit>/scripts/latex_check.py main.tex --list-files lists main.tex and every file it \inputs or \includes. The other scanners do not follow \input, so always pass them that list. Below, FILES stands for $(python3 <kit>/scripts/latex_check.py main.tex --list-files) written inline in the command; do not store the list in a shell variable (zsh would pass it as one argument).
   • python3 <kit>/scripts/latex_check.py main.tex --build (add --engine xelatex or --engine lualatex when the thesis loads fontspec).
   • python3 <kit>/scripts/consistency_scan.py FILES
   • python3 <kit>/scripts/rules_lint.py thesis-work/rules/global.md --apply FILES
   • python3 <kit>/scripts/prose_metrics.py FILES (wording repeated across chapters, repeated openers)
   • Numbers in the front and back matter: for each file F that holds the abstract, preface, introduction or conclusion, run python3 <kit>/scripts/check_numbers.py F --all --source chapters/<a>.tex --source chapters/<b>.tex ... with one --source per paper chapter, never F itself or a folder that contains it. A match only means the number appears in some chapter; the front-matter agent checks that it is the same quantity.
   • Numbers in each chapter: python3 <kit>/scripts/check_numbers.py chapters/<ch>.tex --source thesis-work/papers/<paper id>/ with one --source for each paper in the chapter's "source paper(s)" column of plan.md (paper ids are the folder names in thesis-work/papers/).
   • The scan does not see names inside math ($F_1$). Grep each metric, model and method name from plan.md across FILES.
2. Reading passes. Start three fresh agents in one message. Each prompt is the paragraph under "Every agent" in references/briefs.md, then one of its sections (front and back matter, wording and notation, seams), then the paths and the report path (thesis-work/consolidate/<date>/agent-<1|2|3>.md).
3. Decide each finding (you, the coordinator), in one table.
   • Apply directly: mechanical variants (use the form a global rule fixes, else the form most chapters use), citation commands, broken references and labels, duplicate bib entries, and copying errors: a number, name or venue the thesis states differently from the paper, where the paper states it for the same configuration. Quote the paper's line in the report.
   • Decisions for the student: everything else that changes a claim. That includes a number no chapter or paper states (a relative gain, an average), a claim's strength, a contribution added to or removed from the abstract or conclusion, a renamed method, and cutting or moving duplicated background. Do not apply these. Record each one in the report and in thesis-work/escalations.md.
   • A fix inside a passage listed in any thesis-work/rounds/*/<ch>/student-edits.md is a decision for the student: they wrote it.
   • Keep acronym definitions in the abstract and at the first use in each chapter, even when the scan lists them as repeated: those are read on their own.
   • A new thesis-wide convention: add it to rules/global.md as one block.
4. Apply the direct fixes in small edits. Run step 1 again and build. Look at every page with a problem: render_pages.py main.pdf --find "<phrase from the source line>" gives the PDF page (page numbers in the LaTeX log are printed labels, not PDF pages), then render_pages.py main.pdf --pages <n> and open the PNG.
5. Report to thesis-work/consolidate/<date>/report.md with the layout below. Then go through the decisions with the student. Apply only what they approve, run step 1 and the build again, and mark each decision approved, declined or changed in the report and in escalations.md. Then copy each edited chapter to its latest thesis-work/rounds/r<N>/<ch>/end.tex, so a later thesis-write round does not take these edits for the student's.

When thesis-work/config.md says Commits: allowed, commit each category of applied fixes as its own commit (that answer is the student's request), staging only the files you edited (never .aux, .log or the PDF). Otherwise leave the changes uncommitted.

Report layout

# Consolidation report (<date>)
Scope, files, and the state of the checks before and after.

## Applied
| # | Location (before this pass) | Original | Fix | Reasoning (with the paper or rule) |

## Decisions for the student
| # | Location | Original | Proposed fix | Reasoning and evidence |

## Left as is
| # | Location | What the scan or an agent flagged | Why it stays |

Red flags

Thought	Do this instead
"This number looks wrong, I'll change it to match the table."	Check the paper first. The chapter's table may be the wrong one.
"The chapter overclaims, I'll soften it."	That changes the claim. List it under decisions for the student, with the evidence.
"A rule says so, so I'll restructure every chapter."	Rules fix wording and conventions. Moving sections or cutting text is a decision for the student.
"Spelling variants are trivial, skip the scan."	Readers miss them and examiners notice them. Run the scan on FILES.
"I'll make the openers match."	Make them consistent in content (role, RQ, publication note) and varied in wording.
"The build passed, so references are fine."	Also read the undefined-reference list and the pages showing ??.