Thesis production orchestrator

Thesis Production Orchestrator

Manage the thesis as a versioned evidence system. Do not begin by rewriting prose.

First-run sequence

1. Determine whether the user is starting, restructuring, writing one chapter, revising, formatting, plotting, auditing, or recovering.
2. Run the intake questionnaire in references/onboarding.md.
3. Generate the answers JSON and execute guided_intake.py; do not require the user to construct manifests by hand.
4. Route school rules, outline, scope, and chapter contracts to thesis-requirements-planning.
5. Ask the author to identify the authoritative manuscript when it cannot be established from a written decision. Never infer authority from final, version numbers, timestamps, page count, or folder location.
6. Record SHA-256 hashes before any edit and complete material, conflict, gap, and terminology ledgers.
7. Use Superpowers brainstorming for scope/design, writing-plans for multi-stage work, and verification-before-completion before any completion claim.
8. Route work to the narrowest specialist Skill and run its deterministic gate.
9. Deliver new files plus a report of inputs, changes, validation, unresolved items, and required human approvals.

Routing

• School rules, thesis structure, supervisor framework, scope, and staged plan: use thesis-requirements-planning.
• Review search, field mapping, authoritative reviews, primary studies, publication figures, or ChatGPT web research handoffs: use thesis-literature-review.
• Zotero, references, DOI checks, evidence matrix, experimental facts, or factual support: use thesis-evidence-engineering.
• Materials, preparation, characterization conditions, controls, replicates, statistics, or method-result coverage: use thesis-research-methods.
• Raw data, OriginPro, Python/R plots, fitting, error bars, graph templates, or plot specifications: use thesis-data-analysis-plotting.
• Chapter outline, research logic, section integration, or prose: use thesis-chapter-engineering.
• Figures, panels, captions, tables, or visual readability: use thesis-figure-table-audit.
• DOCX, school template, page layout, equations, TOC, headers, or references layout: use thesis-docx-production.
• Reviewer, defense, supervisor, or blind-review comments: use thesis-review-revision.
• CFD, MD, finite-element, numerical models, source terms, validation, or simulation figures: optionally use thesis-computational-evidence only when the research requires it.

Load only the selected specialist Skill and relevant reference files.

Authority rules

Apply the hierarchy in references/versioning.md. A lower-ranked artifact may reveal a conflict but may not silently override a higher-ranked source.

Treat these as separate categories:

• verified literature fact;
• author-provided experimental fact;
• completed computational result;
• inference consistent with evidence;
• recommendation or future work.

Do not merge the categories in prose or reports.

Edit modes

Choose one mode before editing:

• draft: create new Markdown or DOCX from controlled inputs.
• restructure: change chapter organization while preserving registered evidence and assets.
• content-patch: modify only declared paragraphs or sections.
• format-patch: preserve text and modify only Word structure/style.
• review-pack: leave the manuscript untouched and produce paste-ready revisions.
• recovery: compare versions, restore lost text/figures, and establish a new baseline.

Never combine restructure, content-patch, and format-patch without an explicit change scope.

Deterministic tools

Initialize a project:

python scripts/init_thesis_project.py /path/to/project --title "Title"

Preferred guided initialization:

python scripts/guided_intake.py /path/to/project --answers intake-answers.json

Record a baseline:

python scripts/snapshot_project.py /path/to/project \
  --output /path/to/project/versions/baseline.json

Run a stage gate:

python scripts/quality_gate.py /path/to/project --stage evidence \
  --report /path/to/project/reports/evidence-gate.json

Read references/project-schema.md before changing artifact fields. Read references/gates.md before declaring a stage complete.

Completion rule

Do not call the thesis or a stage complete because a document was generated. Require fresh audit output, visual inspection where applicable, unchanged baseline verification, and an explicit list of unresolved human decisions.