Start a thesis
Set up a Multilo project for a whole thesis: bring in your chapters, build your library, write the rules the AI follows, plan the chapters, and draft and check your first section.
A thesis runs for months or years, across many chapters and hundreds of sources. This tutorial sets up a Multilo project built for that: one place for every chapter, a library your agents cite from, rules the AI follows in every chat, and a first section drafted and checked. Work through it once at the start, and every later writing session is faster.
Before you start
- Multilo is installed and connected to your account.
- Have to hand anything you’ve already written (Word chapters, notes), your sources (PDFs, or an export from your reference manager), and your department’s style rules.
1. Create one project for the thesis
Click New Project and name it after your thesis. Use one project for the whole thesis, not one per chapter: agents see the whole project, so they can keep terms consistent across chapters and cite from every source you’ve gathered. See your first project.
A layout that works well for a thesis:
My thesis/
├── chapters/ # one document per chapter
├── library/ # PDFs and reference files you cite from
├── notes/ # outline, meeting notes, supervisor feedback
├── data/ # results, tables, figures
└── .multilo/ # created by Multilo: rules, voice, memory2. Bring in what you already have
- Existing chapters: drag your Word
.docxfiles intochapters/. Multilo opens them with their headings, footnotes, tables, and citations intact. See working with Word. - Chapters you haven’t started: create a new, blank document for each one, so the structure of the thesis is visible from day one.
- Notes and feedback: put them in
notes/. Agents can read them when you point them there.
3. Build your library
Your library is what agents write from and cite. A thesis lives or dies on it, so fill it before you draft:
Add your PDFs
Drop the papers you have intolibrary/. New files are picked up within seconds.Add your reference manager's export
Add a.bib,.ris, or CSL-JSON file to the library. Each entry becomes its own citable reference.Or import straight from Zotero
With Zotero 7 or later running, and Allow other applications on this computer to communicate with Zotero turned on in Zotero’s Settings → Advanced, ask in chat: “Import my Thesis collection from Zotero into my library.” Multilo shows what would come across and asks before importing anything.Fill the gaps
Open Sources Hub to find the references inside your papers and search for what’s missing.
4. Write down your thesis rules
Create .multilo/AGENTS.md with the rules every chat and agent should follow for this thesis. Keep it short and specific:
# Thesis
- Research question: [How does remote work affect trust in small teams?]
- Department style: [APA 7], British spelling, numbered headings.
- Chapters: 1 Introduction, 2 Literature review, 3 Methods, 4 Results, 5 Discussion.
# Rules
- Cite only sources from my library.
- Call participants "respondents", never "subjects".
- Chapter 1 is approved by my supervisor. Don't edit it unless I ask.Update it as the thesis evolves. See store instructions and memories.
5. Set your voice and integrity
- Voice: let Multilo learn your writing voice from samples of your own work — an earlier paper or an approved chapter — so drafts sound like you.
- Integrity: turn on strict mode, so the AI refuses to invent a citation and tells you when it can’t find a real source.
Set both from Settings. See author voice & integrity.
6. Plan the chapters
Before writing, agree on the structure. Turn on plan mode with Shift+Tab in the chat box (or type /plan) and ask:
Propose a chapter-by-chapter outline for my thesis, using the sources in my library and the chapters already in chapters/. For each chapter, list its sections and the key sources for each. Write it to notes/outline.md.Nothing changes until you approve. Ask for changes in chat, or click Edit on the plan card to change it yourself, then Approve & run. Share the outline with your supervisor before you draft.
7. Draft your first section
Open the chapter document and ask for one section at a time — a thesis is too big for a single request:
Draft section 2.1 of the literature review from the outline in notes/outline.md, about [900] words, citing sources from my library.For a whole chapter at once, use the Full Draft Writer: it researches, shows you the outline first, then drafts section by section with citations. Either way, treat the result as a first draft to revise in your own words.
8. Check it and save to Word
Review the changes
The bar above the chat box lists every file the session changed. Keep or undo each change.Check every citation
Run Claim Check. It fetches each cited source and tells you whether it supports the claim.Save as Word
Save the chapter as.docxfor your supervisor. Headings, footnotes, tables, and citations come through intact.
9. Keep the thesis safe for the long haul
- Back it up with Git. Multilo’s history keeps the last 40 versions of each document for 14 days — great for undoing a bad edit, but not a multi-year backup. Commit milestones (an approved chapter, a submitted draft) to Git or GitHub. See versions & safety.
- One session per chapter. Rename sessions after the chapter you’re working on and pin the active ones. See manage sessions.
- Record decisions. When you and your supervisor decide something, tell an agent to remember it: “Remember that we excluded the 2019 pilot data.”
Your name is on it
Agents speed up the writing; they don’t replace your judgment. Read every section you keep, and check its sources, before it goes to your supervisor or examiners.