How to draft a thesis chapter with verified citations

A chapter is bigger than a paragraph and scarier than a blank page. The Thesis Editor is built for exactly that middle distance: getting a full, defensible first draft down, keeping every claim tied to a real source as you go, and never losing a word across the weeks it takes. This guide walks the mechanics of drafting one chapter end to end, deeper than the one-section getting-started path.

One thing stays true at every step: the AI drafts only from the full text of papers in your library, and every claim it writes arrives with a citation that resolves to a real paper. There is no free-text reference anywhere in the editor.

1. Two ways to draft, and when to use each

There are two drafting paths, and they are complementary. The whole-chapter path drafts an empty chapter from the right upstream source for its type: the Introduction from your pinned question, the Literature Review from your synthesis, the Methodology from your study design, the Results from your analyses. It runs first-draft-only (it never overwrites a chapter that already has prose or grounded claims), so it turns a blank chapter into a grounded starting draft without any risk to work you already have.

The per-section path is "Write with AI" on a single section. Use it to refine one part at a time, or to write a section the whole-chapter handoff does not cover. If an upstream step is missing (say you try to draft a Literature Review before building a synthesis) the editor shows the reason and a link to the tool that fixes it, rather than a button that would fail.

2. Read the grounding as you write

Every section header carries a small badge that reads how many of its paragraphs are grounded (for example "6/7 paragraphs grounded"). Green means every paragraph is backed; amber means one or more are not yet. The Outline dropdown mirrors the same signal per section, so you can see at a glance which parts of the chapter still need a source.

Each citation chip in your running text is toned by its verification verdict, and selecting one opens the provenance rail on the right. That rail shows the exact passage from the cited paper's stored full text that supports the claim, down to the character span, so you can confirm the source really says what your sentence says before you move on.

3. Cite what you choose, not just what the AI drafted

Drafting is not the only way a citation lands in a chapter. A searchable citation picker puts every paper in your library one keystroke away, and a quote bank holds the passages you highlighted while reading, each still bound to its exact source span (page, section, offsets). Drop a saved quote into a paragraph and it arrives with its real citation attached.

The Fact Checker guards every insertion the same way it guards AI-drafted prose. A citation you add by hand is checked against its source's full text just like one the model wrote, so "cite it yourself" never means "skip verification".

4. Verify the whole chapter in one pass

When the draft is down, "Verify all" re-checks every cited sentence against its source. On a long chapter it runs section by section and shows real progress ("Verifying section 2/6") instead of a silent multi-minute wait, and the results settle straight into the per-paragraph badges and chip tones.

Fixing a flag is usually quick. The most common repair is narrowing an overclaim: "X causes Y" often becomes supported once it reads "X was associated with Y in two trials". The next most common is adding the full text (an uploaded or open-access PDF) for a paper you cited from its abstract, so verification has something to read. A flagged sentence is the product being honest, not the draft failing.

5. Never lose a draft

Months of writing need a safety net, so the editor keeps several. Typing marks a section dirty and a debounced autosave persists it in the background; there is a manual Save button when you want a deliberate checkpoint, and a browser guard warns you before a tab close would drop unsaved prose. Every save adds a timestamped entry to that section's version history, and one click restores any earlier version. Restoring is itself saved as a new version, so nothing is ever truly gone.

Underneath the chapter, the References pane renders your bibliography in the project's citation style (APA, MLA, Chicago, or IEEE), one entry per distinct source and numbered to match the chips in your text.

Where to go next

A drafted chapter is a starting draft, not a finished one. When the prose needs tightening, move to the Proof Reader (its revisions cannot break your citations); read "Revise without breaking your citations" for that path. When every chapter is drafted and verified, the Thesis Assembler binds them into a submittable document behind the trust gate.