One root file, many chapters

A thesis in a single .tex file becomes miserable to work in somewhere around the second chapter: scrolling replaces thinking, and every compile processes everything. The standard cure is one root file that holds the class and preamble, with each chapter in its own file. The root file stitches them together.

The root file

% main.tex
\documentclass{report}
\begin{document}
\include{chapters/intro}
\include{chapters/methods}
\include{chapters/results}
\end{document}

main.tex is the only file you ever compile. Each \include names another file without its .tex extension, using forward slashes on every platform, and pulls its contents in at that point. The chapter files themselves contain only content, typically starting with \chapter{...}; they have no \documentclass and no document environment of their own, because they are fragments of this document, not documents.

include versus input

The two inclusion commands behave differently, and the differences decide which to use where. \include starts a new page before the material, which suits chapters, and writes a separate .aux file for each included file, which is what makes selective compilation possible. \input is a plain textual paste: no page break, no separate .aux, and it can be nested inside another input. That makes \input the right tool for fragments smaller than a chapter, such as a large table kept in its own file or a shared macros file. One structural rule to remember is that \include cannot be nested inside an included file, while \input can be used anywhere.

Drafting one chapter at a time

\includeonly{chapters/methods}

Placed in the preamble, \includeonly tells LaTeX to process only the listed files while still reading the saved .aux data of all the others. The compile gets dramatically faster, and because the other chapters’ labels and page counts are replayed from their .aux files, cross-references and numbering in the chapter you are drafting stay correct. That second half is the reason to prefer this over commenting out \include lines, which forgets the other chapters entirely and turns every \ref into them into ??.

Comment the \includeonly line out for full builds, and always run a complete compile before sharing a PDF, since stale .aux data can lag behind edits made in excluded chapters. For which files in the resulting folder are yours and which are generated, see the files in a real project.