What is the difference between input and include in LaTeX?

Input inserts content exactly where called and can be nested. Include starts on a new page, creates auxiliary files, and works with includeonly for selective compilation. Use input for small insertions like preambles and include for major sections like chapters.

How do I compile only one chapter of my thesis for faster editing?

Use includeonly in your preamble to specify which chapters to compile. For example, includeonly followed by chapters/methods in braces will only compile the methods chapter. Cross-references from other chapters are preserved from previous full compilations.

How should I organize figures in a large LaTeX project?

Create a figures folder with subfolders for each chapter, like figures/chapter-3/. Use graphicspath to tell LaTeX where to look. This keeps your project organized and makes it easy to find and update specific figures later.

Why is my large document compiling so slowly?

Large documents with many figures compile slowly. Speed it up by using includeonly to compile single chapters, enabling draft mode to skip images, externalizing TikZ graphics, and using lower resolution images during drafting. Compile the full document only when needed.

Taming 200-Page Monsters: How to Organize Large LaTeX Projects

When One File Isn't Enough

A 10-page paper? Open one file, write, compile. Simple.

A 200-page thesis with 12 chapters, 50 figures, and 300 references? That's not a file. That's a project.

Single files become unwieldy. Scrolling takes forever. Compilation slows to a crawl. Your editor chokes. And if you need to reorganize chapters, you're in for a world of pain.

The solution: multi-file LaTeX architecture. One master document, separate files for each chapter, intelligent compilation that rebuilds only what changed. Here's how to set it up from the start—or retrofit an existing monster document. (See also our thesis templates for pre-organized project structures.)

File Organization

The Master Document Pattern

Create a main file that includes others:

thesis/
├── main.tex              # Master document
├── preamble.tex          # Packages and settings
├── chapters/
│   ├── introduction.tex
│   ├── literature.tex
│   ├── methods.tex
│   ├── results.tex
│   └── conclusion.tex
├── frontmatter/
│   ├── abstract.tex
│   ├── acknowledgments.tex
│   └── dedication.tex
├── appendices/
│   ├── appendix-a.tex
│   └── appendix-b.tex
├── figures/
│   ├── chapter-3/
│   └── chapter-4/
└── references.bib

The Master File

% main.tex
\documentclass[12pt, a4paper]{book}
 
\input{preamble}
 
\begin{document}
 
\frontmatter
\input{frontmatter/titlepage}
\input{frontmatter/abstract}
\input{frontmatter/acknowledgments}
\tableofcontents
\listoffigures
\listoftables
 
\mainmatter
\include{chapters/introduction}
\include{chapters/literature}
\include{chapters/methods}
\include{chapters/results}
\include{chapters/conclusion}
 
\backmatter
\appendix
\include{appendices/appendix-a}
\include{appendices/appendix-b}
 
\bibliographystyle{apalike}
\bibliography{references}
 
\end{document}

\input vs \include

\input

Inserts content exactly where called:

\input{sections/intro}
% Content of intro.tex appears here

Characteristics:

Can be nested (input within input)
Can be used anywhere
No page break before or after
Cannot be selectively included

\include

For major document sections:

\include{chapters/methods}
% Starts new page, includes chapter

Characteristics:

Cannot be nested
Starts on new page
Creates .aux file per include
Works with \includeonly

\includeonly

Compile only specific chapters:

\includeonly{chapters/methods, chapters/results}
 
% In document:
\include{chapters/introduction}  % Skipped
\include{chapters/literature}    % Skipped
\include{chapters/methods}       % Compiled
\include{chapters/results}       % Compiled
\include{chapters/conclusion}    % Skipped

Benefits:

Much faster compilation
Cross-references preserved (from aux files)
Switch quickly between sections

Comment out \includeonly for final compilation.

Compilation Strategies

Draft Mode

Speed up compilation during writing:

\documentclass[draft]{book}

Draft mode:

Shows overfull/underfull box warnings
Replaces images with placeholders
Faster compilation

Selective Compilation

Using \includeonly:

% Working on methods chapter
\includeonly{chapters/methods}
 
% Later, working on results
\includeonly{chapters/results}
 
% Final compilation (comment out)
% \includeonly{...}

Parallel Compilation

Some build systems compile parts in parallel. Check if your setup supports:

latexmk with appropriate configuration
IDE-specific parallel compilation
Custom build scripts

Managing Cross-References

Labels Across Files

Labels work across included files:

% In chapters/methods.tex
\section{Data Collection}
\label{sec:data-collection}
 
% In chapters/results.tex
As described in Section \ref{sec:data-collection}...

Checking References

Find undefined references:

grep "LaTeX Warning.*undefined" main.log

Or search your PDF for "??" symbols.

The \ref* Command

With hyperref, \ref* creates non-hyperlinked reference:

\ref{sec:intro}   % Hyperlinked
\ref*{sec:intro}  % Plain number

Bibliography Management

Single Bibliography

Most common approach:

% At end of main.tex
\bibliographystyle{apalike}
\bibliography{references}

Per-Chapter Bibliographies

Using biblatex with refsection:

\usepackage[refsection=chapter]{biblatex}
 
% Each chapter gets its own bibliography
\begin{refsection}
\include{chapters/literature}
\printbibliography[heading=subbibliography]
\end{refsection}

Large Bibliography Files

Organize .bib files by topic:

\bibliography{general, methods, datasets}

Or keep one file but organize internally:

%%% FOUNDATIONAL PAPERS %%%
@article{...}
 
%%% METHODOLOGY %%%
@article{...}
 
%%% DATASETS %%%
@misc{...}

Handling Figures

Figure Organization

figures/
├── chapter-1/
│   ├── overview.pdf
│   └── timeline.pdf
├── chapter-3/
│   ├── setup.pdf
│   ├── results-1.pdf
│   └── results-2.pdf
└── chapter-4/
    └── comparison.pdf

Graphics Path

\graphicspath{
    {figures/}
    {figures/chapter-1/}
    {figures/chapter-3/}
    {figures/chapter-4/}
}
 
% Then in text:
\includegraphics{overview}  % Found in figures/ or subfolders

External Figure Files

For complex TikZ figures, externalize:

\usetikzlibrary{external}
\tikzexternalize[prefix=tikz-cache/]

TikZ figures compile once and are cached as PDFs.

Custom Commands and Styles

The Preamble File

Keep customizations in one place:

% preamble.tex
 
% Packages
\usepackage{amsmath, amssymb}
\usepackage{graphicx}
\usepackage{booktabs}
\usepackage{hyperref}
\usepackage{cleveref}
 
% Custom commands
\newcommand{\todo}[1]{\textcolor{red}{TODO: #1}}
\newcommand{\myterm}{Technical Term}
 
% Document settings
\setlength{\parindent}{0pt}
\setlength{\parskip}{1em}

Class Files

For extensive customization, create a class file:

% mythesis.cls
\NeedsTeXFormat{LaTeX2e}
\ProvidesClass{mythesis}[2025/01/01 My Thesis Class]
 
\LoadClass[12pt, a4paper]{book}
 
\RequirePackage{...}
% Additional configuration

Use in main:

\documentclass{mythesis}

Version Control

Git for LaTeX

Git works excellently with LaTeX:

git init
git add .
git commit -m "Initial structure"

.gitignore for LaTeX

# LaTeX auxiliary files
*.aux
*.log
*.bbl
*.blg
*.out
*.toc
*.lof
*.lot
*.fls
*.fdb_latexmk
*.synctex.gz
 
# Build output (optional)
*.pdf
 
# Editor files
*.swp
.DS_Store

Meaningful Commits

git commit -m "Complete first draft of methods chapter"
git commit -m "Add figures for experimental results"
git commit -m "Revise introduction based on advisor feedback"

Branching for Major Revisions

git checkout -b major-revision
# Make significant changes
git commit -m "Restructure literature review"
git checkout main
git merge major-revision

Compilation Workflows

Using latexmk

Automate the compile sequence:

latexmk -pdf main.tex

latexmk automatically runs LaTeX, BibTeX, and recompiles as needed.

Makefile

For complex builds:

all: main.pdf
 
main.pdf: main.tex chapters/*.tex references.bib
	latexmk -pdf main.tex
 
clean:
	latexmk -c
 
distclean:
	latexmk -C

Continuous Compilation

Watch for changes and recompile:

latexmk -pdf -pvc main.tex

Common Problems

Slow Compilation

Solutions:

Use \includeonly
Enable draft mode
Externalize TikZ graphics
Reduce image resolution during drafting

Auxiliary File Pollution

Solution: Redirect to build folder:

latexmk -pdf -auxdir=build -outdir=build main.tex

Cross-Reference Errors

Symptom: Wrong chapter/section numbers after using \includeonly.

Solution: Compile full document occasionally to update all .aux files.

Bibliography Issues

Symptom: Citations show [?] after adding new references.

Solution: Full compile sequence: LaTeX → BibTeX → LaTeX → LaTeX.

Project Templates

Thesis Template Structure

thesis/
├── main.tex
├── preamble.tex
├── mythesis.cls          # Optional custom class
├── frontmatter/
│   ├── titlepage.tex
│   ├── abstract.tex
│   ├── acknowledgments.tex
│   └── symbols.tex       # List of symbols/abbreviations
├── chapters/
│   ├── 01-introduction.tex
│   ├── 02-background.tex
│   ├── 03-methods.tex
│   ├── 04-results.tex
│   └── 05-conclusion.tex
├── appendices/
├── figures/
├── tables/               # Optional: external table files
├── references.bib
├── .gitignore
└── Makefile

Book Template Structure

book/
├── main.tex
├── preamble.tex
├── parts/
│   ├── part1.tex
│   └── part2.tex
├── chapters/
├── appendices/
├── frontmatter/
│   ├── preface.tex
│   └── foreword.tex
├── backmatter/
│   └── index.tex
├── figures/
└── references.bib

Quick Reference

File Inclusion Commands

| Command | New Page | Nestable | \includeonly | |---------|----------|----------|--------------| | \input{} | No | Yes | No | | \include{} | Yes | No | Yes |

Compilation Optimization

| Technique | Speed Gain | |-----------|-----------| | Draft mode | High | | \includeonly | High | | TikZ externalize | Medium-High | | Reduced image quality | Medium | | SSD storage | Medium |

Essential Commands

% Structure
\frontmatter, \mainmatter, \backmatter
\appendix
 
% File inclusion
\input{file}, \include{file}
\includeonly{file1, file2}
 
% Graphics
\graphicspath{{path/}}
 
% References
\tableofcontents
\listoffigures
\listoftables

Conclusion

Large documents require organization:

Split into logical files using \include
Use \includeonly for fast partial compilation
Organize figures and references systematically
Version control with Git
Automate builds with latexmk or Makefile

The initial setup takes time, but pays off across months of writing. A well-organized project is easier to navigate, faster to compile, and more maintainable.

Start organized. Stay organized. Finish successfully.

When One File Isn't Enough

A 10-page paper? Open one file, write, compile. Simple.

A 200-page thesis with 12 chapters, 50 figures, and 300 references? That's not a file. That's a project.

Single files become unwieldy. Scrolling takes forever. Compilation slows to a crawl. Your editor chokes. And if you need to reorganize chapters, you're in for a world of pain.

File Organization

The Master Document Pattern

Create a main file that includes others:

thesis/
├── main.tex              # Master document
├── preamble.tex          # Packages and settings
├── chapters/
│   ├── introduction.tex
│   ├── literature.tex
│   ├── methods.tex
│   ├── results.tex
│   └── conclusion.tex
├── frontmatter/
│   ├── abstract.tex
│   ├── acknowledgments.tex
│   └── dedication.tex
├── appendices/
│   ├── appendix-a.tex
│   └── appendix-b.tex
├── figures/
│   ├── chapter-3/
│   └── chapter-4/
└── references.bib

The Master File

% main.tex
\documentclass[12pt, a4paper]{book}
 
\input{preamble}
 
\begin{document}
 
\frontmatter
\input{frontmatter/titlepage}
\input{frontmatter/abstract}
\input{frontmatter/acknowledgments}
\tableofcontents
\listoffigures
\listoftables
 
\mainmatter
\include{chapters/introduction}
\include{chapters/literature}
\include{chapters/methods}
\include{chapters/results}
\include{chapters/conclusion}
 
\backmatter
\appendix
\include{appendices/appendix-a}
\include{appendices/appendix-b}
 
\bibliographystyle{apalike}
\bibliography{references}
 
\end{document}

\input vs \include

\input

Inserts content exactly where called:

\input{sections/intro}
% Content of intro.tex appears here

Characteristics:

Can be nested (input within input)
Can be used anywhere
No page break before or after
Cannot be selectively included

\include

For major document sections:

\include{chapters/methods}
% Starts new page, includes chapter

Characteristics:

Cannot be nested
Starts on new page
Creates .aux file per include
Works with \includeonly

\includeonly

Compile only specific chapters:

\includeonly{chapters/methods, chapters/results}
 
% In document:
\include{chapters/introduction}  % Skipped
\include{chapters/literature}    % Skipped
\include{chapters/methods}       % Compiled
\include{chapters/results}       % Compiled
\include{chapters/conclusion}    % Skipped

Benefits:

Much faster compilation
Cross-references preserved (from aux files)
Switch quickly between sections

Comment out \includeonly for final compilation.

Compilation Strategies

Draft Mode

Speed up compilation during writing:

\documentclass[draft]{book}

Draft mode:

Shows overfull/underfull box warnings
Replaces images with placeholders
Faster compilation

Selective Compilation

Using \includeonly:

% Working on methods chapter
\includeonly{chapters/methods}
 
% Later, working on results
\includeonly{chapters/results}
 
% Final compilation (comment out)
% \includeonly{...}

Parallel Compilation

Some build systems compile parts in parallel. Check if your setup supports:

latexmk with appropriate configuration
IDE-specific parallel compilation
Custom build scripts

Managing Cross-References

Labels Across Files

Labels work across included files:

% In chapters/methods.tex
\section{Data Collection}
\label{sec:data-collection}
 
% In chapters/results.tex
As described in Section \ref{sec:data-collection}...

Checking References

Find undefined references:

grep "LaTeX Warning.*undefined" main.log

Or search your PDF for "??" symbols.

The \ref* Command

With hyperref, \ref* creates non-hyperlinked reference:

\ref{sec:intro}   % Hyperlinked
\ref*{sec:intro}  % Plain number

Bibliography Management

Single Bibliography

Most common approach:

% At end of main.tex
\bibliographystyle{apalike}
\bibliography{references}

Per-Chapter Bibliographies

Using biblatex with refsection:

\usepackage[refsection=chapter]{biblatex}
 
% Each chapter gets its own bibliography
\begin{refsection}
\include{chapters/literature}
\printbibliography[heading=subbibliography]
\end{refsection}

Large Bibliography Files

Organize .bib files by topic:

\bibliography{general, methods, datasets}

Or keep one file but organize internally:

%%% FOUNDATIONAL PAPERS %%%
@article{...}
 
%%% METHODOLOGY %%%
@article{...}
 
%%% DATASETS %%%
@misc{...}

Handling Figures

Figure Organization

figures/
├── chapter-1/
│   ├── overview.pdf
│   └── timeline.pdf
├── chapter-3/
│   ├── setup.pdf
│   ├── results-1.pdf
│   └── results-2.pdf
└── chapter-4/
    └── comparison.pdf

Graphics Path

\graphicspath{
    {figures/}
    {figures/chapter-1/}
    {figures/chapter-3/}
    {figures/chapter-4/}
}
 
% Then in text:
\includegraphics{overview}  % Found in figures/ or subfolders

External Figure Files

For complex TikZ figures, externalize:

\usetikzlibrary{external}
\tikzexternalize[prefix=tikz-cache/]

TikZ figures compile once and are cached as PDFs.

Custom Commands and Styles

The Preamble File

Keep customizations in one place:

% preamble.tex
 
% Packages
\usepackage{amsmath, amssymb}
\usepackage{graphicx}
\usepackage{booktabs}
\usepackage{hyperref}
\usepackage{cleveref}
 
% Custom commands
\newcommand{\todo}[1]{\textcolor{red}{TODO: #1}}
\newcommand{\myterm}{Technical Term}
 
% Document settings
\setlength{\parindent}{0pt}
\setlength{\parskip}{1em}

Class Files

For extensive customization, create a class file:

% mythesis.cls
\NeedsTeXFormat{LaTeX2e}
\ProvidesClass{mythesis}[2025/01/01 My Thesis Class]
 
\LoadClass[12pt, a4paper]{book}
 
\RequirePackage{...}
% Additional configuration

Use in main:

\documentclass{mythesis}

Version Control

Git for LaTeX

Git works excellently with LaTeX:

git init
git add .
git commit -m "Initial structure"

.gitignore for LaTeX

# LaTeX auxiliary files
*.aux
*.log
*.bbl
*.blg
*.out
*.toc
*.lof
*.lot
*.fls
*.fdb_latexmk
*.synctex.gz
 
# Build output (optional)
*.pdf
 
# Editor files
*.swp
.DS_Store

Meaningful Commits

git commit -m "Complete first draft of methods chapter"
git commit -m "Add figures for experimental results"
git commit -m "Revise introduction based on advisor feedback"

Branching for Major Revisions

git checkout -b major-revision
# Make significant changes
git commit -m "Restructure literature review"
git checkout main
git merge major-revision

Compilation Workflows

Using latexmk

Automate the compile sequence:

latexmk -pdf main.tex

latexmk automatically runs LaTeX, BibTeX, and recompiles as needed.

Makefile

For complex builds:

all: main.pdf
 
main.pdf: main.tex chapters/*.tex references.bib
	latexmk -pdf main.tex
 
clean:
	latexmk -c
 
distclean:
	latexmk -C

Continuous Compilation

Watch for changes and recompile:

latexmk -pdf -pvc main.tex

Common Problems

Slow Compilation

Solutions:

Use \includeonly
Enable draft mode
Externalize TikZ graphics
Reduce image resolution during drafting

Auxiliary File Pollution

Solution: Redirect to build folder:

latexmk -pdf -auxdir=build -outdir=build main.tex

Cross-Reference Errors

Symptom: Wrong chapter/section numbers after using \includeonly.

Solution: Compile full document occasionally to update all .aux files.

Bibliography Issues

Symptom: Citations show [?] after adding new references.

Solution: Full compile sequence: LaTeX → BibTeX → LaTeX → LaTeX.

Project Templates

Thesis Template Structure

thesis/
├── main.tex
├── preamble.tex
├── mythesis.cls          # Optional custom class
├── frontmatter/
│   ├── titlepage.tex
│   ├── abstract.tex
│   ├── acknowledgments.tex
│   └── symbols.tex       # List of symbols/abbreviations
├── chapters/
│   ├── 01-introduction.tex
│   ├── 02-background.tex
│   ├── 03-methods.tex
│   ├── 04-results.tex
│   └── 05-conclusion.tex
├── appendices/
├── figures/
├── tables/               # Optional: external table files
├── references.bib
├── .gitignore
└── Makefile

Book Template Structure

book/
├── main.tex
├── preamble.tex
├── parts/
│   ├── part1.tex
│   └── part2.tex
├── chapters/
├── appendices/
├── frontmatter/
│   ├── preface.tex
│   └── foreword.tex
├── backmatter/
│   └── index.tex
├── figures/
└── references.bib

Quick Reference

File Inclusion Commands

| Command | New Page | Nestable | \includeonly | |---------|----------|----------|--------------| | \input{} | No | Yes | No | | \include{} | Yes | No | Yes |

Compilation Optimization

| Technique | Speed Gain | |-----------|-----------| | Draft mode | High | | \includeonly | High | | TikZ externalize | Medium-High | | Reduced image quality | Medium | | SSD storage | Medium |

Essential Commands

% Structure
\frontmatter, \mainmatter, \backmatter
\appendix
 
% File inclusion
\input{file}, \include{file}
\includeonly{file1, file2}
 
% Graphics
\graphicspath{{path/}}
 
% References
\tableofcontents
\listoffigures
\listoftables

Conclusion

Large documents require organization:

Split into logical files using \include
Use \includeonly for fast partial compilation
Organize figures and references systematically
Version control with Git
Automate builds with latexmk or Makefile

The initial setup takes time, but pays off across months of writing. A well-organized project is easier to navigate, faster to compile, and more maintainable.

Start organized. Stay organized. Finish successfully.

When One File Isn't Enough

File Organization

The Master Document Pattern

The Master File

\input vs \include

\input

\include

\includeonly

Compilation Strategies

Draft Mode

Selective Compilation

Parallel Compilation

Managing Cross-References

Labels Across Files

Checking References

The \ref* Command

Bibliography Management

Single Bibliography

Per-Chapter Bibliographies

Large Bibliography Files

Handling Figures

Figure Organization

Graphics Path

External Figure Files

Custom Commands and Styles

The Preamble File

Class Files

Version Control

Git for LaTeX

.gitignore for LaTeX

Meaningful Commits

Branching for Major Revisions

Compilation Workflows

Using latexmk

Makefile

Continuous Compilation

Common Problems

Slow Compilation

Auxiliary File Pollution

Cross-Reference Errors

Bibliography Issues

Project Templates

Thesis Template Structure

Book Template Structure

Quick Reference

File Inclusion Commands

Compilation Optimization

Essential Commands

Conclusion

Frequently Asked Questions

Related Articles

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AI Writing Assistant for LaTeX: Write Better Papers Faster

When One File Isn't Enough

File Organization

The Master Document Pattern

The Master File

\input vs \include

\input

\include

\includeonly

Compilation Strategies

Draft Mode

Selective Compilation

Parallel Compilation

Managing Cross-References

Labels Across Files

Checking References

The \ref* Command

Bibliography Management

Single Bibliography

Per-Chapter Bibliographies

Large Bibliography Files

Handling Figures

Figure Organization

Graphics Path

External Figure Files

Custom Commands and Styles

The Preamble File