Scimax VS Code

✅ Overview

When writing academic papers in LaTeX, e.g. with Overleaf, it is common to organize figures into a separate directory, and sometimes to include files in directories to keep the main directory well-organized. Some publishers do not like this, however, and it is extremely annoying to have to manually copy all the files into a single directory with simple names, inline the bibliography, and flatten all the \input and \include commands into a single .tex file.

The manuscript module helps prepare LaTeX documents for journal submission by creating a self-contained, flattened version of your manuscript.

When submitting papers to journals, you often need:

  • A single .tex file (no \input or \include commands)

  • Bibliography inlined from the .bbl file

  • All figures in the same directory with simple names

  • Local style files (.sty, .cls, .bst) included

This module automates that process while preserving your original files.

✅ Commands

✅ Flatten Manuscript

Command: scimax.manuscript.flatten

Opens from Command Palette: "Scimax: Flatten Manuscript for Submission"

This is the main command that:

  1. Optionally compiles your document to generate/update the .bbl file

  2. Flattens all \input{} and \include{} commands

  3. Inlines the bibliography (.bbl content)

  4. Renames figures sequentially (1.pdf, 2.png, etc.)

  5. Detects and copies local support files (.sty, .cls, .bst, data files)

  6. Creates a timestamped submission directory

✅ Preview Flattening

Command: scimax.manuscript.preview

Opens from Command Palette: "Scimax: Preview Manuscript Flattening"

Shows what would happen without making changes:

  • Number of included files

  • Number of figures to rename

  • Support files to copy (.sty, .cls, .bst, data files)

  • Whether compilation is needed

  • Any warnings

✅ Flatten to Directory

Command: scimax.manuscript.flattenToDirectory

Opens from Command Palette: "Scimax: Flatten Manuscript to Directory"

Same as flatten, but lets you choose the output directory.

✅ Output Structure

Given a project structure like:

paper/
├── main.tex
├── sections/
│   ├── intro.tex
│   └── methods.tex
├── figures/
│   ├── plot1.pdf
│   └── results.png
├── refs.bib
└── main.bbl

After flattening, you get:

paper/
├── submission-2026-01-20/
│   ├── main.tex      # Flattened, all paths updated
│   ├── 1.pdf         # was figures/plot1.pdf
│   └── 2.png         # was figures/results.png
└── (original files unchanged)

✅ Figure Naming

Figures are renamed sequentially with smart padding based on the total count:

Total FiguresNaming Pattern
1-91.pdf, 2.png, ...
10-9901.pdf, 02.png, ...
100-999001.pdf, 002.png, ...

This ensures correct sorting in file managers.

✅ Support Files

The module automatically detects and copies local support files that your document needs:

✅ Style Files (.sty)

Custom LaTeX packages in your project directory. Detected from \usepackage{...} commands.

✅ Class Files (.cls)

Custom document classes. Detected from \documentclass{...}.

✅ Bibliography Style Files (.bst)

Custom bibliography styles. Detected from \bibliographystyle{...}.

Standard styles (plain, unsrt, alpha, IEEEtran, etc.) are not copied since they're available on most LaTeX installations.

✅ Data Files

Files used by packages like pgfplots:

  • \pgfplotstableread{data.csv}

  • \DTLloaddb{name}{data.csv}

  • \input{data.dat}

✅ Bibliography Handling

The module supports both traditional BibTeX and biblatex:

✅ BibTeX

  • Replaces \bibliography{refs} with the contents of main.bbl

  • Keeps \bibliographystyle{...} in place

✅ Biblatex

  • Replaces \printbibliography with the contents of main.bbl

  • Comments out \addbibresource{...} lines

✅ Compilation

Before flattening, the module checks if your .bbl file is up-to-date by comparing modification times of:

  • The .tex file

  • The .bib file(s)

  • The existing .bbl file

If compilation is needed, you'll be prompted:

  • *Compile first* - Runs pdflatex + bibtex/biber to update the .bbl

  • *Use existing .bbl* - Uses the current .bbl as-is

The module auto-detects whether to use bibtex or biber based on your document's packages.

✅ Configuration

SettingDefaultDescription
scimax.manuscript.autoCompile"ask"When to compile: always, if-needed, never, ask
scimax.manuscript.pdflatexPath"pdflatex"Path to pdflatex executable
scimax.manuscript.bibtexPath"bibtex"Path to bibtex executable
scimax.manuscript.biberPath"biber"Path to biber executable

✅ Workflow Example

  1. Open your main .tex file

  2. Run "Scimax: Flatten Manuscript for Submission" from Command Palette

  3. Choose whether to compile first (recommended if you've made recent changes)

  4. Wait for processing

  5. Find your submission-ready files in submission-YYYY-MM-DD/

✅ What Gets Flattened

✅ Included

  • \input{file} - Content inserted directly

  • \include{file} - Content inserted with \clearpage before and after

  • \includegraphics[opts]{path} - Figures renamed and paths updated

  • \bibliography{refs} - Replaced with .bbl content

  • \printbibliography - Replaced with .bbl content (biblatex)

✅ Ignored (Not Processed)

  • Commands inside % comments

  • Commands inside verbatim environments (verbatim, lstlisting, minted)

  • \input commands that can't be resolved (warning issued)

✅ Warnings

The module issues warnings for:

  • Missing included files

  • Missing figure files

  • Missing .bbl file

  • Circular includes (A includes B, B includes A)

  • Maximum include depth exceeded (default: 20 levels)

Warnings are shown after flattening completes. You can review them by clicking "Show Warnings" in the success notification.

✅ Limitations

The module handles most common manuscript scenarios but has some limitations:

✅ Not Supported

FeatureDescriptionWorkaround
\graphicspathCustom figure search paths are not parsedUse relative paths in \includegraphics
Custom fontsFont files (.ttf, .otf) are not copiedManually copy font files to submission directory
TikZ externalizeExternalized TikZ figures (.pdf cache) not handledDisable externalize or manually copy
Index files.ind files from makeindex not copiedManually copy if using index
Glossary files.gls files from makeglossaries not copiedManually copy if using glossaries
Multiple bibliographiesOnly one .bbl file supportedCombine bibliographies before flattening
Subfiles package\subfile commands not processedUse \input instead

✅ Encoding

The module assumes UTF-8 encoding for all files. Non-UTF-8 files may cause errors or produce garbled output.

✅ Figure Detection

Only \includegraphics commands are detected. Other figure inclusion methods are not handled:

  • \pgfimage

  • \pdfximage

  • Raw PDF includes via \pdfpages

✅ Path Resolution

  • Paths are resolved relative to the directory of the file containing the command

  • Absolute paths are not modified

  • Paths with special characters may not resolve correctly

✅ Bibliography Edge Cases

  • Multiple \printbibliography commands: only the first is replaced with content; others are commented out

  • refsection environments (biblatex): not handled, may produce incomplete bibliographies

  • Custom .bbl locations: the module looks for .bbl alongside the main .tex file

✅ Support Files

Standard LaTeX packages from TeX distributions are not copied (they're assumed to be available). The module only copies files that exist in your project directory.