Zettlr edits ordinary Markdown files and organizes their folders in a writing workspace. A single file can be exported directly, while a folder marked as a project gains an ordered source list and project-specific publishing settings. Export creates a separate output through Pandoc or another configured command. It does not rewrite the Markdown sources into the destination format.
A project is a folder with export settings
Enabling Project stores a title, selected output profiles, included files, their order and optional citation or template choices. Project export collects only those listed files in the configured sequence. Adding, renaming or removing a Markdown file does not update that list automatically.
A stale entry may remain unnoticed until export checks it, and a new chapter can stay out of the result until the user adds it. Disabling Project immediately deletes the saved project settings, and the removal has no built-in undo. The Markdown files remain in the folder, but their export order and template selections disappear.
Profiles send the text through Pandoc
An export profile is a YAML Pandoc defaults configuration that selects an output format and transformations. Single-file export combines the current file, selected profile and destination. Project export invokes Pandoc once for every selected profile, so one project can generate several output types.
Zettlr creates a temporary defaults file and adjusts selected fields before Pandoc runs. It can add filters, apply link and tag behavior or override profile title and template settings with project choices. The order of added filters has no guarantee, which matters when two filters expect to transform the same element in sequence. Relative paths inside the temporary defaults file are also unsafe because that file lives outside the source folder.
Simple PDF does not use the LaTeX path
Simple PDF first converts Markdown to HTML and then prints through a browser-style process. A LaTeX PDF template does not control that result. Citation libraries and CSL styles can also change rendered text, while templates may add content around the source. The output word count can therefore differ from the count in the Markdown editor.
Project settings have their own scope, so some global export choices do not apply to project output. When appearance differs between one-file export and project export, comparing the active profile, project template and citation settings is more useful than editing the source text blindly.
A custom command replaces the standard exporter
A custom export command must be available in the system path or use an absolute executable path without spaces. Zettlr passes absolute source-file paths to it and bypasses the normal exporter. The command becomes responsible for conversion, output location and error handling.
This path can support a private publishing toolchain, but it does not inherit Zettlr’s ordinary Pandoc transformations automatically. Testing the command on copies also reveals whether it respects the project file order and handles citations before it becomes the only route to a finished document.
