tufte-org-mode VS org-thesis

https://github.com/tsdye/tufte-org-mode (org + tufte-latex environment)

I have used Org mode in tandem with LaTeX for displaying inline statistical equations when taking notes for data science topics and have found it works very well, although I am by no means a LaTeX expert. I have, however, read where Ph.D students have used Org mode to write their theses using LaTeX.

Check out https://github.com/dangom/org-thesis

Not barebones, but I would consider looking at scimax, which is an emacs configuration that likely is similar to your work flow. You can also look to PhD theses written in org-mode and shared on github, there are a few with sensible configurations you might want to just copy.

The include has the ability to specify lines. Here is an article I saved that goes into how this could be used for a thesis and reuse parts for journal articles. That sounds similar to your use case. https://github.com/dangom/org-thesis

As a sibling parent mentioned, you can tag an element by inserting it into it's own heading and adding the :ignore: tag.

I feel this functionality is overlooked, and it is in my opinion one of the most powerful features implemented in org, as it allows you to add "meta" groupings to your org document without any effect on the content.

Without the :ignore: tag, there is a strict semantic relation between org-mode document headings, as physically indicated by the * at the beginning of a line, and the corresponding hierarchical level of the heading's content.

With the :ignore: tag, however, you separate content from form. Headings with :ignore: work just as headings for your file.org document: you can search for headings, link to them, add IDs and properties and whatever else you can do with headings. But when you export your document, the heading no longer exists and thus has no impact on the hierarchical level of its content.

Why is this interesting? Well, because if content is separated from form, we can build things where the same content assume multiple forms depending on whatever context we define.

I used this in combination with other org-mode tags, "#+exclude_tags" and "#+include" directives to build my Ph.D. thesis with org mode and have my thesis chapters be exportable both as thesis chapters as well as standalone publications. Shameless plug: https://github.com/dangom/org-thesis

It should be straightforward to extend the idea to presentations and other formats as well.

https://github.com/dangom/org-thesis (org mode phd solution) https://write.as/dani/writing-a-phd-thesis-with-org-mode (explaining his solution)

I wrote my thesis with org mode and wrote about it here: https://write.as/dani/writing-a-phd-thesis-with-org-mode. Repo here: https://github.com/dangom/org-thesis