Dear members of the Forum,
I apologize for the long post, but I thought you would find it helpful if I gave as many details as possible.
I have been, and still am, writing academic manuscripts with Multimarkdown Composer. Typically, I have one file for the Abstract, one for the Introduction and one for each of the different parts of the Results, Discussion, Materials & Methods and Figure Legends sections. For each manuscript, all those files are stored in a private git repository, so I don’t need to save multiple versions of each file: I save over top of the previous one and use version control to manage the changes. I then create an Index file, which is used by Marked to combine, in the order I want, the different parts of the manuscript into one single markdown file. I use Pandoc from the terminal to turn the markdown file into a docx file, which is what the journals we submit our manuscripts to require. I have a series of docx templates for different journals that Pandoc uses, so I can quickly reformat a manuscript for a new journal if it gets rejected by different one.
It seems to me that the idea of breaking down a long text into smaller, more manageable sections, which is what I have always been doing, is one of the core principles of Scrivener, so some time ago I purchased it, and slowly — unfortunately, I cannot take time off to learn how to use it, and as I explore Scrivener in my spare time, I keep on using my old system to avoid delays in publishing our research — I have been trying to understand how to use it best.
So far, it seems to me that by using Scrivener I could have all the different parts of each manuscript into a single Scrivener project instead of having them as separate files in a git repository. Further, Snapshots in Scrivener could be considered the equivalent of version control, and I would not need to create an Index file that tells Marked how to combine all those parts of the manuscript and export them as a single markdown file. Finally, I could still use all my docx templates with Pandoc in Scrivener, whether I write in Scrivener in markdown or in rich text (against which I have nothing).
So I have tried to put together a Scrivener template for our manuscripts, trying to recreate what I do with Multimarkdown Composer. My use of Multimarkdown is not orthodox: for example, manuscripts formatted for submission to a journal must have a page break between the title, authors, affiliation, etc. section and the Abstract; in order to achieve that, for the Abstract heading I use a level 4 heading, which I use nowhere else in our manuscripts. In my docx templates, this is styled exactly like a level 2 heading, which is what the Abstract, Introduction, Results, Discussion, Materials & Methods and Figure Legends sections would require, but has a page break before it. Even though nonorthodox, this stratagem has allowed me to overcome limitations of Multimarkdown. I reproduced this system “verbatim” in Scrivener (please see attached .scriv project file), which results in a perfectly formatted docx file (attached in PDF format) by compiling for Multimarkdown and by processing with Pandoc using my templates. Only, as you will notice, the structure of the Manuscript folder in the Scrivener binder is a bit awkward — with all those untitled documents — and I wondered whether there were a simpler way to achieve in Scrivener what I am trying to do, without necessarily trying to recreate “verbatim” in Scrivener my old system, including its stratagems to overcome Multimarkdown limitations. For example, I have tried to use Separators to achieve that space break between the title, authors, affiliation, etc. section and the Abstract but was unable to make it work. So I thought I would turn for advice to the members of this forum, who clearly know more about Scrivener than I do, and see whether they had any suggestions on how to achieve what I am trying to achieve in Scrivener.
Finally, if it matters for your feedback, we don’t have math equations in our manuscripts; I have no use for the Research section in Scrivener (all my research material is in Bookends and Tinderbox); the References section in our manuscripts is created by adding Bookends citations in Scrivener (or, at the moment, in Multimarkdown Composer) and by scanning the final docx with Bookends; and figures are never inserted in the docx file: they are created in other programs and uploaded directly on the website of the journal’s submission system, which from the docx file and the figure files produces a PDF that is used for peer-review.
Thank you very much for your consideration.