Below please find my final setup for writing a scientific paper/book. Although my requirements seemed to be clear&simple, it took me app. 40 hours to put everything together. And here it is: my final set-up ready :)

I want my system to support me in:

1. Managing scientific sources and citations
2. Insert and enumerate simple equations
3. Export the final document to MS Word docx format, keeping all Styles (like headings).

1. Storing all documents and drafts: Google Drive
2. Managing scientific sources: Zotero (https://www.zotero.org/)
3. Making notes and structuring content: MindManager (https://www.mindjet.com/mindmanager/)
4. Writing: Scrivener (https://www.literatureandlatte.com/scrivener/overview)
5. Exporting: Pandoc (https://pandoc.org/).

1. Initiate the project:
   1. set-up a Google Drive folder and create subfolders:
      1. {book title}
         1. ... {book chapters}...
      2. Setup
   2. set-up a Zotero folder for all needed resources {book title}
      1. export this folder to Setup Google Drive folder in a BibTex format using Better Bibtex plugin (how to can be found in points 1-5 here) > mylibrary.bib
   3. in the Setup Google Drive folder store:
      1. a docx template for Your book (with all proper styles)
      2. mylibrary.bib
      3. Your preferred citation style: choose sth from https://www.zotero.org/styles, eg. https://www.zotero.org/styles/chicago-author-date-16th-edition
2. Scientific sources
   1. Gather all necessary knowledge resources (books, papers, websites, reports etc.) using:
      1. Zotero web plugin
      2. Zotero ISBN search
      3. Just drag&drop files from Your folders
   2. Organize them using TAGS
   3. Make notes:
      1. annotate PDFs and then export notes to Zotero using ZotFile
      2. integrate key notes into MindManager
   4. Make draft structure (paragraph-detail level) in MindManager
3. Writing:
   1. organize all the writing in Scrivener using folders
   2. control targets and writing progress with meta-tags
   3. compile to docx via MultiMarkdown and Pandoc (see compile presets below).

1. Install Zotero (from www.zotero.org)
2. Install useful plugins:
   1. Better Bibtex plugin (see installation instructions here) > to export Your reference library as a BibTex file
   2. ZotFile > for efficient PDF management, especially exporting annotations from PDF to Zotero
3. Zotpick-applescript > for a possibility of calling Zotero citation during writing with a single click
   1. Mac-OS only: Create a dedicated app with Workflow Manager (see installation instructions https://raphaelkabo.com/blog/posts/markdown-to-word/)

I suggest to purchase it driectly from https://www.literatureandlatte.com/scrivener/overview - an AppStore version has some limitations.

For markdown to docx conversion.

1. from terminal with

   brew install pandoc
   

2. from this page.

3. Additionally, install the following pandoc extensions:

   1. pandoc-citeproc: for managing citation. Installation instructions here, or:

      brew install pandoc-citeproc
      

   2. pandoc-eqnos: for enumarating equations. Installation instructions here, or:

      pip install pandoc-fignos
      

The only, and the most difficult to, setup you need is Scrivener.

1. (suggested, but not required): import my Scrivener preferences and theme settings from scrivener settings github folder

2. Compile presets. This is the most important - magic happens here!

   1. from scrivener settings import My Markdown.scrformat.

      1. click File > Compile
      2. drag and drop My Markdown.scrformat into the Formats panel on the right. Choose "My Formats" option

   2. To see it's presets: right-click > Edit

      1. I made a lot of changes to Styles, basing mostly on Scrivomatic MarkDown exports (see: https://github.com/iandol/scrivomatic)

      2. The most important settings are in Processing script. It took me app 30 hours to get there :). When you click Processing > Edit Script you will see sth like that:

         

      3. The script itself is below (for Your Copy-Paste convenience - some fine tuning will be necessary):

         fullfilename=$1
         filename=$(basename "$fullfilename")
         fname="${filename%.*}"
         
         pandoc --filter pandoc-citeproc --filter /Applications/Anaconda/anaconda/bin/pandoc-eqnos --bibliography '/Users/Andy/Dysk Google/Scrivener/setup/! final setup/github/setup/mylibrary.bib' --csl '/Users/Andy/Dysk Google/Scrivener/setup/! final setup/github/setup/ee.csl' $filename -f markdown-auto_identifiers+tex_math_dollars --reference-doc '/Users/Andy/Dysk Google/Scrivener/setup/! final setup/github/setup/MS Word - Cambria.docx' -o $fname.docx
         

   3. IMPORTANT: update paths to Your local settings:

      1. /Applications/Anaconda/anaconda/bin/pandoc-eqnos <<< Your pandas-eqnos installation. Attention: I don't know why, but even if pandoc-eqnos works perfect from Your terminal, here the full path is needed...
      2. /Users/Andy/Dysk Google/Scrivener/setup/! final setup/github/setup/mylibrary.bib - this is a path to Your Google Drive/.../setup/mylibrary.bib file.
      3. /Users/Andy/Dysk Google/Scrivener/setup/! final setup/github/setup/ee.csl - this is a path to Your Google Drive/.../setup/{preferred style sheet} file.
      4. /Users/Andy/Dysk Google/Scrivener/setup/! final setup/github/setup/MS Word - Cambria.docx - this is a path to Your Google Drive/.../setup/{preferred docx style} file.

      That's it! It should work, although it maybe very cumbersome...

1. Create a New Scrivener Project
2. Write sth
3. Compile:
   1. Compile for: MultiMarkdown
   2. Presets: My Markdown

1. Open draft project from main girhub folder
2. Compile
3. And check the output. I put my sample in the output folder.

1. My inspirations:
   1. https://raphaelkabo.com/blog/posts/markdown-to-word/
   2. http://davepwsmith.github.io/academic-scrivener-howto/
   3. https://www.simondcoll.com/references-markdown-zotero/
2. Zotero, Markdown and Pandoc:
   1. All videos on Zotero, Markdown and Pandoc from Nicholas Cifuentes-Goodbody, starting from https://www.youtube.com/watch?v=Gm2MbYB3k4o&list=PLXt-tu7G1H3vlRXLmGyOzeAp7ZKDK0pty&index=1. Great!
3. Scrivener has their own really great tutorials here.

https://github.com/wodecki/writing

Happy writing :)