Looking for advice about using Scrivener for writing a scientific PhD thesis

Scrivener Markdown & LaTeX
4

Answering my own question here after a whole day of googling and experimenting:

I’ve created my own Pandoc-style format.
For figures, they are in a directory on the same level as my *.scriv, *.md files. I’m using the Pandoc and pandoc-fignos format to put them into the document, e.g.:

![Caption](figures/my_fig.png){#fig:fig_id}

and referencing it using clever referencing (needed the cleveref.sty package installed), like +@fig:fig_id.

Equations were similar, using pandoc-eqnos, so in the document:

 $$ y = mx + c $$ {#eq:eq_id}

referenced like +@eq:eq_id.

I’ve put my bibliography in the same directory, and added a script to do the Pandoc md -> pdf conversion. The only things I’ve found were that unlike the command line, I needed to put the full pathnames for pandoc-citeproc and pandoc-xnox.
I also had to add a --pdf-engine option with the full path of pdflatex.

I wanted to avoid the Scrivomatic approach as it seems incredibly complicated and I don’t really have the time to work out what it’s doing. This seems to be working OK so far.