Emacs with org mode, helm, and projectile as a starting point would hit all of your asks (although org syntax has differences from markdown, it's still quite intuitive).

I use org mode for: my tasks (gtd style), food log (using org columns), notes (easy export to any other format), habits. Alongside beorg for iOS for quick capturing on the go, I cannot imagine I would be any happier elsewhere.

Same here, org-mode is going nowhere, it's one of those things that just works. From wikis, todos, document authoring, agendas, code notebook, ... On mobile, there's a few options, I made one, a web app called filestash: https://demo.filestash.app/s/hn . It has a lot of the org mode candies: agenda, todos, and the real org-mode exporters: HTML, PDF, Markdown, TXT, Latex, iCal, ODT and even beamer

And literate programming too with Babel!

Org-mode, Helm, and Projectile as a "starting point," is pretty steep. Org alone probably covers the bases.

I’ve been using Quiver for a few years, and love it. Totally replaced Evernote for me. Not sure if they have syntax highlighting though — there is a “code” cell, but I haven’t used it.

http://happenapps.com

I also use Quiver, I just wish I could have my notes on my Android phone. No one has yet brought together quite everything -- there's always tradeoffs between the various note apps, even though there doesn't have to be.

Perhaps Boostnote? https://boostnote.io/

Been using it for a work journal for a while, and it's pretty reasonable. I used to use RedNotebook before that, but I finally got fed up with the lack of Markdown syntax.

Bootsnote and Joplin works great for notes, but Joplin was less than ideal last time I checked. Hugo is really the tool I think will get me closest to what I'm looking for.

Could you expand on why it's less than ideal? I'm considering moving, so far it looks good.

Because the way it backs up your files isn't symbolic with the file system. The Hugo template I'm working on does this for you. Their are some minor annoyances, but it is the most powerful tool that I know of to get setup quickly. Wish there was some more standardization around Templates though, and the ability to do custom output templates for section lists that create paginated sections of content based on grouping, custom parameters and more. Best thing is it is all managed in a logical folder (section) and file (page) hierarchy and so far I've just about got a infinitely nested template setup with paginated sections and pages throughout, with the ability to add custom paginated sections using specific layouts for custom sections.

It's a bit less than ideal, overall. I would like to see you be able to assign a custom output format, so for each index and section kinds it would be nice to automatically create paginated sections that you want for specific layouts. I've tried this and it only sort of works, but expects them to be the pages as your lists.html or index.html, and can't paginate a path.

Also, built in client-side search. I'm working on Mermaid.js, Chart.js and Reveal.js short-code integration next.

zim? http://zim-wiki.org/ with the "source view" plugin?

It sounds like a private git repo would suite you fine. You'll only need an internet connection to update when you've made changes on a different device.

The interface is that of a notes app rather than a board like Notion, but I just started using Joplin for this and have been really liking it so far.

I use Quiver for this purpose. http://happenapps.com/

Seconded that org-mode sounds like a good place to start.