As a person who builds software, a decent chunk of the content I would like to gather in a second brain or zettelkasten system is about code (in multiple languages). But the systems I see popping up here are 95% text focused. They typically let you write code snippets, but to run them, or see anything about how they interact, you have to copy them somewhere else and create a suitable environment in which to run them.
The best solution I've managed to set up so far is emacs org-roam set up alongside a set of toy projects, where note files can link to specific lines (it's brittle) in files in those toy projects. I found org-babel too cumbersome to configure, and too hard to deal with code snippets that depend on libraries.
But I hope someone builds something like a zettlekasten + repl.it mashup which removes the setup burden, such that it can be fast and easy to take notes which include a snippet of code from a paper, without having to stop to create a project with a list of dependencies, a build script, etc.