[KyleOS]

Have you ever considered Kyso (https://kyso.io) (disclaimer - I'm a co-founder)? I could be way off, and it would be a corner case for us right now, but it seems we'd fit all your requirements:

* We sit on top of git, which remains the single source of truth for your code - versioning, reproducibility, etc.

* Python & R notebooks or simple markdown (also on the web app itself).

* Show or hide code.

* Simple links for sharing reports.

* Tagging.

* Comprehensive search - by tag, keyword and content (soon).

Would be really interesting to hear your thoughts on the fit.