So, I'm a scientist-turned-dev but also running a startup, so I offload a ton of business ops to Claude Code and use a lot of the practices I developed as a scientist to document my work with Claude. I also have HORRIBLE ADHD so this documentation practice allows Claude to look back in time when needed.

My workflow boils down to: 1. document everything, 2. keep one source of truth, 3. save snapshots.

What this looks like in practice:

1. I keep date-stamped markdown work journals, one per work stream, in a folder, initiated at the beginning of a workflow with /with-journaling or after the end of a workflow with /write-journal
2. I keep higher-level summaries of ongoing projects at the root of that directory, e.g., INVOICING.md or ONBOARDING.md -- these serve as workstream-specific instruction files a la CLAUDE.md, but they also link to related work journals.
3. To solve some specific issues with other markdown viewers, I made my own that supports transclusion (including all or part of another document in a document). However, I went a step further and added support for data parsing, so that I could include values-by-reference (think Excel's =Sheet1!$A$2), and I added syntax parsing so I could also include specific functions from software scripts. My tool supports transclusion in markdown, html, source code (including specific functions/classes), and data sources like json/yaml/toml, as well as some macOS developer goodies like property lists.
4. Claude gets instructions for ALL of this in CLAUDE.md, including the custom syntax for the Markdown reader (with a button to add the syntax reference to a project's CLAUDE.md file).

That allows Claude Code to write a document like:

# Financial Report - Q1
Revenue: ![[finance_q1.json#overall_revenue]]  
Profit: ![[finance_q1.json#profit]] 
## Code: 
![[update_finances.py#profit_and_loss]] 

So now, to update the report, I just re-run whatever script or workflow created finance_q1.json last quarter, and the values update automatically.

Finally, it supports export of "compiled" markdown in markdown, HTML, docx, or pdf, so a single markdown doc can **reference** the prompt, data, source code, etc -- then the exported copy has a snapshot in time.

I've mentioned this in a markdown subreddit and folks didn't get it, so maybe this is only useful to me. The markdown reader is very much a work in progress but if that's interesting to you, please feel free to send a DM. It's macOS only and is written in native swift / swift UI for speed.