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My custom second brain setup, part 4: Limitations as strengths

The main limitations (and strengths) of my second brain setup come from Markdown and Git:

There's no great way to handle images, which can be useful for design inspiration (user interfaces, home interior design, etc.). Luckily I rarely need them for notes or reference, so I usually just transcribe the information in text for things like diagrams and visual explanations. If I do need them, I co-locate images in the same folder as the related note, and can preview them in VSCode or with the file explorer.

I don't have a solution for linking between Markdown files. Sometimes I'll just create a link in Markdown with the file name and path, which I'll use to simply search for the file using the command palette in VSCode or the file tree. Having backlinks like Obsidian, Roam, or Dendron offer would be cool, but I'm not sure I want to invest in making custom tooling or finding an extension for this.

My second brain setup doesn't allow for any sharing or collaboration. For me, that's fine and intentional as this is a private workspace for all areas of my life, and I can use other collaboration tools as needed.

Exporting and migrating Markdown files from Readwise and converting voice notes isn't automatic and introduces friction in the CODE workflow. It's not ideal, but I rarely have an urgent need for specific highlights I haven't imported yet that disrupts my work.

Valuable constraints

These limitations are mildly inconvenient, but I'm continuously refining my setup and have full control over it. In fact, I find these limitations worthwhile and even beneficial, as they allow me to keep my setup simple, lightweight, and flexible. Everything is about tradeoffs, and this setup provides immense value to me without requiring much overhead or complexity.

I'm guessing my current setup offers 95% of what I could ever want in my second brain. In fact, the only improvements I have or currently plan to make involve simple adjustments to the folder structures and how I scope/limit my work in progress.


Here's a final overview of my custom second brain setup.


  • Capture highlights and notes from source material (eBooks, articles, videos, podcasts)
  • Organize with PARA method using folders and files
  • Distill using Markdown syntax for progressive summarization
  • Express with new writing and notes for creating other content


  • Kindle (eBook highlights and notes)
  • Readwise Reader (article highlights and notes)
  • Readwise (export highlights and notes to Markdown)
  • VSCode (creating and editing notes)
  • Git Journal (creating and editing notes on mobile)
  • Git (version control)
  • Version control and automatic file backup services (use multiple for redundancy, privacy, and security)


  • Readwise and Readwise Reader: $99/year
  • Cloud storage for file backups: $49/year
  • Everything else is free and open-source
  • This setup saves me countless hours per year, while an hour of consulting covers the annual costs

Second brain resources

There's a growing personal knowledge management community that's focused on building a second brain.

Here are some resources I've gotten a lot of value from: