My Vault Hit 367 Pages — And I Couldn’t See the Forest for the Trees

My Vault Hit 367 Pages — And I Couldn’t See the Forest for the Trees

A few weeks ago I realised something uncomfortable: my Obsidian vault had grown to over 367 pages, and I had no idea what was actually in it anymore. I knew individual pages existed — I wrote most of them — but the overall shape, the clusters, the orphaned notes that never got linked to anything… that was invisible to me. It felt like owning a library where you remember every book you put on the shelf, but you’ve lost the catalogue.

This vault started as a simple second brain experiment. A place to dump ideas, log daily Hermes sessions, and keep track of my homelab config. But somewhere between the 100th and 200th page, it turned into something bigger. Wiki pages about AI tools, nightly synthesis reports, CRM entries for people I met, system documentation, journal entries, inbox clippings — it all accumulated. And the bigger it got, the harder it became to discover what I already knew.

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The Discovery Problem

Here’s the thing about a second brain: it only works if you can retrieve what you put in. I had pages about MCP protocol changes, Hermes agent upgrades, DNS server config, battery storage research, and a dozen AI tool comparisons. But when I needed that one page about the Technitium DNS setup I wrote three months ago, I had to search blindly or scroll through the file tree. The vault had become a write-only archive.

That’s when I stumbled on the Obsidian Second Brain CLI skill by Eugeni Ghelbur — a 45-command cross-CLI tool that works in Hermes, Claude Code, OpenCode, and Gemini CLI. One command in particular caught my attention: /obsidian-visualize. It generates a visual canvas of your vault — hub nodes centred, colour-coded by type, orphaned notes highlighted in red. Exactly what I needed.

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What I Learned From the Visual Canvas

Running the visualizer on my vault revealed three things I hadn’t noticed:

• Clusters I didn’t know existed: My Hermes agent pages formed a dense, well-connected cluster. But my AI tools pages were scattered — no links between them, even though they’re about the same topic.
• Orphaned notes: About 15 pages had zero incoming links. Ideas I captured once and never connected to anything. Some were genuinely useful — they just needed a few [[wikilinks]] to become findable.
• A missing index: The vault had no central hub page that linked to the major topic areas. Everything was organised by folder, but folders don’t show relationships.

I spent an afternoon fixing the orphans and adding cross-links between the AI tools pages. The vault feels different now — more like a connected web, less like a pile of files.

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Why This Matters for Your Own Vault

If you’re running a second brain — whether in Obsidian, Notion, or plain markdown files — I’d bet you have the same problem. You write more than you retrieve. The vault grows, but the connections don’t keep up. A visual canvas tool, or even a simple backlink audit every few weeks, can make a huge difference.

I installed the Obsidian Second Brain CLI skill in Hermes and added /obsidian-visualize to my weekly vault maintenance routine. It takes 30 seconds to run and shows me exactly what I need to fix. If you use Obsidian, I’d recommend giving it a try — or at least running a backlink check on your own vault. You might be surprised what you find.

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Over to You

How big is your second brain? And do you actually know what’s in it? Drop a comment below — I’m curious if I’m the only one who let their vault grow wild before taming it.