My Obsidian Vault Made 21 Permanent Notes in 3.5 Years, So I Redesigned It

What I use Obsidian for, and what went wrong

I adopted Obsidian to build knowledge for myself.

• Take in lots of personal knowledge through all kinds of methods, and turn it, one by one, into Permanent Notes: finished pieces of my own wisdom
• Build up those Permanent Notes and hand them down as a body of explicit knowledge for those who come after me

Above all, I believed Obsidian's job was to keep producing solid Permanent Notes out of the collective knowledge I'd gathered. Or so I thought.

But the Permanent Notes just weren't growing. At all. It was a disaster. Obsidian had been reduced to a plain old diary.

I'd also assumed, on my own, that the reason Permanent Notes weren't growing was that "the notes aren't connected to each other." But when I dug into the vault with Claude Code's help, the cause turned out to be somewhere else. What was missing was a step where I write down my own claims, and the time to actually do it every day.

21 notes in three and a half years, zero in the last 90 days

What I want from Obsidian is to keep producing solid Permanent Notes, one at a time, from the knowledge I collect. Each note is meant to be about the size of an index card, something my future self or people coming after me can reuse.

When I actually counted, here's what I found:

Aspect	Actual
Number of Permanent Notes	21 (over roughly three and a half years since February 2023)
Last Permanent Note update	August 2025. Zero in the last 90 days
Inflow over the last 90 days	79 Clippings, 142 AI conversations and summaries, 1 Fleeting Note, 6 Inbox

What comes in is other people's writing and AI's writing. There are almost none of my own insights in Obsidian. My Daily Note has a section called "Thoughts in my mind," but I've kept it empty the whole time. Meanwhile, the KPI section where I log sleep hours and running distance gets filled in every day. The sections measured in numbers stuck; the free-writing section didn't.

Adding links didn't grow my Permanent Notes

In March 2026, I built a Claude skill, /zettelkasten, that automatically adds tags and links to Fleeting Notes, and ran it on 99 of 281 notes. Each note also got a list of related notes appended at the end. That was seven months ago. Not a single note has been promoted since.

The reason was obvious the moment I opened the Fleeting Notes. Most of them are just a title. Terrible. One note I wrote in February 2024, "Transcribing from memos is what really matters, so set up a time to transcribe," had an empty body too. I'd written down the answer myself two years earlier, then left it there without ever making time to transcribe. Truly terrible.

The notes that did have a body had problems too. "Architecture is just one hypothesis" still contained an AI reply, "Thank you for your understanding," verbatim. Worse and worse. Before I could even connect anything, the things I'd be connecting weren't in my own words.

The bar of "unshakable intelligence" was what kept me from writing

I had selfishly defined a Permanent Note as "definitive, unshakable intelligence." With that bar, the day I could call a note finished was never going to come.

My existing 適応度関数.md (fitness function) note was a textbook example. The title says "fitness" (適応度), yet the body says "goodness of fit" (適合度) nine times, for some mysterious reason. The title and the content don't even fit each other. It cited no sources, and the second half just restated the first. I hadn't touched it since May 2024. The note that was supposed to be unshakable had, in reality, become a note nobody revisits, or even looks at.

So I lowered the bar to "correct as of the verification date, and revisable later," and set six criteria:

• The title is a single-sentence claim
• The body is in my own words and covers the claim, the reasoning, a concrete example, and the scope (around 200–400 Japanese characters)
• There's at least one piece of supporting evidence
• The verification result and the verification date are recorded
• The note makes sense when read on its own
• Its visibility (visibility) is set

I added the last one to check whether the content trips any confidentiality concerns: words meant only for me should be explicitly marked as never to be seen by anyone else. If you're going to let arbitrary readers see your notes, you need to decide, note by note, whether each one is okay to publish.

I write the claims; AI handles verification

I chose who writes the body from three options. Letting AI write it and just approving would be the fastest and produce the most notes. But that's the same as building one more "storehouse of AI-written text," just like what I already had. I chose the option where I write the claims and reasoning myself. Obviously. Claude Code can't be expected to understand what's obvious to me, but I think I should be grateful that it catches the biases humans like me let slip by.

Since these are my claims and my own knowledge in the first place, I narrowed the AI's role down to the minimum:

• Check factual statements against primary sources
• Present the strongest counterargument to the claim
• Suggest related notes

I don't let the AI rewrite the body. It only points out what to fix; I'm the one who rewrites. With this setup, about 100 notes a year is the ceiling, but only knowledge I can explain myself gets properly kept.

Keep the writing entirely inside Obsidian

The first system that came out of this was one Claude Code proposed to suit itself: a flow driven by conversation with Claude Code. It asks me questions, I answer, and I get verification results on the spot. It's comfortable enough when you use it, but you can't run it from inside Obsidian. That didn't match my premise: right after reviewing my Daily Note, spend 15 minutes writing, right there in Obsidian.

Breaking the process into steps, the only part of this flow that actually needs AI is verification. The questions are the same every time, so I realized I could just put them in a template. So I moved the writing into Obsidian and turned verification into a batch job that runs in the background.

My daily flow looks like this:

1. Look at the "Today's one" section I newly added to my Daily Note. It lists notes awaiting review of their verification results, drafts in progress, and Permanent Note candidates.
2. If anything is awaiting review, read that note's "Verification" section. If something needs fixing, fix the body, and for each counterargument, check either "reflected in scope" or "not reflected."
3. If nothing is awaiting review, pick one candidate and write a new note from the Permanent Note template.

In the template, right after the field for the claim, I put three questions:

• Why do I think so?
• What experience of mine led me to this, or matched it?
• In what cases does it not apply?

For verification, I run the following command in the vault folder. It inspects all drafts at once and writes the results into each note's "Verification" section.

claude -p "/zettelkasten verify --all" --allowedTools "Read,Glob,Grep,Edit,Write,WebSearch,WebFetch"

Verification takes time, so I stop working for the moment, and the back-and-forth in the moment goes away. In exchange, writing can continue even when the AI isn't running, and I can write from my iPhone or iPad. I set it up so it doesn't depend on where I am or what device I'm on.

For Permanent Note candidates, besides Fleeting Notes and the Inbox, I also included the directory where I save my AI conversations. I'm starting to feel this is the downside of splitting things into too many directories. If you're just starting out with Obsidian, I recommend keeping directories to a minimum. A single inbox is the easiest place to operate for stashing information and dropping insights.

The first note was carved out of a published article

Alongside writing new Permanent Notes from candidates, I decided to also carve them out of articles I've already published. Those articles are already in my own words. They're backed by research and already in publishable shape, so they become finished notes much faster than writing from a candidate from scratch.

I made the very first one from my Zenn article on Copier. Verification confirmed two points. First, a repository created from a GitHub template can't merge updates. Second, Copier can pull updates into a project after it has been generated.

Two counterarguments came back. One was that the update mechanism itself takes effort to maintain. I reflected that by adding "when there are few downstream projects" to the scope. The other pointed out that the update mechanism hasn't yet been tested with a major change. I finalized that one as-is, and I'll revise the note after trying updates with TypeScript 7.1 or 7.2. Being able to assume revision is thanks to lowering the bar. I'm grateful for that. There are times I just can't help wanting perfection, and at times like that, it becomes a shackle.

What I dropped, and what I haven't confirmed yet

There are two things I decided not to do:

1. Processing the remaining 182 Fleeting Notes. Two-year-old title-only memos can't be decoded even by the person who wrote them. I'll start from new insights and only pick up old memos when they become relevant.
2. Consolidating directories. I do think I split things too much, but stages can be managed with a property called status, so I leaned on Dataview to run things without moving any folders.

There are also things I haven't confirmed yet. The template and the list are brand new, and I haven't run the whole thing end to end inside Obsidian. Whether everything from entering a claim, to recording the seed, to moving it into a folder works as expected will take a few days of testing. I've also only tried the batch verification with zero drafts. I plan to set up scheduled runs myself once the system has been running for a while.

I'll judge whether this works by whether I have at least 8 verified Permanent Notes four weeks from now. By then, I should be able to share the verification results too.