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💡 The Big Idea: A Healthy Vault Isn’t a Tidy One; It’s One That Actually Helps You Think

When did you last open a note in your vault just to think? Not to organize, not to file, not to tag. When’s the last time your vault surprised you with a connection you’d forgotten you made?

If you’re drawing a blank, it may be a sign that your Obsidian vault is in need of some TLC.

It happens. Most people eventually fall into the same trap when it comes to their PKM system: they assume their vault is underperforming because something’s missing. The right plugin, the right folder structure, the right template. So they go find it, install it, tweak it.

The vault gets cleaner, more organized, and somehow even less useful.

A tidy vault is not a signal of strength. In fact, often it’s a warning sign.

A pristine Obsidian vault usually means you’re maintaining it instead of using it. You’re collecting articles for future you to read instead of capturing what actually makes you think right now.

Here’s the truth: A vault that looks immaculate in a screenshot probably isn’t doing much heavy lifting.

But if we can’t judge how healthy our vault is based on how organized it is, what metrics can we use to get a more accurate picture of our vault health?

I’ve spent the last few weeks thinking about that. In this newsletter, I want to share what I came up with.

Orphan Notes

Orphan notes are notes with no links in or out. These notes can accumulate as dead weight in your vault, floating in isolation with no connection to anything else. If you have a lot of orphan notes, it’s evidence that your vault is a pile of files, not a true knowledge system.

Think about how ideas actually arrive in your PKM system. Something resonates. You’re reading an article or listening to a conversation, and a thought catches you. You don’t know exactly where it fits yet; you just know it matters. So you capture it. That’s the whole point. A vault that only contains notes you already fully understood isn’t a thinking tool; it’s a filing cabinet for things you already know.

Some of those orphaned notes will link up eventually, once you write the surrounding context. Some are pure reference – a book summary, a technical definition – that was never meant to link anywhere. It just needed to exist. Reference material doesn’t have to be woven into a web to be useful. Sometimes a note just needs to be findable when you go looking.

The best captures come from following curiosity, not from having a plan. Orphans are proof you captured what resonated instead of just what seemed “important.” That’s the right instinct.

Your orphan notes are often seeds. Some just haven’t germinated yet. That’s not necessarily a failure state, but if those seeds never mature and the orphan notes accumulate, it could be a sign that they’re not developing properly (you’re not getting full value out of your notes and ideas).

Stale Notes

Stale notes are notes you haven’t touched in six months or more. On the surface, a pile of them can look like your vault is rotting through neglect. And it can be an indication of things you captured and never went back to, dead ideas collecting dust.

But stale notes can also be notes that finished their job. Think about what you hire a book note to do. You read the book, you capture the ideas that mattered to you, and then… you’re done. The note sits there. You pull it up when you’re writing something adjacent, or when someone asks you about the topic, or when you’re working through a problem and remember something relevant. The rest of the time it just exists, quietly waiting to be opened again.

That’s not neglect. In fact, a lot of finished notes are going to hit that threshold – and that’s fine.

The only time stale notes should actually concern you is if you’re finding stale notes on topics you’re actively thinking about. If there’s a note titled “My Business Strategy” and you haven’t opened it since last year but it’s supposed to be a living document, that’s a different thing. But that’s about the type of note, not the date alone. Stale usually means done – and done is often good.

Broken Links

Broken links are links that point to notes that don’t exist yet. They look like errors – typos, or things you meant to build and never got around to, and can be a sign that you’re abandoning your notes before they’re done.

But in Obsidian, an unresolved link is often an intention, not a mistake. Frequently it’s a note you linked to deliberately before you wrote it. You didn’t get distracted; you were thinking ahead – you knew the concept deserved its own note, you created the connection while the thought was fresh, and the destination will come when you have something worth saying.

That’s completely fine. The idea arrived before the articulation. That’s how thinking works.

Some broken links, though, are typos, and those are worth a few minutes to fix. If you wrote [[Fleeting Notes]] in one place and [[Fleting Notes]] somewhere else, clean it up when you see it. It’ll be done in five minutes, and it’ll make working with your notes easier in the future.

But if you’ve got [[On asymmetric bets in career planning]] sitting as an unresolved link, that’s not a bug. That’s future-you dropping a thought marker.

So before you delete a broken link, ask whether it’s a typo or a breadcrumb. The answer changes everything.

New Notes Per Week

New notes per week is a way to measure your capture cadence (how many notes you’ve added recently). It’s easy to read this as a productivity quota or a number you’re supposed to hit. But if you’re not careful, it can become a judgment on whether you’re using your system enough, whether you’re thinking enough, whether you’re “doing PKM right.”

But it can also just be a mirror for how busy you were. A slow capture week isn’t a moral failing. If you spent the month working on a single deep project, or reading slowly, or traveling, or just living life without your laptop open all the time – your note count will reflect that. And it should! The vault is a record of where your attention went, and your attention doesn’t have to be in the vault to be well-spent.

The whole point is to capture what resonates. These are the things that genuinely pique your interest, not a quota of ideas you’re supposed to be generating. If you start creating notes to fill the meter, those notes are hollow. You’ve gamed the metric at the expense of the point.

But if you go long enough without capturing things that are interesting, it will inevitably lead to you feeling stressed when you sit down to create. You need a steady inflow of new ideas if you want to keep the Creativity Flywheel spinning.

So pay attention to your capture rate, but be honest about the job you’re hiring the capture rate to do. If it’s measuring your output against some imaginary standard, fire it from that job. Its actual job is telling you where your curiosity has been living lately. Low this month? You probably had a full life. High? You probably went deep on something interesting. But understand that a series of low months may make it harder to create consistently.

Average Links Per Note

Okay. Here’s where I stop asking you to relax.

Everything above – orphans, stale notes, broken links, a quiet capture week – almost never means what it looks like it means. But this metric is different. This is the one worth protecting.

Average links per note is the signal. Links are the whole game. They’re what turns Obsidian from a searchable folder of documents into something that actually thinks alongside you. When notes connect, ideas compound. You start noticing patterns you didn’t plan for – a thing you captured eight months ago in a completely different context suddenly becomes relevant to what you’re working on today. That only happens when the notes are talking to each other.

When this number is low, your notes aren’t talking. You’ve got an archive full of documents, not a vault full of ideas.

The reason this number is worth paying attention to is that it isn’t a quick fix. A low number of links limits the usefulness of your connected notes, but links without meaning are even worse. You can’t just have Claude create a bunch of links for you to fix this. You need to add them manually and intentionally. Your links need to mean something.

So the solution is simple, but not necessarily easy: start adding links consistently as part of a note-making practice. If you’re looking for a place to start, pick five notes you’ve written in the last 90 days. Open each one and ask yourself: “Does this note or idea connect to something else in my vault?” If so, update the note and add the links.

That’s it! Easy. Don’t try to tackle your entire vault, just those five notes. One connection per note is enough to start. The habit builds from there.

Second-Tier Metrics

Those are the five metrics I’d really pay attention to, but there are a handful of others that can be useful:

• Hollow notes (under ~30 words): Almost always seeds or stubs. Leave them alone until you have more to say. Hollow now doesn’t mean hollow forever.
• Unfiled notes in the vault root: If you’re using the root as an inbox, this is the feature working, not a bug. Just make sure things flow out of it occasionally.
• Sparse folders (fewer than 3 notes): Mostly a non-issue, but can be a sign of over-engineered organizational structure.
• Orphaned attachments: This one is worth an occasional cleanup pass. Images and PDFs with no associated note clutter without contributing. A quick sweep every few months is enough.
• Single-use tags: Mostly harmless, but can be an indication of a lack of clarity in your tagging structure. You don’t need to aggressively prune tags used once. They’re probably fine.
• Daily note cadence: Daily notes are an indication of a lived-in vault, but they’re a rhythm, not a report card. Gaps are normal. Life isn’t linear, and your daily notes don’t have to be either.
• Community plugin count: This is the one place where less is genuinely healthier. More plugins means more cognitive overhead, more potential conflicts, and more time maintaining the system instead of using it. If you haven’t used it in six months, uninstall it. The vault breathes better when it's lighter.

I Built a Tool to Help You Diagnose Your Vault Health

The vibe-coding continues 😂 This time, I built a tool to help you diagnose your vault health. Here’s how it works:

First, access the tool at vaulthealth.practicalpkm.com and click the button to get started:

The next step is to copy a DataviewJS code snippet and paste it into a blank note in your vault. Note: this does require you to have the Dataview plugin installed.

Once you paste the snippet in Obsidian, you can deselect any archive folders that happen to be in your vault. This controls which notes get analyzed and makes sure that the report is accurate. Once you have the folders selected, click the button to analyze your notes.

At the bottom of the code block, you’ll get some numbers. This is the raw data, but it’s not that useful yet, so click the button at the bottom to copy the plain text results for the web tool to analyze.

Back at the website, you can paste that code into the bottom box and click the button to get a detailed report of your vault health.

The report will give you an overall score, a breakdown of each of the five major metric areas, as well as all of the secondary metrics (which are still weighted, but not as heavily).

The goal is to give you an accurate diagnosis of what’s going on in your vault so you can make sure your PKM system is performing well.

The Bottom Line: Give Your Vault a Checkup

The health check doesn’t exist to tell you your vault is broken. It exists to show you what your vault actually looks like – how you actually use it, where your attention actually goes, what your thinking has been. A red number isn’t necessarily something that’s broken, but it might be something worth paying attention to.

Run the check. Then read your numbers with this in hand – not as a neat freak chasing green, but as a thinking person looking for the one place real leverage actually lives.

It’s free, takes about two minutes, and you get to pick which folders to include: vaulthealth.practicalpkm.com​

— Mike