Most advice about taking notes falls apart at the same spot. Saving something is easy — you drop a link, a voice memo, or a half-formed thought into a folder and move on. Going back later to make sense of it is the hard part: reading it again, pulling out what matters, filing it where you’ll find it, and connecting it to what you already know. That second step is the one almost nobody does, and it’s where most note-taking habits quietly fall apart.

My fix is a pair of tools. Obsidian is where my notes live — a simple app that stores everything as plain text files on my computer. Claude is the assistant that keeps those files in order, like a librarian who reshelves and cross-references everything I bring in. (For how I use Claude beyond my notes, see How I Use Claude.)

I’ve been running this particular setup since the middle of June. Long enough to know what works, and long enough to have thrown a few things away.

Two vaults, on purpose

I keep work and personal separate — two vaults that never mix. The work one is large and project-shaped, organized around what’s active and what’s finished. This article is about the other one, which I called Time: the personal vault, for faith, technical curiosity, DIY, and anything else worth keeping.

The split matters more than it sounds. A vault organized around projects wants to know what’s due. A vault organized around interests doesn’t have deadlines at all — a note about chainmail weaves isn’t late. Trying to run both through one structure made both worse, so I stopped.

What I actually built

I started nearly from scratch and asked Claude to lay out a structure. What we landed on is deliberately dull: a handful of numbered top-level folders, nothing nested deeper than it needs to be.

00 Inbox      capture zone — anything unsorted lands here
10 Faith
20 Technical
30 DIY
40 Notes      catch-all for things that don't fit yet
50 Writing    drafts and finished articles
_Indexes      the maps that actually organize things
_Templates
_Attachments
_Meta         conventions, backup script, notes about the vault itself

The numbers exist only to control sort order. That’s it. Six weeks in I haven’t needed a seventh folder, and I take that as a good sign.

The important part isn’t the folders — it’s that folders aren’t how anything is organized. A note belongs to a subject by being linked from that subject’s map, not by where it sits on disk. Those maps live in _Indexes, one per domain, and they’re hand-curated: I decide what goes on them. Nothing is auto-generated, because an automatic index lists everything and tells you nothing.

Every note carries a few labels at the top — title, date, tags, and a status: seedling, growing, or evergreen. A seedling is a thought I had once. An evergreen is something I’d stand behind. Most notes never make the trip, and that’s fine.

The one file that makes it work

The single most useful thing in this vault isn’t a note. It’s a file called CLAUDE.md sitting at the root, which Claude reads every time we start working.

It says who I am, what each folder is for, how notes should be named, what the tags mean, and — most importantly — what not to do. Without it every session started from zero and the structure drifted a little each time. With it, the vault stays consistent whether I touched it yesterday or three weeks ago.

Two companion files do the rest. Conventions.md holds the same information written for a human, so I can read my own rules without parsing instructions meant for a machine. And About Jeff.md describes who I am and how I write — which is why drafts come back sounding like me instead of like a press release.

The guardrails matter more than the features

The rules in that file are mostly restrictions, and that’s deliberate.

Claude has full write access to the whole vault. What it doesn’t have is permission to be clever with it. It never deletes, overwrites, or renames an existing note without showing me exactly what will change and waiting for an answer. When it isn’t sure where something belongs it goes to 00 Inbox rather than guessing. It doesn’t reorganize folders on its own initiative.

That restraint is the whole reason I trust it with the vault. An assistant that occasionally tidies things away is worse than no assistant, because you stop being able to believe what you’re looking at.

There’s one hard-won rule in there too. Claude works partly through a Linux sandbox, and early on it tried to run git — the version-control system that keeps a full history of every change — from inside that sandbox. Git needs to create and delete small lock files as it works, the sandbox wouldn’t allow it, and the history ended up in a broken state. So the rule now reads: git runs natively on Windows, never through the sandbox. The kind of thing you only learn by breaking it once.

The weekly rhythm

Day to day, capture is deliberately stupid. Something interesting turns up, it goes in the Inbox, I don’t think about where it belongs. Thinking about filing at capture time is how you stop capturing.

Once a week, about fifteen minutes:

  1. Empty the Inbox. Claude proposes a title, folder, labels, and which map to link each note from — as a list, for me to approve. Nothing moves until I say so.
  2. Promote a couple of notes. Anything that’s genuinely grown gets bumped up a status level.
  3. Run the backup. A script snapshots the whole vault, git history included, to a different physical drive.

That review is generated for me now — a scheduled job writes a dated checklist every week listing exactly what’s sitting in the Inbox and which notes look ready for promotion. I open it and work down the list.

What changed along the way

The setup I’ve described isn’t what I started with. A few things worth reporting.

The backup script broke on day one. It tried to zip the vault while Obsidian had files open, and failed on the locked ones. It now copies everything to a staging folder first, then zips that. Boring fix — but the first version would have quietly produced bad backups, which is worse than no backups.

I got the tags wrong and had to go back. Clipped web articles were tagged clippings. The convention said source. A small inconsistency, but exactly the kind that compounds; a year of it and searches stop working.

One note turned into forty in an afternoon. I inherited my mother’s gemstone collection, started a note about a single stone, and by the end of the day there was a material note per gem type, an inventory with ID numbers, and a triage checklist for sorting the unlabeled ones. That’s the part I couldn’t have done alone at that speed — not because the writing is hard, but because staying consistent across forty notes is.

Some tools outgrew the vault entirely. I’d built bench calculators — ring blank lengths, bezel strips, metal weights — as live widgets inside a note. Useful, but only at my desk. They became a standalone web app that installs on a phone and works with no signal, and last week it moved onto my own website where anyone can use it. It started life as a note.

And the vault now feeds this site. There’s a folder called To Publish. A draft goes in, a script converts it from vault conventions to web format, and it goes live. This article went through it.

Is it working?

Enough that I want to keep making it better rather than start over.

Ninety-three notes. The Inbox is empty, which is the metric I actually care about — it means the weekly review is happening rather than being something I intend to do. The links between notes are real, and clicking one usually takes me somewhere worth going.

But a third of those notes are still seedlings and most of them will stay that way. And I over-built in places: I made four HTML dashboards for viewing the vault at a glance, and I use one of them regularly. The other three were interesting to build.

The thing I’d tell anyone trying this: the structure is not the hard part, and it’s the part you’ll be tempted to keep fiddling with. Capture has to stay frictionless and review has to stay short. Everything else is decoration. I have the decoration to prove it.

  • obsidian
  • claude
  • note-taking