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Where should your notes live when AI agents need to read them?

Your notes now have a second reader: an AI agent. Four questions to judge a notes app for agents, and how six tools answer them, checked on each vendor's site.

· Updated · 8 min read
A folder of Markdown notes read by three readers: you in the browser, a script in the terminal, and an AI agent
In short
  • Your notes have a new reader: the AI agent you ask to look things up or write things down.
  • Before you hand your notes to one, ask four questions.
  • Where do the files live? Can every device reach them? Can an agent write safely? Can you undo its mistakes?
  • Below: how six popular tools answer, checked at each vendor's own site, and where each one is the right pick.

In 2023, Steph Ango wrote File over app: keep your writing in open files, not locked inside the app that made it. His test looks far ahead. Do you want your writing readable on a computer from the 2060s or 2160s? Then your notes should be readable on a computer from the 1960s.

Today there's a new kind of reader. It's the AI agent you ask to "check my notes on the migration" or "add this to my reading list". Most notes-app comparisons still rank themes and plugins. This one asks what matters once an agent is reading and writing.

Four questions to ask any notes app

1

Where do the files live?

Plain .md files, a database, or someone's cloud. Plain files can be read by any agent, grep, git and your next app. Anything else needs an official interface.

plain files in a folder you control.

2

Can every device reach them?

Agents run in your terminal, on a server, on a schedule at 3 a.m. If notes live on one laptop, every other place needs a copy, and copies drift.

one copy, reachable from anywhere, without a sync bill.

3

Can an agent write safely?

Look for an official MCP server, CLI or API, not only a community plugin. Then ask what happens when you and the agent save at the same time.

edits that can't overwrite yours (see below).

4

Can you undo its mistakes?

Agents make confident mistakes: a wrong edit, a deleted section, a note "tidied" into something wrong. You want to see what changed and roll it back days later.

per-note history, on by default.

How an agent can overwrite your edit

The usual way an agent edits a note is: read it, change it, write the whole file back. If you saved in between, your change is silently gone. The fix is a conditional write: the agent says which version it read, and the save is refused if the note has changed since. (In HTTP, that version is sent in an If-Match header.)

Top: the agent reads version 1, you save version 2, the agent writes the whole file and your change is lost. Bottom: the agent writes only if the note is still version 1, the server refuses with 409, and your change is kept.
If a tool's agent interface can only overwrite whole files, it will eventually overwrite you.

How six notes apps answer the questions

Checked on 30 September 2026 (prices and history limits re-checked on 13 October 2026) at each project's own website, docs or repository. Sources are at the end. Tell us if something has changed.

1 · Plain files 2 · Every device 3 · Official agent access 4 · History Live co-editing
mdnest ✓ ✓one server, any browser ✓MCP, CLI, API ~needs git sync or the git backend ✓
Obsidian ✓ ~paid Sync or DIY ~CLI needs the app open ~7 days on device; more with Sync ✗
SilverBullet ✓ ✓one server, any browser ✗community only ?not documented ?not documented
Logseq ✓DB version in beta ~built-in sync in alpha ✗none official found ?not checked ~alpha
Joplin ~Markdown, via its apps ✓Cloud (paid) or own server ~MCP is off by default, needs the Web Clipper service ✓90 days ?not documented
Notion ✗Notion's cloud ✓Notion's apps ✓hosted MCP ~7 to 90 days by plan ✓

✓ yes~ partly, or with a catch✗ no? not documented or not checked

The details behind every cell
Where the notes live Every device Several people, live Official agent access History
mdnest Plain .md files in folders on your server One self-hosted server, opened in any browser Yes: live co-editing, SSO, per-namespace access MCP server, CLI and REST API Per-note history with compare and restore in the app, once git sync (or the git storage backend) is set up; git sync commits every 10 minutes by default. Off by default
Obsidian Plain .md files in a vault on your device Obsidian Sync (Standard $4 or Plus $8 per user per month, billed yearly) or your own sync No, single-user app CLI, which needs the desktop app running; MCP only through community plugins File recovery snapshots on each device (7 days by default); Sync keeps 1 month (Standard) or 12 months (Plus)
SilverBullet Plain .md files in a folder on your server One self-hosted server, opened in any browser Accounts with per-space read/write; live co-editing not documented MCP only through community projects Not documented; the files work with git
Logseq Markdown files; a new database (SQLite) version is in beta Built-in device sync is part of an alpha feature; the files work with any file sync Real-time collaboration is in alpha No official MCP server found (checked 30 September 2026) Not checked
Joplin Markdown notes that you work with through the Joplin apps Joplin Cloud (paid, from €2.99 a month, no free plan), self-hosted Joplin Server, or Nextcloud, Dropbox or OneDrive Notebook sharing on the Joplin Cloud Pro and Teams plans; live co-editing not documented MCP server built into the desktop app (off by default, runs on the Web Clipper service), plus a Data API Built in, 90 days by default
Notion Notion's cloud Notion's own apps and web; hosted by Notion, no self-hosted option documented Yes, many people on one page at once MCP server hosted by Notion Page history: 7 days (Free), 30 (Plus), 90 (Business)

Which row has plain files, your own server, live co-editing and an official agent interface that doesn't need a desktop app open? Only one, and its history needs one setup step. You'd expect that from a post on mdnest's own site, so here is where the others win.

Which notes app to pick

ObsidianYou write on one machine, want everything offline, and love plugins. Its native apps are fast and its plugin ecosystem is the largest here.
NotionYou want nothing to run. Any number of people can edit a page at once, and Notion hosts its MCP server for you. The catch: notes live in Notion's cloud, and free history is a week.
JoplinYou want mature open-source apps with end-to-end encrypted sync and 90 days of history by default. Joplin Server's license is for personal, non-commercial use.
SilverBulletYou want queries over your pages and Lua scripts next to the text, on your own server.
LogseqYou want an open-source, privacy-first knowledge base with PDF annotation and tasks, in Markdown or Org-mode. Read the beta warning before trying the database version: data loss is possible.
mdnestYou want one copy of your notes that you, your team and your agents all use, from any device. The catch: it's a server, so it doesn't work on a plane.

mdnest's own README says it plainly:

Just want a local vault on one Mac? Obsidian is great.

What mdnest does about each question

The mdnest editor in the browser: a folder tree of Markdown notes on the left and a note with a table and a checklist on the right
The same .md files, opened in the browser. Agents and the CLI work on this exact copy.

mdnest keeps your notes as plain .md files on a machine you own, and opens that one copy from everywhere.

  • 🗂️ One copy, no sync. Every device opens the same server. On a private network like Tailscale, nothing is exposed to the internet (phone guide).
  • 🤖 Agents use the same interfaces you do. The MCP server lets Claude Desktop, Cursor and others search, read and write notes as you, with your permissions. The CLI does the same from any script.
  • 🛡️ Edits that can't overwrite you. edit_note (MCP) and mdnest edit (CLI) change one exact piece of text. They also send the version they read, as in the bottom half of the picture above.
  • ⏪ History per note, once git sync (or the git storage backend) is set up. It's off by default (setup). Then right-click a note → History to preview or compare versions and restore one, and restores are versioned too. Git sync commits every 10 minutes by default, so history is per commit, not per save. An agent's bad edit and your fix in the same 10 minutes become one version.
  • 📂 Your folders stay yours. Point mdnest at an existing folder, even an Obsidian vault, and keep using both.

Want the head-to-head? See mdnest vs Obsidian vs SilverBullet.

A checklist for your own notes app

Copy this and run it against whatever you use today:

  • My notes are plain files in a folder I control.
  • Every device, and every agent, reaches the same copy without a sync bill.
  • Agents use an official interface, and their writes can't overwrite mine.
  • I can see what changed and roll back a single note, days later, and that history is actually switched on.

Editors and agents will change. The file format and where the files live will outlast them. To try the setup described here, the Quick Start gets mdnest running from one Docker Compose file.

Sources

Checked 30 September 2026.

Written by Engineering leader; mdnest is one of his open-source projects.