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What is NoteDiscovery?
NoteDiscovery is a self-hosted Markdown knowledge base: you run it on your own server, and your notes stay there as plain Markdown files in folders. It is aimed at people who want note-taking control without a hosted subscription — developers, researchers, writers, and privacy-conscious teams — and it combines standard note features (search, tags, templates, outline navigation, graph view, themes) with extras like LaTeX rendering, Mermaid diagrams, an in-browser drawing editor, code highlighting, and a plugin system.
Its distinguishing feature is AI assistant integration through MCP, which lets tools such as Claude and Cursor search, create, and organize your notes. If you already use an AI coding assistant and want it to read your notes, that is the main reason to pick this over a plain Markdown folder. If you just want simple local notes, the AI layer is optional weight.
Who it fits
- Privacy-first users: notes never leave your server, and there is no vendor lock-in because storage is plain Markdown.
- Technical note-takers: LaTeX, Mermaid, code highlighting, and a plugin system suit engineering and scientific notes.
- AI-assisted workflows: MCP integration connects your knowledge base to Claude or Cursor.
- Multi-device users: responsive design and PWA installation cover desktop, tablet, and mobile.
Trade-offs to weigh
- You maintain it. Self-hosting means running Docker and handling your own backups and updates.
- Sync is your problem. Plain files make backups easy, but cross-device syncing depends on your own setup.
- Feature depth varies. Drawing, templates, and graph view are present, but a mature hosted tool may go deeper in specific areas.
Next step
Try the live demo first — it resets daily, so treat it as a feel test rather than a real workspace. If the interface and graph view click for you, deploy your own instance with Docker and import a small folder of existing Markdown notes to confirm search and tags behave as expected. For alternatives, see Obsidian for local-first Markdown notes and Logseq for outliner-style knowledge management.
How do I install NoteDiscovery on my own server?
Install NoteDiscovery by running its Docker image on your server, then opening the web interface in a browser. The project is designed for quick self-hosting: the official page describes setup as "run with Docker in seconds" and offers a one-click deployment option alongside the source on GitHub. Because notes are stored as plain Markdown files in folders, you keep direct access to your data and can back it up with normal file tools.
H3 Practical steps
- Confirm Docker (and Docker Compose, if you prefer a compose file) is installed on the server.
- Pull or build the NoteDiscovery image and start a container, mapping a port for web access and a volume for your notes directory.
- Open the mapped address, create your first note, and verify that a
.mdfile appears in the mounted folder. - If you want AI assistance, connect an MCP-compatible client such as Claude or Cursor to the running instance.
- Put the service behind HTTPS (reverse proxy) before exposing it beyond your local network, and schedule backups of the notes volume.
H3 What to check before you start
- Storage location: Decide where the Markdown folder lives; this is your backup unit.
- Access model: Local-only, LAN, or public. Public access needs TLS and authentication in front of the app.
- AI integration: MCP is optional; skip it if you don't want external AI tools reading your notes.
- Extras: LaTeX/MathJax, Mermaid diagrams, drawing editor, tags, templates, graph view and PWA installation are built in, so no extra services are required for those.
For exact commands and current container details, use the project's own instructions at NoteDiscovery or its GitHub repository. If you already run other self-hosted tools, compare deployment patterns with Obsidian (local-first, not server-hosted) to decide whether a server-based knowledge base fits your workflow.
How does NoteDiscovery integrate with Claude and Cursor through MCP?
NoteDiscovery connects to Claude and Cursor through MCP (Model Context Protocol), an open standard that lets AI tools talk to external data sources. Per the site's own description, the integration lets those assistants "search, create, and organize your notes" in your NoteDiscovery instance. In practice, that means you can ask your AI assistant a question and have it pull relevant notes, or instruct it to draft and file a new note, without copying text in and out of a browser tab.
NoteDiscovery
What the integration actually covers
The page frames MCP as one of several built-in capabilities rather than a separate product, alongside Markdown storage, wikilinks, graph view, LaTeX, Mermaid and a drawing editor. The stated scope is three actions: search, create, organize. That is a narrower, more predictable surface than a general "AI writes your whole vault" pitch — useful if you want an assistant to retrieve context or capture a quick note, and less useful if you expect it to restructure your entire knowledge base unattended.
What it does not tell you
The page doesn't specify the transport (local stdio vs. remote HTTP), the exact configuration steps, authentication, or whether write access is scoped or all-or-nothing. Those details matter before you point an assistant at a folder of private notes, so check the project's GitHub documentation for the current setup instructions rather than assuming.
A concrete scenario
Say you keep research notes in NoteDiscovery and use Claude while drafting. With MCP configured, you could ask it to find your notes on a topic and summarise the open questions, or have it create a new file from your meeting-notes template. Because the underlying files are plain Markdown in folders, you can inspect or revert anything the assistant writes with normal file tools — a meaningful safety net that proprietary note databases don't offer.
Decision criteria
- Choose it if you already self-host and want AI access to notes you own outright, with no vendor lock-in.
- Be cautious if you need fine-grained permissions, audit logs, or a hosted service where you don't manage the server.
- If you mainly want a polished, zero-maintenance notes app, a hosted alternative may suit you better; if you want an open-source, self-hosted option with a plugin system, this is aimed at you.
Next step: read the project's MCP setup section on GitHub, then test the integration against a throwaway notebook before connecting your main vault.
Can NoteDiscovery import my existing Obsidian vault or Markdown files?
Yes, with a caveat: NoteDiscovery stores notes as plain Markdown files in folders, so pointing it at an existing vault or Markdown directory is the natural way to bring notes in. The site describes "plain markdown files in folders, no vendor lock-in, easy backups" — that's the storage model that makes migration practical.
What usually transfers cleanly
.mdfiles and folder structure- YAML frontmatter tags, which NoteDiscovery reads for its smart tags and properties panel
- Standard Markdown formatting, code blocks with language hints, and LaTeX math
- Mermaid diagram code blocks
- Wikilinks, which the site lists as a supported feature — Obsidian's
[[Note Name]]syntax is the same family, so most internal links should resolve once the files are in place
What may need cleanup
- Obsidian-specific plugins and their syntax (Dataview queries, Canvas files, Excalidraw drawings) have no stated equivalent. NoteDiscovery has its own drawing editor, but that's a separate tool, not a converter.
- Attachments: NoteDiscovery saves drawings as PNGs alongside notes, so an existing attachments folder should still work if links point to it correctly.
- Themes and workspace layout don't carry over — those are per-app settings.
Practical approach
- Back up the vault first.
- Test with a subset — copy one folder of notes into your NoteDiscovery data directory and check that links, tags and math render.
- If something breaks, the original vault is untouched, since you're copying plain files rather than converting formats.
Who this suits: someone already comfortable with Docker or self-hosting who wants their notes to stay as files on their own server. If you'd rather not run a server, this isn't the right fit — the trade-off is that all the privacy and ownership benefits come with setup and maintenance work on your side.
For the exact folder location and any import steps, check the project's own documentation: NoteDiscovery.
Is NoteDiscovery a good free alternative to Obsidian for privacy-focused note-taking?
Yes, for a particular kind of user. NoteDiscovery is a strong free, self-hosted alternative to Obsidian if your priority is that notes live as plain Markdown on a server you control, and you want AI tools to read and write them. It is a weaker fit if you rely on Obsidian's mature plugin ecosystem, mobile sync, or long-term polish.
Where it fits well
- Privacy and ownership: Notes are plain Markdown files in folders on your own server, so there is no vendor lock-in and backups are straightforward. The page states notes never leave your server.
- AI-assisted workflows: MCP integration is the standout. Claude, Cursor and other MCP-capable tools can search, create and organize notes — useful for developers who already work in those tools.
- Technical writing: LaTeX via MathJax, Mermaid diagrams, code highlighting, an embedded drawing editor that saves PNGs beside notes, and YAML frontmatter tags.
- Navigation: Wikilinks, graph view, outline panel with anchor links, smart search, card view and templates.
- Access: Runs via Docker, works on desktop, tablet and mobile, and installs as a PWA.
Where Obsidian still wins
| Need | NoteDiscovery | Obsidian |
|---|---|---|
| Local-first desktop app | Server-hosted, browser/PWA access | Native desktop and mobile apps |
| Plugin ecosystem | Extensible, but smaller | Very large community plugins |
| Sync | You host and manage it | Paid sync or self-managed |
| Setup effort | Docker deployment required | Install and go |
A practical scenario: A developer running a home server or VPS who wants notes searchable by Claude or Cursor, writes math and diagrams, and is comfortable maintaining Docker. They get privacy and AI access in one place. Someone who mainly takes notes on a phone and expects instant, effortless sync across devices will find Obsidian's official apps smoother, or may prefer a hosted option like Obsidian.
Next step: Try the live demo on the site first — it resets daily, so it is safe for testing. If the editor, graph and search feel right, deploy your own instance via Docker and confirm MCP works with your AI tool of choice before migrating a large vault.
How do I back up and sync my NoteDiscovery notes across devices?
NoteDiscovery stores your notes as plain Markdown files in folders, so backup and sync are mostly a file-management problem rather than a product feature. You keep a folder on your server; anything that copies or mirrors that folder gives you a backup, and anything that keeps two folders in step gives you cross-device sync.
Backup: copy the folder
Because the storage is plain Markdown, a backup is just a copy of the notes directory. Practical options:
- A scheduled
rsyncorrclonejob to another disk, NAS, or object storage. - A Git repository, which gives you version history as a bonus. Commit on a timer with
cronif you want automatic snapshots. - Your existing backup tool, pointed at the notes folder.
Keep at least one copy off the machine that runs NoteDiscovery. If you also store drawings, remember that PNG sketches are saved alongside the notes, so back up the whole directory tree rather than only .md files.
Sync: choose one writer per file
Sync is where most setups go wrong. Two-way sync tools can create conflict copies when the same file changes in two places before either sync completes. Safer patterns:
| Approach | Good for | Trade-off |
|---|---|---|
| Git pull/push | Technical users, version history | Manual or scripted; merge conflicts on simultaneous edits |
| Syncthing / file sync tool | Always-on devices, near-real-time | Conflict files if you edit offline on two devices |
| Single server + browser/PWA access | Most people | Requires the server to be reachable |
The simplest reliable model: treat the server as the single source of truth, and access it from other devices through the browser or the installable PWA rather than syncing a second copy of the files. You get one writer, no conflicts, and your backup job handles durability.
If you do want offline copies on a laptop, sync one direction (server → laptop) for reading, and edit on the server.
A concrete starting setup
- Put the notes folder under Git and push to a private remote daily.
- Add a weekly
rclonecopy to separate storage. - Access notes from phone and tablet via the PWA instead of a sync client.
- Test a restore once: clone the repo into a fresh instance and confirm the notes and images appear.
For background on the file-and-folder model that makes this work, see NoteDiscovery. If you want to compare how another Markdown tool handles sync, Obsidian documents its own sync and file-based approach.
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