Mycel

The local-first Markdown knowledge base that feels like a desktop app — because it is one.

Plain .md files on disk. A real Rust + Tauri shell. Wikilinks, a force-directed graph, inline databases, GitHub-backed sync, and a global hotkey that turns a fleeting thought into a note in under a second.

_{Above: editor + inline mycel-db block. Below: the vault graph.}

✨ Why Mycel?

Most "second brains" lock your notes in a proprietary format, a slow Electron container, or somebody else's cloud. Mycel makes the opposite bet:

📂 Your files, your folder. Mycel writes plain Markdown to a directory you pick. iCloud, Syncthing, Git, grep — they all keep working. Uninstall Mycel tomorrow and your notes are still there.
⚡ Native, not a browser tab. Rust backend + a real OS window via Tauri 2. Cold start under a second, no Chromium tax.
🧠 Built for thinking. Wikilinks, backlinks, a live outline, tag navigation, an inline relational database, a graph that actually shows structure — the tools knowledge workers reach for, without the bloat.
🔐 Optional encrypted sync. When you want sync, point Mycel at a private GitHub repo. Your token lives in your OS keyring, never in a config file.

Status: active development (v0.1). The features listed under "What's in the box" are all working today. Items in the roadmap are the next things on the bench.

🚀 Quick start

git clone https://github.com/Mycel-AI-notes/Mycel.git
cd Mycel
npm install
npm run tauri dev

First launch shows the vault picker — point it at any folder. Mycel remembers it and auto-opens it next time.

Prereqs: Rust (stable), Node.js 18+, and Tauri's system dependencies for your OS (Xcode CLT on macOS, build-essential + webkit2gtk on Linux, MSVC + WebView2 on Windows).

Build a release binary:

npm run tauri build
# bundles under src-tauri/target/release/bundle/ (.app, .dmg, .deb, .AppImage, .msi)

📦 What's in the box

Writing & navigation

✍️ CodeMirror 6 editor with Markdown syntax, inline preview decorations, fenced code blocks with per-language highlighting, and autocomplete.
🔗 Wikilinks — [[Like this]] autocomplete, click-to-navigate, missing targets are created for you. Renaming a note rewrites every link to it across the vault — aliases, anchors, embeds and folder paths included — so a rename never leaves a trail of broken references.
🪟 Embeds — ![[Note]] shows the note right in the editor as a read-only card; ![[Note#Heading]] shows just that section, and ![[pic.png]] shows the picture wherever it lives in the vault. Click the card's title to open the note. Embeds go one level deep (a nested ![[…]] renders as a link), so notes embedding each other can't loop, and they count as links in backlinks.
🏷️ Aliases — aliases: [ML, Machine learning] in frontmatter (a YAML list or a single string works too) lets [[ML]] reach the note. Aliases show up in [[ autocomplete and count in backlinks and the graph. A note actually named ML still wins — aliases never steal links.
⚡ Slash menu — type / for quick inserts (tables, code, headings, callouts…).
📅 Daily notes (⌘/Ctrl+Shift+D) — opens today's daily/YYYY-MM-DD.md, creating it from your daily template when it doesn't exist yet (an existing note is never overwritten). Previous / Next daily note in the palette step through the days you actually wrote. Folder and template are set in Settings → Notes.
🧩 Templates — drop .md files in templates/ (folder configurable in Settings → Notes), then /template or Insert template… in the palette inserts one at the cursor. Variables: {{title}}, {{date}}, {{time}}, and {{date:DD.MM.YYYY HH:mm}} with the tokens YYYY MM DD HH mm.
📊 Editable GFM tables rendered as styled blocks; inline Markdown (links, wikilinks, bold) renders inside cells and stays clickable.
💾 Autosave — edits land on disk about a second after you stop typing, and are flushed when you leave a tab or close the window. ⌘/Ctrl+S still works and still pins a preview tab; it's just no longer the only thing between a thought and losing it.
🗂️ Tabs done right — single click opens a preview tab (italic). Switching files replaces it, so you don't drown in junk tabs. Save (⌘/Ctrl+S) or double-click to pin.
🔍 Quick switcher (⌘/Ctrl+O) — fuzzy search across note titles and paths.
🔎 Full-text search (⌘/Ctrl+Shift+F) — search the contents of every note, as you type, fully offline and without an AI key. A local SQLite FTS5 index (.mycel/search.db) kept fresh by the file watcher; Cyrillic and Latin alike, accent- and ё/е-insensitive, prefix matching. Operators: "exact phrase", -exclude, a OR b, plus path:, file: and tag: filters. Results are grouped by note with highlighted snippets; Enter jumps straight to the matching line. Encrypted notes are never indexed.
🎛️ Command palette (⌘/Ctrl+P) — every action in the app, fuzzy-searchable, with its hotkey shown next to it. Commands and hotkeys come from one registry, so nothing is reachable only by mouse.
⌨️ Configurable hotkeys — Settings → Hotkeys: click a shortcut, press the new keys. Conflicts are caught before they happen (you're asked before a key is taken from another command), Backspace unbinds, one click resets to the default. Bindings follow the physical key, so they keep working on a non-Latin keyboard layout. The global quick-note shortcut is fixed.
⚡ Quick notes (⌘/Ctrl+Shift+N, global — works even when the app is minimised) — drops a timestamped note in quick/YYYY-MM-DD/ so a thought never gets away.

Sense-making

🕸️ Spore graph view (⌘/Ctrl+G) — full-screen force-directed graph. Folders cluster as spores, wikilinks become edges, tag and structural connections toggle on or off from the toolbar.
📍 Live outline panel — every heading in the current note, click to jump.
↩️ Backlinks panel — folder-aware incoming references, plus outgoing wikilinks and external URLs.
🏷️ Tag system — #tags autocomplete in the editor, dedicated tag panel, tag search across the vault, tag nodes in the graph.
📥 Quick-note auto-filing — with Insights enabled, Mycel finds the note each quick capture belongs to and offers a one-click, confirmed merge (with a provenance trail). The quick/ folder stops being a graveyard. See docs/specs/quick-note-filing.md.

Structured data

🧱 Inline databases. Notion-style fenced mycel-db blocks render typed tables (text, number, date, select, multi-select, checkbox, page link…) right in the note.
🗃️ Vault picker with recents. Switch between vaults; Mycel remembers your last one and the last few you used.
🗑️ Recoverable deletes. Deleting a note or folder moves it to .mycel/trash/<timestamp>/, keeping its original path — restoring is a move back. Nothing is unlinked outright.

Sync & sharing

☁️ GitHub vault sync — push and pull your vault to a private GitHub repo. Fine-grained PAT, stored in the OS keyring (macOS Keychain / Windows Credential Manager / Secret Service), with auto-sync, manual sync, and clean conflict reporting.
📥 Clone a remote vault straight from the vault picker — point Mycel at a repo and it bootstraps the local folder.

Security

🔐 Per-note encryption — convert any note to *.md.age with one click. Uses age (X25519 + ChaCha20-Poly1305), the modern crypto format by Filippo Valsorda and Ben Cartwright-Cox; we depend on the Rust implementation str4d/rage. Encrypted notes still sync through GitHub as opaque ASCII-armored blobs.
🗝️ Hardware-backed identity — your X25519 secret is wrapped twice: with a passphrase you choose (inner) and a random 256-bit KEK in your OS keyring (outer, Secure Enclave on macOS / TPM-backed DPAPI on Windows). Both factors required to unlock. Plaintext key never touches disk, wiped on lock or after 5 min idle.
👥 Multi-device — each device has its own identity. Add another machine's pubkey to recipients.txt and notes are readable on both. Existing notes can be re-encrypted to the new recipient set with one button.

Look & feel

🎨 Color palettes — Moss, Amber, Azure, Plum, Coral, Classic. Light/dark/system. Picker in the status bar.
🍎 Native window chrome. macOS traffic lights blend into the title bar; the toolbar is fully drag-region aware.
↔️ Resizable sidebar — drag the edge, double-click to reset.

⌨️ Keyboard shortcuts

Shortcut	Action
`⌘/Ctrl + P`	Command palette
`⌘/Ctrl + O`	Quick switcher (fuzzy file finder)
`⌘/Ctrl + Shift + F`	Full-text search across note contents
`⌘/Ctrl + Shift + N`	Quick note (works globally, even when Mycel is unfocused)
`⌘/Ctrl + G`	Toggle graph view
`⌘/Ctrl + S`	Save current note (also pins a preview tab)
`⌘/Ctrl + Shift + P`	Present the current note
`⌘/Ctrl + Shift + D`	Open today's daily note
`⌘/Ctrl + ,`	Settings
`⌘/Ctrl + I`	Garden quick capture
`⌘/Ctrl + Shift + A`	Garden: Next Actions
⌘/Ctrl + `	Garden: toggle the sidebar section
`/` in the editor	Slash command menu (`/template` inserts a template)
`[[` in the editor	Wikilink autocomplete
Double-click a tab	Pin a preview tab
Double-click sidebar resize handle	Reset sidebar width

Every shortcut except the global quick note can be changed in Settings → Hotkeys; the table lists the defaults.

🧰 Stack

Layer	Tech
Shell	Tauri 2
Backend	Rust (parser, file watcher, full-text index, keyring, Git sync)
Frontend	React 19 + TypeScript + Vite
Editor	CodeMirror 6
Graph	`d3-force`
State	Zustand (with `persist` for UI prefs, recent vaults, sync config)
Styling	Tailwind CSS
Icons	`lucide-react`
Markdown	`pulldown-cmark`, `gray_matter` (frontmatter)
Secrets	`keyring` (OS-native credential storage)

📖 How to use it

Pick a vault. Any folder works. Mycel doesn't move or rename your files; everything stays as plain .md.
Create notes. Use the + icons in the sidebar header (root) or hover a folder row to create inside it.
Link notes. Type [[ to autocomplete. Click a rendered wikilink to follow it. If the target doesn't exist, Mycel creates it.
Find notes. ⌘/Ctrl + O for the fuzzy switcher.
Capture a fleeting thought. ⌘/Ctrl + Shift + N — anywhere on the system — and start typing.
Zoom out. ⌘/Ctrl + G opens the spore graph.
Sync (optional). Open the sync panel, paste a GitHub PAT, point at a private repo. Auto-sync keeps it tidy in the background.
Switch vaults. The folder icon in the status bar takes you back to the picker.

Vault layout

my-vault/
├── .mycel/              # Mycel's working files (gitignored automatically)
├── quick/
│   └── 2026-05-11/
│       └── 14-32-08.md  # quick notes are filed by date and time
├── projects/
│   └── garden.md
└── inbox.md

The .mycel/ folder holds app metadata: the AI index, the insights store, Garden data, and the trash. Mycel's own GitHub sync adds it to .gitignore for you — nothing in there belongs on a remote, and the AI index in particular holds your notes' text in the clear. If you sync the vault with Git separately, add .mycel/ to .gitignore yourself.

Note format

Plain Markdown, optional YAML frontmatter, plus optional fenced databases:

---
title: My note
tags: [ideas, ml]
---

# My note

Supports [[WikiLinks]], #tags, **bold**, `code`, GFM tables, and fenced databases.

```mycel-db
view: table
source: inline
columns:
  - { id: name, name: Name, type: text }
  - { id: done, name: Done, type: checkbox }
rows:
  - { name: Sketch idea, done: true }
  - { name: Wire backend, done: false }
```

Encrypted notes (`*.md.age`)

Click the shield icon in the toolbar to set up encryption. You'll be asked for a passphrase (≥ 8 chars, optional but strongly recommended). Mycel generates a fresh X25519 keypair for this device and wraps the secret half twice: with your passphrase (inner, scrypt) and with a random 256-bit key-encryption-key (KEK) in your OS keyring (outer, scrypt). Both factors are required to unlock — the keyring alone is not enough, so a per-Lock passphrase prompt actually means something.

The vault auto-locks after 5 minutes of idle. Layout under .mycel/crypto/:

.mycel/crypto/
├── recipients.txt        # COMMITTED. All public keys allowed to decrypt
│                         # notes in this vault. One device = one pubkey.
├── .gitignore            # COMMITTED. Excludes the per-device files below.
├── local-identity.age    # GITIGNORED. This device's X25519 secret,
│                         # double-wrapped (scrypt(KEK, scrypt(passphrase, …))).
└── local-pubkey.txt      # GITIGNORED. This device's public key.

To encrypt an existing note, hover its row in the sidebar and click the lock icon — the file becomes <name>.md.age. Encrypted notes still appear in the file tree (with a lock badge), get a banner above the editor showing what's on disk, and sync through GitHub as opaque ASCII-armored blobs.

Encryption is not retroactive. Clicking the lock icon on an existing .md only protects writes from that moment on. Anything you saved or pushed beforehand is still plaintext in git history, in iCloud / Time Machine / Windows backups, in the GitHub remote. Mycel warns you on the encrypt action; the only guarantee is to click the lock before typing anything sensitive.

Adding a second device

Device 1 runs Set up. recipients.txt is created with pubkey-1.
Sync to GitHub. Device 2 clones.
Device 2 opens the vault — the shield icon shows "This device has not joined the vault". Click → choose a passphrase (your own, independent of device 1's) → generates pubkey-2, appends to recipients.txt.
Sync. Now both pubkeys are in recipients.txt; any note encrypted going forward is readable on both.
For notes encrypted before device 2 joined: on device 1, open the shield panel → Re-encrypt all notes → re-wraps every .md.age to the current recipient set. Push. Device 2 pulls and reads them.

Credits: the on-disk format is plain age, so encrypted notes round-trip through the upstream age CLI and any other age-compatible tool. Thanks to Filippo Valsorda and Ben Cartwright-Cox for the spec, and to @str4d for the Rust implementation we depend on.

🗺️ Roadmap

The big things on the bench, roughly in priority order (details and rationale in docs/roadmap.md):

🔎 Full-text search & a real index — SQLite FTS5 over the vault with path: / tag: / - operators, fed incrementally by the file watcher. Free, offline, and it makes backlinks, tags and the graph queries instead of vault walks.
🤖 Local-first AI by default — embeddings and chat through Ollama / llama.cpp / LM Studio; OpenRouter stays as an opt-in. Ask questions grounded in your vault.
🔌 MCP server — let Claude Code, Codex and other agents search and write your vault, with encrypted notes locked out, writes scoped to chosen folders, and every change recoverable (git + trash).
⌨️ Obsidian-user habits — command palette, configurable hotkeys, daily notes and templates, ![[embeds]], aliases, unlinked mentions, local graph, a properties editor.
📦 Signed releases & auto-update — notarized macOS, signed Windows builds, Tauri updater, Obsidian vault import.
🧱 Databases, next level — kanban and calendar views, relations, CSV import.
🧩 Plugin API — slash commands, panels, decorations.
🌳 KB hierarchy, 🎨 community themes, 📱 mobile companion (read-only + capture first).

✅ Already shipped (previously listed here): semantic search, encrypted notes with hardware-backed identity, LaTeX, image support, Garden/GTD, present mode, KB directories, quick-note auto-filing.

📋 The full roadmap lives in GitHub Issues — that's where the granular tickets, design discussions, and "good first issue" tags live. Everyone is invited to contribute — pick a ticket, drop a comment, send a PR. New ideas welcome too.

🤝 Contributing

Mycel is open to contributors and we'd love your help. PRs, issues, design feedback, themes, screenshots, blog posts — all welcome.

Good first issues:

Hunt for a bug in the issues tab — we tag beginner-friendly ones.
Add a color palette (a few entries in src/stores/ui.ts and matching CSS variables).
Add a slash-menu entry (see src/components/editor/SlashCompletion.ts).
Improve the empty-state hero (src/components/editor/EmptyEditor.tsx).

Workflow:

# fork on GitHub, then:
git clone https://github.com/<you>/Mycel.git
cd Mycel && npm install
npm run tauri dev      # iterate

# before pushing — CI runs all of these on every PR
npm run lint
npm test
npm run build
cd src-tauri && cargo fmt --check && cargo clippy --all-targets -- -D warnings && cargo test

On Linux the Rust checks need Tauri's system libraries (libgtk-3-dev, libwebkit2gtk-4.1-dev and friends) — without them the build fails inside gdk-sys with a pkg-config error that gives no hint a system package is what's missing. See .github/workflows/ci.yml for the exact list.

Open a PR against main with a short summary of why the change matters. Commits roughly follow Conventional Commits (feat(editor): …, fix(graph): …).

📝 Contributor License Agreement

Before your first PR is merged, please sign the Mycel CLA — it's short, modelled on the Apache ICLA 2.0, and exists so the project stays legally clean as it grows (including future commercial editions that fund development). You keep full copyright in your contribution. The CLA Assistant bot will prompt you automatically on your first PR; a one-line manual statement also works.

Frontend-only dev (no Tauri shell)

If you just want to hack on the UI:

npm run dev   # Vite on http://localhost:1420

File-system commands won't be available (the vault picker needs the Tauri runtime), but components render fine.

🏗️ Project structure

.
├── src/                       # React frontend
│   ├── components/
│   │   ├── editor/            # CodeMirror editor, tabs, slash menu, wikilinks
│   │   ├── sidebar/           # File tree
│   │   ├── ui/                # Right panel, palette picker, primitives
│   │   ├── graph/             # Force-directed graph view
│   │   ├── search/            # Quick switcher, tag search
│   │   ├── sync/              # GitHub sync panel, clone dialog
│   │   ├── database/          # Inline mycel-db blocks
│   │   ├── table/             # GFM table editor
│   │   ├── markdown/          # Inline Markdown rendering
│   │   ├── onboarding/        # Vault picker
│   │   └── brand/             # Logo, spore visuals
│   ├── stores/                # Zustand stores (vault, ui, sync, recentVaults)
│   ├── hooks/                 # useTheme, useQuickNote
│   └── lib/                   # Editor / database helpers
├── src-tauri/                 # Rust shell
│   ├── src/commands/          # Tauri commands (notes, vault, search, graph, sync, database)
│   └── src/core/              # Vault, parser, file watcher, full-text index, sync, keyring
└── package.json

⭐ If Mycel helps you, star the repo

It's the cheapest way to say thanks, and it genuinely moves the needle on what gets prioritised next. Tell a friend, share a screenshot, file an issue — every bit counts.

📜 License

AGPL-3.0 — Mycel is free software. Use it, modify it, share it. If you run a modified version as a network service, you must publish your changes under the same license.

Built with ❤️ by people who'd rather own their notes.

Name		Name	Last commit message	Last commit date
.github		.github
docs		docs
public		public
scripts		scripts
src-tauri		src-tauri
src		src
.eslintrc.cjs		.eslintrc.cjs
.gitignore		.gitignore
CLA.md		CLA.md
LICENSE		LICENSE
README.md		README.md
index.html		index.html
package-lock.json		package-lock.json
package.json		package.json
postcss.config.js		postcss.config.js
rust-toolchain.toml		rust-toolchain.toml
tailwind.config.js		tailwind.config.js
tsconfig.json		tsconfig.json
tsconfig.node.json		tsconfig.node.json
vite.config.ts		vite.config.ts

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Mycel

✨ Why Mycel?

🚀 Quick start

📦 What's in the box

Writing & navigation

Sense-making

Structured data

Sync & sharing

Security

Look & feel

⌨️ Keyboard shortcuts

🧰 Stack

📖 How to use it

Vault layout

Note format

Encrypted notes (`*.md.age`)

Adding a second device

🗺️ Roadmap

🤝 Contributing

📝 Contributor License Agreement

Frontend-only dev (no Tauri shell)

🏗️ Project structure

⭐ If Mycel helps you, star the repo

📜 License

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Mycel

✨ Why Mycel?

🚀 Quick start

📦 What's in the box

Writing & navigation

Sense-making

Structured data

Sync & sharing

Security

Look & feel

⌨️ Keyboard shortcuts

🧰 Stack

📖 How to use it

Vault layout

Note format

Encrypted notes (*.md.age)

Adding a second device

🗺️ Roadmap

🤝 Contributing

📝 Contributor License Agreement

Frontend-only dev (no Tauri shell)

🏗️ Project structure

⭐ If Mycel helps you, star the repo

📜 License

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Encrypted notes (`*.md.age`)