second-brain-mcp

MCP server that exposes a personal Obsidian vault over stdio. Lets Claude Desktop, Claude Code, or any stdio-capable MCP client search, read, browse, and write to the vault without depending on a running Obsidian instance.

Tools

| Tool | What it does | |---|---| | search_vault | Keyword search — INDEX.md first, grep fallback if fewer than 3 INDEX hits. Excludes inbox. | | read_note | Read a note by relative path, filename stem, or frontmatter alias. Returns metadata + body. | | list_folder | Top-level folder summary (no arg) or note listing for a specific folder. | | create_inbox_note | Write a new note to inbox/ with auto-generated frontmatter and optional prefix. |

Prerequisites

uv — Python package manager and runner. Install with:
```
curl -LsSf https://astral.sh/uv/install.sh | sh
```
Claude CLI — only needed if installing for Claude Code (not required for Claude Desktop)

Note: You do not need to install Python manually. uv will download and manage Python 3.13 automatically when the server first runs.

Installation

git clone https://github.com/victormacaubas/second-brain-mcp.git
cd second-brain-mcp
uv sync

Quick start

The install script registers the server with your preferred Claude client in one command:

# Claude Code — current project only (default)
./install.sh ~/path/to/your/vault

# Claude Code — available in all sessions
./install.sh ~/path/to/your/vault --global

# Claude Desktop
./install.sh ~/path/to/your/vault --desktop

Run ./install.sh --help for full usage details.

Connecting to Claude Code

Project-scoped (default)

Registers the server for the current project directory. Writes to .claude/settings.json:

./install.sh /absolute/path/to/vault

Global

Registers the server for all Claude Code sessions. Writes to ~/.claude/settings.json:

./install.sh /absolute/path/to/vault --global

Verify

After installing, restart Claude Code and run:

claude mcp list

You should see second-brain-mcp listed with status connected.

Connecting to Claude Desktop

./install.sh /absolute/path/to/vault --desktop

This merges the server entry into your Claude Desktop config file without touching other settings. Quit and reopen Claude Desktop to activate — the server will appear in the MCP tools menu (hammer icon).

Config file locations:

| OS | Path | |---|---| | macOS | ~/Library/Application Support/Claude/claude_desktop_config.json | | Linux | ~/.config/Claude/claude_desktop_config.json | | Windows | %APPDATA%\Claude\claude_desktop_config.json |

Troubleshooting: If the server doesn't connect, check ~/Library/Logs/Claude/mcp*.log (macOS) for startup errors. The most common issues are an incorrect vault path or uv not being found at the expected location.

Manual configuration

If you prefer not to use the install script, you can configure things manually.

Claude Code (via CLI)

claude mcp add second-brain-mcp \
  --scope project \
  --transport stdio \
  -e VAULT_PATH=/absolute/path/to/vault \
  -- "$(which uv)" run --directory /absolute/path/to/second-brain-mcp second-brain-mcp

Change --scope project to --scope user for global installation.

The -- separates Claude's own flags from the command it will run as a subprocess. Everything after -- is what gets executed when the server starts:

$(which uv) — full path to the uv binary
run --directory <path> — tells uv where to find the project (pyproject.toml)
second-brain-mcp — the entry point name from [project.scripts]

Claude Desktop (manual JSON)

Edit the config file at the path for your OS (see table above) and add:

{
  "mcpServers": {
    "second-brain-mcp": {
      "command": "/path/to/uv",
      "args": [
        "run",
        "--directory", "/absolute/path/to/second-brain-mcp",
        "second-brain-mcp"
      ],
      "env": {
        "VAULT_PATH": "/absolute/path/to/vault"
      }
    }
  }
}

If the file already exists with other servers, merge the second-brain-mcp entry into the existing mcpServers object.

Running standalone (for testing)

The server speaks MCP over stdio — it is not meant to be invoked directly. But you can verify it starts:

VAULT_PATH=~/path/to/vault uv run second-brain-mcp

It will hang waiting for stdio input — that's correct. Press Ctrl+C to exit.

Development

Test with MCP Inspector before connecting to a real model:

VAULT_PATH=~/path/to/vault \
  npx @modelcontextprotocol/inspector \
  uv run --directory /absolute/path/to/second-brain-mcp second-brain-mcp

Vault conventions

The server expects the vault to follow these conventions:

Kebab-case .md filenames
YAML frontmatter on every note (title, date, description, tags, aliases)
INDEX.md at vault root with title/alias/description/tag entries per note
inbox/ as staging — excluded from search, only target for writes

Writes go to inbox/ only.

MCP Servers