Synapse

Standalone MCP server for semantic search over your markdown knowledge vault. Generates embeddings via Ollama with automatic indexing and live file watching.

Prerequisites

Ollama must be running on your system. Install from ollama.com, then pull the embedding model:

ollama pull nomic-embed-text

Server Setup

npm install
VAULT_PATH=/path/to/your/vault bun run start

Server runs on http://0.0.0.0:3939 by default.

On first run, Synapse will:

1. Scan your vault for markdown files
2. Generate embeddings via Ollama
3. Store embeddings in SQLite database
4. Start a file watcher for live updates

Environment Variables

Variable	Required	Default	Description
VAULT_PATH	Yes	-	Path to markdown vault
ENV_PATH	No	$VAULT_PATH/.synapse	Where embeddings.db is stored
MCP_PORT	No	3939	HTTP port
MCP_HOST	No	0.0.0.0	Bind address
OLLAMA_URL	No	http://localhost:11434	Ollama API endpoint
OLLAMA_MODEL	No	nomic-embed-text	Embedding model name

Client Setup (Local Machine)

claude mcp add --scope user --transport sse synapse http://<remote-host>:3939/sse

Replace <remote-host> with the IP/hostname of the machine running the server.

Endpoints

Endpoint	Method	Description
/sse	GET	SSE connection for MCP
/messages?sessionId=X	POST	Client-to-server messages
/health	GET	Health check

Tools

• search_notes - Keyword search in note paths
• get_similar_notes - Semantic similarity using embeddings
• get_connection_graph - Multi-level connection exploration

How It Works

Initial indexing: On startup, Synapse scans your vault and generates embeddings for all markdown files using the specified Ollama model. These embeddings are stored in a local SQLite database.

Live updates: The built-in file watcher automatically detects changes, additions, and deletions in your vault, re-embedding modified files in real-time.

Semantic search: Tools use embeddings to find semantically related notes and build multi-hop connection graphs across your vault.