Simple-Index MCP Server

A Python Model Context Protocol (MCP) server for indexing projects, files, and folders using embeddings. Provides semantic search capabilities to help AI agents understand and navigate your codebase.

Features

• Semantic Indexing: Uses embeddings (via Ollama) to create a searchable index of your project files
• Single Index File: All indexes are stored in projectIndex.si (in project root or global location)
• Incremental Updates: Only re-indexes files that have changed (based on content hash)
• Extensible Provider System: Easy to add new embedding providers beyond Ollama
• MCP Tools: Exposes powerful tools for indexing, searching, and retrieving context

Installation

Prerequisites

• Python 3.10 or higher
• Ollama installed and running locally
• nomic-embed-text model pulled in Ollama: ollama pull nomic-embed-text

Setup

1. Create a virtual environment:

python -m venv venv
source venv/bin/activate  # On Windows: venv\Scripts\activate

2. Install dependencies:

pip install "mcp>=1.2.0" aiohttp

3. Place simple_index_server.py in your project directory

Configuration

Claude Desktop Configuration

Add to your Claude Desktop config (~/Library/Application Support/Claude/claude_desktop_config.json on macOS):

{
  "mcpServers": {
    "simple-index": {
      "command": "python",
      "args": [
        "/path/to/simple_index_server.py",
        "/path/to/your/project"
      ],
      "env": {
        "OLLAMA_MODEL": "nomic-embed-text",
        "OLLAMA_URL": "http://localhost:11434"
      }
    }
  }
}

  }
}

} }

### Global Index Mode (Optional)

If you prefer to store the index file in a central location (instead of the project root), set the `SIMPLE_INDEX_ROOT` environment variable.

```json
{
  "mcpServers": {
    "simple-index": {
      "command": "python",
      "args": ["/path/to/simple_index_server.py"],
      "env": {
        "SIMPLE_INDEX_ROOT": "/path/to/central/indexes",
        "OLLAMA_MODEL": "nomic-embed-text"
      }
    }
  }
}

Alternative Configuration Options

You can also specify the Ollama model and URL as command-line arguments:

{
  "mcpServers": {
    "simple-index": {
      "command": "python",
      "args": [
        "/path/to/simple_index_server.py",
        "/path/to/your/project",
        "nomic-embed-text",
        "http://localhost:11434"
      ]
    }
  }
}

Available Tools

1. index_file

Index a single file with embeddings.

Parameters:

• file_path (string, required): Path to the file to index
• force (boolean, optional): Force reindexing even if file hasn't changed

Example:

Claude, please index the file /path/to/my/script.py

2. index_directory

Index all matching files in a directory recursively.

Parameters:

• directory (string, required): Path to directory to index
• patterns (array of strings, optional): File patterns to match (default: ["*.py", "*.js", "*.ts", "*.md", "*.txt"])
• exclude_patterns (array of strings, optional): Patterns to exclude (default: ["*/node_modules/*", "*/.git/*", "*/venv/*"])

Example:

Claude, index all Python and JavaScript files in my project, excluding the tests directory

3. search

Search for files similar to a query using semantic search.

Parameters:

• query (string, required): Search query describing what you're looking for
• top_k (integer, optional): Number of results to return (default: 10)

Example:

Claude, search for files related to "database connection logic"

4. get_context

Get full file contents for the most relevant files to a query.

Parameters:

• query (string, required): Query describing what context you need
• top_k (integer, optional): Number of files to include in context (default: 5)

Example:

Claude, get context for "authentication implementation"

5. list_indexed_files

List all files currently in the index.

Example:

Claude, show me all indexed files

6. get_index_stats

Get statistics about the current index.

Example:

Claude, what are the index statistics?

7. remove_file

Remove a file from the index.

Parameters:

• file_path (string, required): Path to file to remove from index

Example:

Claude, remove the file /path/to/old/file.py from the index

Index File Format

The projectIndex.si file is stored in JSON format with the following structure:

{
  "version": "1.0",
  "created_at": "2026-01-31T10:00:00Z",
  "updated_at": "2026-01-31T12:30:00Z",
  "project_root": "/path/to/project",
  "metadata": {
    "total_files": 42,
    "total_size": 150000,
    "embedding_model": "ollama:nomic-embed-text"
  },
  "files": {
    "src/main.py": {
      "path": "src/main.py",
      "absolute_path": "/path/to/project/src/main.py",
      "hash": "abc123...",
      "embedding": [0.1, 0.2, ...],
      "indexed_at": "2026-01-31T12:30:00Z",
      "size": 1024,
      "metadata": {
        "extension": ".py",
        "name": "main.py"
      }
    }
  }
}

Index Management

• Atomic Writes: The index is written atomically using a temporary file to prevent corruption
• Change Detection: Files are only re-indexed if their content hash changes
• Incremental Updates: You can index new files without affecting existing entries

Usage Examples

Initial Project Indexing

You: Claude, index my entire project directory at /Users/me/myproject

Claude: [Uses index_directory tool]
I've indexed your project. Found 45 files, indexed 42, skipped 3 binary files.

Searching for Relevant Files

You: Find files related to user authentication

Claude: [Uses search tool]
I found these relevant files:
1. src/auth/login.py (similarity: 0.89)
2. src/middleware/auth_check.py (similarity: 0.85)
3. tests/test_auth.py (similarity: 0.78)

Getting Context for Development

You: I need to modify the payment processing logic. Show me the relevant code.

Claude: [Uses get_context tool]
Here's the relevant code from 3 files:

## File 1: src/payments/processor.py (similarity: 0.92)
[Full file contents...]

## File 2: src/payments/validators.py (similarity: 0.87)
[Full file contents...]

Checking Index Status

You: What's the status of the index?

Claude: [Uses get_index_stats tool]
Index Statistics:
- Total files: 42
- Total size: 150 KB
- Last updated: 2026-01-31T12:30:00Z
- Embedding model: ollama:nomic-embed-text

Architecture

Components

1. EmbeddingProvider: Abstract base class for embedding providers

   • OllamaProvider: Implementation using Ollama API
   • Easy to extend with OpenAI, Cohere, etc.

2. ProjectIndex: Manages the projectIndex.si file

   • Loading and saving with atomic writes
   • Adding, removing, and querying files
   • Computing statistics

3. SimpleIndexServer: Main MCP server implementation

   • File reading and hashing
   • Orchestrating indexing operations
   • Semantic search functionality

4. MCP Integration: Standard Model Context Protocol server

   • Tool registration and handling
   • STDIO transport for communication

Adding New Embedding Providers

To add a new provider (e.g., OpenAI):

class OpenAIProvider(EmbeddingProvider):
    def __init__(self, api_key: str, model: str = "text-embedding-3-small"):
        self.api_key = api_key
        self.model = model
    
    async def embed(self, text: str) -> List[float]:
        # Implementation using OpenAI API
        pass

Then modify the main() function to support the new provider.

Best Practices

1. Index Regularly: Run indexing after significant code changes
2. Use Exclude Patterns: Exclude node_modules, venv, build artifacts
3. Semantic Queries: Use descriptive queries like "error handling for API requests" rather than just "error"
4. Monitor Index Size: Large projects may need chunking strategies for very large files

Troubleshooting

Ollama Connection Issues

# Check if Ollama is running
curl http://localhost:11434/api/version

# Pull the embedding model if not available
ollama pull nomic-embed-text

Index Corruption

If projectIndex.si becomes corrupted, simply delete it and re-index:

rm projectIndex.si
# Then ask Claude to re-index the directory

Logging

The server uses Python's logging module and writes to stderr (MCP requirement). Check your MCP client's logs for debugging information.

Performance Considerations

• Embedding Generation: ~100-500ms per file depending on size
• Index Size: ~4KB per file (768-dim embeddings + metadata)
• Search Speed: <100ms for typical project sizes (hundreds of files)

License

MIT License - Feel free to use and modify as needed.

Contributing

This is a reference implementation. Feel free to fork and extend with:

• Additional embedding providers
• Chunking strategies for large files
• Multi-language support
• Custom metadata extraction
• Integration with other tools

Credits

Built with:

• Model Context Protocol
• Ollama
• nomic-embed-text