Feat/add docker setup support

[RyanNg1403]

Fix MCP Endpoint Routing for Remote Client Access

🔍 Root Cause

Issue #174: MCP Client Connection Problems

MCP clients (Cursor, Windsurf, Claude Code) could not connect to Cipher's MCP endpoints when deployed remotely.

Problems identified:

1. Hardcoded /api prefix: All API routes were mounted under /api, making MCP endpoints available at /api/mcp instead of the expected /mcp
2. Misleading logs: Startup messages showed "MCP endpoints available at /mcp/sse and /mcp" but actual paths were /api/mcp/sse and /api/mcp
3. Client expectations: MCP clients expect standard endpoints at /mcp and /mcp/sse, not prefixed versions

✅ Solution

Core Changes for MCP Routing

Implemented configurable API prefix to enable flexible endpoint routing:

• Added apiPrefix configuration to ApiServerConfig interface
• Environment variable support: CIPHER_API_PREFIX="" disables prefix
• CLI flag support: --api-prefix "" command line option
• Dynamic route building: All routes now use configurable prefix
• Fixed startup logs: Show actual endpoint URLs with correct prefix

Usage Examples

Docker Setup for Remote MCP Access

Step 1: Clone and Configure

git clone <repository-url>
cd cipher
cp .env.example .env

Step 2: Set API Keys in .env

# Required: Add at least one API key
OPENAI_API_KEY=sk-your-actual-openai-key-here
# OR
ANTHROPIC_API_KEY=sk-ant-your-actual-anthropic-key-here

# Recommended settings for Docker
NODE_ENV=production
CIPHER_LOG_LEVEL=info
VECTOR_STORE_TYPE=in-memory
STORAGE_DATABASE_TYPE=in-memory
STORAGE_CACHE_TYPE=in-memory

Step 3: Build and Start Docker

# Build and start Cipher
docker-compose up --build -d

# Verify it's running
docker-compose logs -f cipher-api

Expected success logs:

✅ [API Server] Using API prefix: '(none)'
✅ [API Server] MCP SSE endpoints available at /mcp/sse and /mcp
✅ API Server started on 0.0.0.0:3000

Step 4: Test Endpoints

# Health check
curl http://localhost:3000/health

# MCP server listing (should work without /api prefix)
curl http://localhost:3000/mcp/servers/

Step 5: Connect MCP Clients

Cursor Configuration:

{
  "mcpServers": {
    "cipher": {
        "type": "sse",
        "url": "http://localhost:3000/mcp/sse",
        "postUrl": "http://localhost:3000/mcp"
    }
  }
}

Other clients: Use http://localhost:3000/mcp as the MCP endpoint URL.

🎯 Result

MCP Routing Fix

• ✅ Backward Compatible: Default /api prefix behavior preserved
• ✅ Standard MCP Endpoints: CIPHER_API_PREFIX="" enables /mcp paths
• ✅ Remote Deployment Ready: Works with Cursor, Windsurf, Claude Code
• ✅ Accurate Logging: Startup messages show correct endpoint URLs
• ✅ Docker Optimized: Simple single-service deployment

[phamleduy04]

@RyanNg1403 I see you remove the build step on while building docker and rely on host.

• This wont work with CI/CD since CI/CD don't have a build step before it.
• This generally not recommend since the node version on host and node version on docker image might be different.
• You might get “works on my machine” surprises.

[RyanNg1403]

@RyanNg1403 I see you remove the build step on while building docker and rely on host.

• This wont work with CI/CD since CI/CD don't have a build step before it.
• This generally not recommend since the node version on host and node version on docker image might be different.
• You might get “works on my machine” surprises.

Note that! I'm working on that right now!