---
id: kb-014
title: MCP Implementation Comparison - atoms-mcp-prod vs agentapi/atomsagent
scope:
  type: project
  id: 4sgm
purpose: analysis-mcp-comparison
tags:
  - mcp
  - architecture
  - analysis
topics:
  - engineering
  - infrastructure
version: 1
created: 2025-11-26
updated: 2025-11-26
author: droid-agent
status: final
related_ids:
  - kb-010
  - kb-012
external_refs: []
---

# MCP Implementation Comparison: atoms-mcp-prod vs agentapi/atomsagent

## Executive Summary

Both directories contain Model Context Protocol (MCP) implementations, but they serve distinct and complementary roles. `atoms-mcp-prod` is the official standalone server for knowledge management, while `agentapi/atomsagent` is an orchestration service that can compose multiple MCP servers.

## Detailed Comparison

| Aspect | atoms-mcp-prod | agentapi/atomsagent |
|--------|----------------|---------------------|
| **Primary Purpose** | Official Standalone MCP Server | FastAPI Service + MCP Management |
| **Tool Count** | 5 Consolidated Tools | 8 Embedded Tools |
| **Focus** | Knowledge Mgmt (Entities, Relationships) | Requirements, Sandbox Execution |
| **Deployment** | Vercel (Serverless) | FastAPI Application |
| **Management** | ❌ No CRUD for servers | ✅ Yes (API endpoints for registry) |
| **OAuth** | Built-in Hybrid Auth | DCR and Callback Management |
| **FastMCP Ver** | `>=2.13.1` (Latest) | `>=0.11.0` (Older) |

---

## Overlap & Complementary Analysis

- **Shared**: Both use FastMCP, integrate with Supabase, and support OAuth flows.
- **Complementary**: `agentapi/atomsagent` serves as the orchestration layer that can manage and compose `atoms-mcp-prod` along with other external servers.

---

## Recommendations

### Keep Both Implementations
- **Rationale**: They serve different architectural layers. Merging them would create a monolithic service that is harder to deploy and maintain.
- **Integration Path**: Register `atoms-mcp-prod` within the `agentapi` registry to allow seamless tool composition. This provides a total of 13 unified tools (5 + 8) to AI agents.

### Alignment Task
- Update `agentapi/atomsagent` to use `fastmcp>=2.13.1` to ensure consistency in protocol features and metadata handling.
