chore: remove orphaned MCP references

The SmartEM MCP server was removed from smartem-decisions in Dec 2025
(PR DiamondLightSource/smartem-decisions#199) but the corresponding
cleanup in smartem-devtools was never done. This removes all stale
references.

Closes #29

Author: vredchenko

claude-code/ARCHITECTURE.md

@@ -69,7 +69,6 @@ SmartEM is the core system. Everything inside the boundary is in scope; everythi
 | smartem_common | (none - leaf) |
 | smartem_backend | smartem_common |
 | smartem_agent | smartem_common, smartem_backend.api_client |
-| smartem_mcp | smartem_common, smartem_backend, smartem_agent |
 | athena_api | (independent - no smartem imports) |
 
 ### Package Summaries
@@ -80,7 +79,6 @@ SmartEM is the core system. Everything inside the boundary is in scope; everythi
 | `smartem_backend` | API server, DB, MQ consumer | FastAPI, PostgreSQL, RabbitMQ, Alembic |
 | `smartem_agent` | EPU file watcher, parser | Watchdog, lxml, Typer CLI |
 | `athena_api` | Microscope hardware client | HTTP client + mock server |
-| `smartem_mcp` | Natural language querying | FastMCP server |
 
 ## API Client Generation
 
@@ -171,7 +169,6 @@ export ARIA_GQL_LOCAL=http://localhost:9002/graphql
 |----------|-----------------|
 | smartem-backend | Rebuild |
 | smartem-agent | Rebuild |
-| smartem_mcp | Rebuild |
 
 ## CI/CD Overview
 

docs/decision-records/backend-agent-communication-system-design.md

@@ -36,9 +36,6 @@ graph TB
                 athena_client["client.py<br/>External API Integration"]
             end
 
-            subgraph mcp["smartem_mcp"]
-                mcp_server["server.py<br/>Model Context Protocol"]
-            end
         end
 
         subgraph infra["Infrastructure Services"]
@@ -119,7 +116,7 @@ graph TB
     classDef equipment fill:#e8f5e8,stroke:#2e7d32,stroke-width:2px
     classDef communication fill:#fff8e1,stroke:#f57f17,stroke-width:2px
 
-    class k8s,packages,backend,common,athena,mcp,infra k8s
+    class k8s,packages,backend,common,athena,infra k8s
     class boundary,agents,agent_pkg,equipment boundary
     class db,mq database
     class scope1,scope2,scopeN,epu1,epu2,epuN,em1,em2,emN,gpfs1,gpfs2,gpfsN equipment

docs/development/index.md

@@ -10,7 +10,6 @@ tools
 generate-docs
 e2e-simulation
 github-labels
-mcp-interface
 ```
 
 ## Topics
@@ -23,7 +22,6 @@ mcp-interface
 
 - [Development Tools](tools.md) - Utility tools for development, testing, and maintenance
 - [E2E Simulation](e2e-simulation.md) - End-to-end development simulation setup
-- [MCP Interface](mcp-interface.md) - SmartEM MCP server for Claude Code integration
 
 ### Documentation and CI/CD