docs: standardize on codegraph-official binary for consistency

Author: jruokola

CLAUDE.md

@@ -92,21 +92,27 @@ cargo doc --workspace --no-deps --open
 
 ### Running the MCP Server
 
+**Note:** The MCP server has two binaries:
+- `codegraph-official` (recommended): Uses official rmcp SDK, supports both STDIO and HTTP transports
+- `codegraph` (legacy): Original implementation, STDIO only
+
+All examples below use `codegraph-official` for consistency.
+
 ```bash
 # Build the MCP server binary (with AutoAgents experimental feature)
-cargo build --release -p codegraph-mcp --bin codegraph --features "ai-enhanced,autoagents-experimental,faiss,ollama"
+cargo build --release -p codegraph-mcp --bin codegraph-official --features "ai-enhanced,autoagents-experimental,faiss,ollama"
 
 # Or use Makefile target
 make build-mcp-autoagents
 
 # Or build without AutoAgents (uses legacy orchestrator)
-cargo build --release -p codegraph-mcp --bin codegraph --features "ai-enhanced,faiss,ollama"
+cargo build --release -p codegraph-mcp --bin codegraph-official --features "ai-enhanced,faiss,ollama"
 
 # Start MCP server (stdio mode - RECOMMENDED)
-./target/release/codegraph start stdio
+./target/release/codegraph-official serve --transport stdio
 
 # Check agentic tool configuration
-./target/release/codegraph config agent-status
+./target/release/codegraph-official config agent-status
 ```
 
 **HTTP Transport (Experimental):**
@@ -477,9 +483,9 @@ sudo apt-get install libfaiss-dev  # Ubuntu
 - Verify SurrealDB connection is working
 
 **MCP tests fail**
-- Check binary exists: `./target/release/codegraph` or `./target/debug/codegraph`
-- Try building with AutoAgents: `cargo build -p codegraph-mcp --bin codegraph --features "ai-enhanced,autoagents-experimental,faiss,ollama"`
-- Or without AutoAgents (legacy): `cargo build -p codegraph-mcp --bin codegraph --features "ai-enhanced,faiss,ollama"`
+- Check binary exists: `./target/release/codegraph-official` or `./target/debug/codegraph-official`
+- Try building with AutoAgents: `cargo build -p codegraph-mcp --bin codegraph-official --features "ai-enhanced,autoagents-experimental,faiss,ollama"`
+- Or without AutoAgents (legacy): `cargo build -p codegraph-mcp --bin codegraph-official --features "ai-enhanced,faiss,ollama"`
 
 ## Additional Resources