fix(cli): fix generated Go MCP server run and doc

This fixes the kmcp run command for mcp servers generated with kmcp init
go and updates the generated README with the accurate file paths

Author: kevdkr

pkg/cli/internal/commands/run.go

@@ -168,11 +168,11 @@ func runMCPGo(projectDir string, manifest *manifest.ProjectManifest) error {
 
 	if noInspector {
 		// Run the server directly
-		fmt.Printf("Running server directly: go run main.go\n")
+		fmt.Printf("Running server directly: go run cmd/server/main.go\n")
 		fmt.Printf("Server is running and waiting for MCP protocol input on stdin...\n")
 		fmt.Printf("Press Ctrl+C to stop the server\n")
 
-		serverCmd := exec.Command("go", "run", "main.go")
+		serverCmd := exec.Command("go", "run", "cmd/server/main.go")
 		serverCmd.Dir = projectDir
 		serverCmd.Stdout = os.Stdout
 		serverCmd.Stderr = os.Stderr
@@ -183,7 +183,7 @@ func runMCPGo(projectDir string, manifest *manifest.ProjectManifest) error {
 	// Create server configuration for inspector
 	serverConfig := map[string]interface{}{
 		"command": "go",
-		"args":    []string{"run", "main.go"},
+		"args":    []string{"run", "cmd/server/main.go"},
 	}
 
 	// Create MCP inspector config

pkg/cli/internal/frameworks/golang/generator.go

@@ -61,7 +61,7 @@ func (g *Generator) GenerateTool(projectroot string, config templates.ToolConfig
 	fmt.Printf("\nNext steps:\n")
 	fmt.Printf("1. Edit internal/tools/%s.go to implement your tool logic\n", toolNameSnakeCase)
 	fmt.Printf("2. Configure any required environment variables in kmcp.yaml\n")
-	fmt.Printf("3. Run 'go run main.go' to start the server\n")
+	fmt.Printf("3. Run 'go run cmd/server/main.go' to start the server\n")
 
 	return nil
 }

pkg/cli/internal/frameworks/golang/templates/README.md.tmpl

@@ -20,7 +20,7 @@ This project was generated with [`kmcp`](https://github.com/kagent-dev/kmcp).
 
 2.  **Run the server:**
     ```bash
-    go run main.go
+    go run cmd/server/main.go
     ```
 
 ### Building the Docker Image
@@ -51,4 +51,4 @@ To add a new tool to your project, use the `kmcp add-tool` command:
 kmcp add-tool <tool-name>
 ```
 
-This will generate a new Go file in the `tools/` directory with a template for your new tool. You will need to add the new tool to the `main.go` file. 
+This will generate a new Go file in the `internal/tools/` directory with a template for your new tool. You will need to add the new tool to the `main.go` file.