diff --git a/cmd/server/main.go b/cmd/server/main.go
index 8d09f524..a4266a00 100644
--- a/cmd/server/main.go
+++ b/cmd/server/main.go
@@ -21,10 +21,6 @@ var (
 		Use:   "server",
 		Short: "GitHub MCP Server",
 		Long:  `A GitHub MCP server that handles various tools and resources.`,
-		PersistentPreRun: func(cmd *cobra.Command, args []string) {
-			// Bind flag to viper
-			viper.BindPFlag("log-file", cmd.PersistentFlags().Lookup("log-file"))
-		},
 	}
 
 	stdioCmd = &cobra.Command{
@@ -50,6 +46,9 @@ func init() {
 	// Add global flags that will be shared by all commands
 	rootCmd.PersistentFlags().String("log-file", "", "Path to log file")
 
+	// Bind flag to viper
+	viper.BindPFlag("log-file", rootCmd.PersistentFlags().Lookup("log-file"))
+
 	// Add subcommands
 	rootCmd.AddCommand(stdioCmd)
 }
diff --git a/go.mod b/go.mod
index 08f1472c..e53b8b6b 100644
--- a/go.mod
+++ b/go.mod
@@ -3,12 +3,13 @@ module github.com/github/github-mcp-server
 go 1.23.7
 
 require (
+	github.com/aws/smithy-go v1.22.3
 	github.com/google/go-github/v69 v69.2.0
 	github.com/mark3labs/mcp-go v0.11.2
 	github.com/sirupsen/logrus v1.9.3
 	github.com/spf13/cobra v1.9.1
 	github.com/spf13/viper v1.19.0
-	github.com/aws/smithy-go v1.22.3
+	golang.org/x/exp v0.0.0-20230905200255-921286631fa9
 )
 
 require (
@@ -29,7 +30,6 @@ require (
 	github.com/subosito/gotenv v1.6.0 // indirect
 	go.uber.org/atomic v1.9.0 // indirect
 	go.uber.org/multierr v1.9.0 // indirect
-	golang.org/x/exp v0.0.0-20230905200255-921286631fa9 // indirect
 	golang.org/x/sys v0.18.0 // indirect
 	golang.org/x/text v0.14.0 // indirect
 	gopkg.in/ini.v1 v1.67.0 // indirect