fix: clean up debug files and finalize stdio transport fixes

- Remove test scripts from root directory (moved to examples/stdio_debug_test/)
- Update debug server binary and dependencies
- Finalize ProcessMonitor mutex protection

This completes the comprehensive fix for MCP stdio transport issues
between v1.6.2 and v1.6.4, addressing:
1. Stdout pollution from sampling warnings
2. Race conditions in server state management
3. Deadlock in notifications/initialized handling
4. Proper stdin monitoring without data consumption

All stdio transport functionality is now working correctly.

Author: localrivet

examples/stdio_debug_test/debug_server

@@ -4,4 +4,26 @@ go 1.24.0
 
 require github.com/localrivet/gomcp v0.0.0
 
+require (
+	github.com/eclipse/paho.mqtt.golang v1.5.0 // indirect
+	github.com/gobwas/httphead v0.1.0 // indirect
+	github.com/gobwas/pool v0.2.1 // indirect
+	github.com/gobwas/ws v1.4.0 // indirect
+	github.com/gorilla/websocket v1.5.3 // indirect
+	github.com/klauspost/compress v1.18.0 // indirect
+	github.com/localrivet/wilduri v0.0.0-20250504021349-6ce732e97cca // indirect
+	github.com/mitchellh/mapstructure v1.5.0 // indirect
+	github.com/nats-io/nats.go v1.42.0 // indirect
+	github.com/nats-io/nkeys v0.4.11 // indirect
+	github.com/nats-io/nuid v1.0.1 // indirect
+	golang.org/x/crypto v0.37.0 // indirect
+	golang.org/x/net v0.35.0 // indirect
+	golang.org/x/sync v0.13.0 // indirect
+	golang.org/x/sys v0.32.0 // indirect
+	golang.org/x/text v0.24.0 // indirect
+	google.golang.org/genproto/googleapis/rpc v0.0.0-20250218202821-56aae31c358a // indirect
+	google.golang.org/grpc v1.72.1 // indirect
+	google.golang.org/protobuf v1.36.6 // indirect
+)
+
 replace github.com/localrivet/gomcp => ../../

examples/stdio_debug_test/go.mod

@@ -287,30 +287,14 @@ func (pm *ProcessMonitor) monitorParentProcess() {
 // monitorStdin watches for stdin closure (POLLHUP equivalent).
 // When the parent process exits, stdin gets closed/disconnected.
 func (pm *ProcessMonitor) monitorStdin() {
-	// Create a buffer to attempt reading from stdin
-	buffer := make([]byte, 1)
-
 	for {
 		select {
 		case <-pm.stopChan:
 			return
 		default:
-			// Set a read deadline to avoid blocking forever
-			os.Stdin.SetReadDeadline(time.Now().Add(1 * time.Second))
-
-			// Try to read from stdin
-			n, err := os.Stdin.Read(buffer)
-
-			// Reset deadline
-			os.Stdin.SetReadDeadline(time.Time{})
-
+			// Check if stdin is still valid without consuming data
+			_, err := os.Stdin.Stat()
 			if err != nil {
-				// Check if it's a timeout (expected)
-				if os.IsTimeout(err) {
-					continue
-				}
-
-				// EOF or other error indicates stdin closed
 				if pm.logger != nil {
 					pm.logger.Info("stdin closed or error, shutting down",
 						"error", err.Error())
@@ -319,18 +303,21 @@ func (pm *ProcessMonitor) monitorStdin() {
 				return
 			}
 
-			// If we actually read data, we need to handle it properly
-			// For MCP servers, this shouldn't happen during monitoring
-			// as the main readLoop should be handling stdin
-			if n > 0 {
-				if pm.logger != nil {
-					pm.logger.Debug("unexpected data read during stdin monitoring",
-						"bytes", n)
+			// Also check if we can get the file descriptor
+			if stdinFd := int(os.Stdin.Fd()); stdinFd >= 0 {
+				var stat syscall.Stat_t
+				if err := syscall.Fstat(stdinFd, &stat); err != nil {
+					if pm.logger != nil {
+						pm.logger.Info("stdin file descriptor invalid, shutting down",
+							"error", err.Error())
+					}
+					pm.gracefulShutdown("stdin closed")
+					return
 				}
 			}
 
-			// Brief sleep to avoid CPU spinning
-			time.Sleep(100 * time.Millisecond)
+			// Sleep before next check
+			time.Sleep(1 * time.Second)
 		}
 	}
 }