play tricks to close fd manually

src/main/java/com/github/shadowsocks/System.java

@@ -46,4 +46,5 @@ public class System {
   public static native void exec(String cmd);
   public static native String getABI();
   public static native int sendfd(int fd);
+  public static native void jniclose(int fd);
 }

src/main/jni/system.cpp

@@ -43,6 +43,10 @@ void Java_com_github_shadowsocks_system_exec(JNIEnv *env, jobject thiz, jstring
     env->ReleaseStringUTFChars(cmd, str);
 }
 
+void Java_com_github_shadowsocks_system_jniclose(JNIEnv *env, jobject thiz, jint fd) {
+    close(fd);
+}
+
 jint Java_com_github_shadowsocks_system_sendfd(JNIEnv *env, jobject thiz, jint tun_fd) {
     int fd;
     struct sockaddr_un addr;
@@ -75,6 +79,8 @@ jint Java_com_github_shadowsocks_system_sendfd(JNIEnv *env, jobject thiz, jint t
 static const char *classPathName = "com/github/shadowsocks/System";
 
 static JNINativeMethod method_table[] = {
+    { "jniclose", "(I)V",
+        (void*) Java_com_github_shadowsocks_system_jniclose },
     { "sendfd", "(I)I",
         (void*) Java_com_github_shadowsocks_system_sendfd },
     { "exec", "(Ljava/lang/String;)V",

src/main/scala/com/github/shadowsocks/ShadowsocksVpnThread.scala

@@ -105,6 +105,9 @@ class ShadowsocksVpnThread(vpnService: ShadowsocksVpnService) extends Thread {
                 val fd = getInt.invoke(fds(0)).asInstanceOf[Int]
                 ret = vpnService.protect(fd)
 
+                // Trick to close file decriptor
+                System.jniclose(fd)
+
                 if (ret) {
                   output.write(0)
                 } else {