diff --git a/README.md b/README.md
index cb4617b..b330830 100644
--- a/README.md
+++ b/README.md
@@ -191,7 +191,7 @@ GDB supports the target writing files in the PC's file system. This is suppored
 
 * `int file_write(int fd, const void *buf, unsigned int count)`
 
-* `int file_system(const char *buf)`
+* `int file_system(const char *buf)`: System calls are disabled by default in GDB. To enable, use the GDB command `set remote system-call-allowed 1`
 
 For example:
 ```C++
diff --git a/TeensyDebug.h b/TeensyDebug.h
index 0c6c5b6..1d1162b 100644
--- a/TeensyDebug.h
+++ b/TeensyDebug.h
@@ -103,7 +103,16 @@ public:
     return gdb_file_io(gdb_io);
   }
   int file_system(const char *buf) {
-    sprintf(gdb_io, "Fsystem,%x/%x", (unsigned int)buf, strlen(buf));
+    if (*buf == 0) {
+      // if we send empty string, return if shell enabled or not
+      // to enable in gdb, use:
+      //    set remote system-call-allowed 1
+      sprintf(gdb_io, "Fsystem,0/0", (unsigned int)buf, strlen(buf));
+    }
+    else {
+      // make sure to add string terminator
+      sprintf(gdb_io, "Fsystem,%x/%x", (unsigned int)buf, strlen(buf)+1);
+    }
     return gdb_file_io(gdb_io);
   }
 };
diff --git a/gdbstub.cpp b/gdbstub.cpp
index 3bf07a6..dc449da 100644
--- a/gdbstub.cpp
+++ b/gdbstub.cpp
@@ -325,6 +325,18 @@ size_t gdb_out_print(const char *msg) {
   return gdb_out_write((const uint8_t *)msg, strlen(msg));
 }
 
+int gdb_wait_for_flag(int *flag, int timeout) {
+  unsigned int endtime = millis()+1000;
+  while(*flag) {
+    if (timeout && millis() > endtime) {
+      return -1;
+    }
+    delay(1);
+    yield();
+  }
+  return 0;
+}
+
 int file_io_result;
 int file_io_errno;
 int file_io_pending = 0;
@@ -333,10 +345,7 @@ int gdb_file_io(const char *cmd) {
   // Serial.println(cmd);
   file_io_pending = 1;
   sendResult(cmd);
-  while(file_io_pending) {
-    delay(1);
-    yield();
-  }
+  gdb_wait_for_flag(&file_io_pending, 1000);
   // Serial.println(file_io_result);
   return file_io_result;
 }
@@ -349,13 +358,10 @@ int gdb_file_io(const char *cmd) {
 #pragma GCC optimize ("O0")
 void process_onbreak() {
   // send the signal
+  halt_state = 1;
   sendResult(signal_text[debug_id]);
   // go into halt state and stay until flag is cleared
-  halt_state = 1;
-  while(halt_state) {
-    delay(1);
-    yield();
-  }
+  gdb_wait_for_flag(&halt_state, 0);
   debug_id = 0;
 }