I'll trust you somehow. But the answers below won't be pleasant, as they'll outline a few very basic mistakes.
Problem 1: the script doesn't run from the scratch directory.
Solution 1: you gave the command "./ns3 run scratch/vr-app/examples/trace-file-burst-application-example.cc", showing that either you did mistype the script name and path, or that you copied an entire folder into the scratch directory. Using sub-folders in the scratch directory is possible, and it is explained in the manual or tutorial (I don't remember where). In any case, this is needed only if you have a script split among multiple source files. If you don't, then the script should be placed in the scratch folder directly.
Problem 2: the xml file is not generated.
Solution 2: in your script YOU wrote:
CommandLine cmd (__FILE__);
cmd.AddValue ("traceFolder", "The folder containing the trace.", traceFolder);
cmd.AddValue ("traceFile", "The trace file name.", traceFile);
cmd.AddValue ("startTime", "The start time offset of the trace [s].", startTime);
cmd.AddValue ("simTime", "Length of simulation [s].", simTime);
cmd.Parse (argc, argv);
[...]
// Allow the user to override any of the defaults and the above
// DefaultValue::Bind ()s at run-time, via command-line arguments
bool enableFlowMonitor = false;
cmd.AddValue("EnableMonitor", "Enable Flow Monitor", enableFlowMonitor);
cmd.Parse(argc, argv);
probably because you did copy-paste from another example without understanding what you did (coding means you do understand, or at least you try to).
The 1st "cmd.Parse (argc, argv);" prevents the 2nd to be executed, so you don't have the option "EnableMonitor" in the command line. The default value for "enableFlowMonitor" is false, so the behavior is to not use FlowMonitor.
This is pure and simple code reading.
Furthermore, I don't see in your logs you trying to use the command line option, so even if you'd fix the coding problem by removing the first " cmd.Parse (argc, argv);", you'd not be generating the FlowMonitor logs.
The correct way (or at least one of the correct ways) would have been "/ns3 run scratch/trace-file-burst-application-example.cc -- --EnableMonitor". Also this is explained in the tutorial and manual.
See? Mistakes that would have been prevented easily, by reading the code and by reading the documentation...