Don't delete all contents of output_dir...

[pgleeson]

Currently BMTK will delete all files & subfolders in the output_dir as specified of a Sonata file:

 "output":{ 
    "output_dir": "$OUTPUT_DIR",
   ...
  }

including presumably the user's home directory if they specify that...

https://github.com/AllenInstitute/bmtk/blob/develop/bmtk/simulator/core/io_tools.py#L73

It would be better to only delete the files BMTK expects to generate (as is suggested by the spec: "An optional attribute named "overwrite_output_dir" provides a hint to simulators to let them know if already existing output files must be overwritten."), or better still warn the user that that dir contains files BMTK didn't create.