Directory creation

Hi @apricePhy,

I would like to suggest to change the logic in main.py:
if nor os.path.exists(output_directory):
os.makedirs(output_directory)

to:
if os.path.exists(output_directory):
print(output_directory+" exists, will be removed and recreated")
try:
shutil.rmtree(output_directory)
except OSError as e:
print("Output directory already exists, but cannot be removed")
print("Error : %s - %s." % (e.filename, e.strerror))
os.makedirs(output_directory)

This ensures a clean directory at the start, if we keep the "old" without cleaning, there might be intereference with old files (eg the KKMCee-default links etc which could lead to behaviour hard to debug.