Add Python code for correct overwriting of files

Use the atomicwrites module to ensure the overwrite happens atomically.

Workaround the permissions being incorrect afterwards.

Workaround the prefix argument not working in some versions.

See-also: https://github.com/untitaker/python-atomicwrites/issues/37
See-also: https://github.com/untitaker/python-atomicwrites/issues/38
See-also: https://github.com/untitaker/python-atomicwrites/issues/39
See-also: https://github.com/untitaker/python-atomicwrites/issues/40
See-also: https://github.com/untitaker/python-atomicwrites/issues/42