Fix file output

[geographika]

Attempt to fix #344 This requires a (root) output folder to already exist when outputting to a folder. Without additional parameters there is no consistent way to tell if a string is a folder or a file across multiple OSs.

[geographika]

After discussions with @jansule a better approach would be to check to see if the input is a folder and if this is the case then assume the output is also a folder. If the input is a file the output will be also.