Reflect file structure when copying files

[Twigonometry]

Currently program copies all files found in the top-level of the directory to the target directory. However it is not built to copy to a subdirectory in that directory (e.g. /path/to/source/subdirectory/file.md will be copied to /path/to/target/file.md)

This does not currently matter as there is currently no recursive mode ( #2 ) but once that is added this issue will need to be completed also.

The option to copy an entire directory will also be added.