Add a flag to select the location of the output files in recurse mode

[walle]

Default should be as is now. All files are outputted to the output dir. But there should be a flag that says to reflect the input structure. eg.

Input

• folder1 -- file1.textile --folder2 ---file2.markdown

And the output dir should have these too.

Output

• folder1 -- file1.pdf --folder2 ---file2.pdf