`include` option applies to all submodules and creates empty directories in each

[ChristofLee]

I have downloaded the phploy.phar from Github (there was a fatal error with league/filesystem in the composer version).

In my options, I have for example include[] = 'assets/dist'.

When I run the deploy, as it recurses through each submodule it looks for the directory and creates it, even if it does not exist in the current submodule.

This results in every submodule containing an empty directory assets/dist after deployment.

#374 This issue seems to relate to the creation of directories.