SharePoint 2013: Having nested folders in site template

I have created a custom site template in visual studio, and in the template I have a folder called CommonDocuments, which as the name suggests, contains several files that are used in a few of the configurations. Now, when I deploy and try to create a site I am told that it cant find the files within this folder.

I look in the 15 hive, and I find that the folder structure that visual studio created is not reflected in the hive. All of these common documents are at the root level with every other file.

Is there a special way I am supposed to create folders?