Git doesn’t track folders, only files, so if you ignore everything in a folder, Git won’t have anything to track. You can add a .gitignore file to each directory (application/cache, application/cache/folder, application/cache/folder/onemorefolder/) with the following contents:
*
!.gitignore
Then, you can add those directories, and only the .gitignore file in each directory will get added — but this means the directories will now be tracked (i.e., created when cloning).