Hidden files and folders
Right now Kiln hides by default every dotfile, so everything that starts with a ., being that a file or a folder, is hidden from the output. This feature cannot be turned off right now.
_hidden_ prefix
If you wish to hide certain files and folders, just use the _hidden_ prefix. An example usage could be hiding your template folder. If you add this prefix to the template folder they will not be processed by kiln.
Info
This current solution will eventually be changed again into a more stable version that works for every situation.