Cleaner removes directory if it only contain subdirectories

[sjoerdmulder]

Hit a problem when working with a directory with subdirectory containing large video files, using jekyll serve -w takes around 20 seconds+ to regenerate the site.

It seems that the cleaner.rb is marking folders for deletion when they contain no other files, it uses @site.each_site_file to find the files and takes the directories only from those files to mark them as being active. So in a structure like:

my-awesome-site
  - video
      - chapter1
      - chapter2

Where the files are only in video/chapter and video/chapter2 it marks the video directory for deletion, causing the whole video folder to be copied again.

When this is fixed probally #1297 is also resolved.

Workaround for now is to have an empty index.html file in the video folder