diff --git a/Rakefile b/Rakefile
index 650d25fe..d725e80d 100644
--- a/Rakefile
+++ b/Rakefile
@@ -218,23 +218,31 @@ end
 
 desc 'prime_site_files'
 task :prime_site_files => [:environment] do
-  Site.where(is_banned: false).select(:id, :username).all.each do |site|
+  Site.where(is_banned: false).where(is_deleted: false).select(:id, :username).all.each do |site|
     Dir.glob(File.join(site.files_path, '**/*')).each do |file|
-      next unless site.username == 'kyledrake'
       path = file.gsub(site.base_files_path, '').sub(/^\//, '')
 
       site_file = site.site_files_dataset[path: path]
 
       if site_file.nil?
-        next if File.directory? file
         mtime = File.mtime file
-        site.add_site_file(
+
+        site_file_opts = {
           path: path,
-          size: File.size(file),
-          sha1_hash: Digest::SHA1.file(file).hexdigest,
           updated_at: mtime,
           created_at: mtime
-        )
+        }
+
+        if File.directory? file
+          site_file_opts.merge! is_directory: true
+        else
+          site_file_opts.merge!(
+            size: File.size(file),
+            sha1_hash: Digest::SHA1.file(file).hexdigest
+          )
+        end
+
+        site.add_site_file site_file_opts
       end
     end
   end
diff --git a/models/site.rb b/models/site.rb
index 69234695..49f1af14 100644
--- a/models/site.rb
+++ b/models/site.rb
@@ -671,6 +671,30 @@ class Site < Sequel::Model
       return 'Directory (or file) already exists.'
     end
 
+    path_dirs = path.to_s.split '/'
+
+    path_site_file = ''
+
+    until path_dirs.empty?
+      if path_site_file == ''
+        path_site_file += path_dirs.shift
+      else
+        path_site_file += '/' + path_dirs.shift
+      end
+
+      site_file = SiteFile.where(site_id: self.id, path: path_site_file).first
+
+      if site_file.nil?
+        SiteFile.create(
+          site_id: self.id,
+          path: path_site_file,
+          is_directory: true,
+          created_at: Time.now,
+          updated_at: Time.now
+        )
+      end
+    end
+
     FileUtils.mkdir_p relative_path
     true
   end
@@ -914,7 +938,7 @@ class Site < Sequel::Model
     path ||= ''
     clean = []
 
-    parts = path.split '/'
+    parts = path.to_s.split '/'
 
     parts.each do |part|
       next if part.empty? || part == '.'
@@ -1243,7 +1267,7 @@ class Site < Sequel::Model
       FileUtils.rm files_path(path)
     rescue Errno::EISDIR
       site_files.each do |site_file|
-        if site_file.path.match /^#{path}\//
+        if site_file.path.match(/^#{path}\//) || site_file.path == path
           site_file.destroy
         end
       end
@@ -1262,7 +1286,7 @@ class Site < Sequel::Model
 
     DB.transaction do
       site_file = site_files_dataset.where(path: path).first
-      if site_file
+      if site_file && !site_file.size.nil? && !site_file.is_directory
         DB['update sites set space_used=space_used-? where id=?', site_file.size, self.id].first
         site_file.delete
       end
@@ -1287,6 +1311,15 @@ class Site < Sequel::Model
       return false
     end
 
+    if pathname.extname.match HTML_REGEX
+      # SPAM and phishing checking code goes here
+    end
+
+    relative_path_dir = Pathname(relative_path).dirname
+    create_directory relative_path_dir unless relative_path_dir == '.'
+
+    uploaded_size = uploaded.size
+
     if relative_path == 'index.html'
       begin
         new_title = Nokogiri::HTML(File.read(uploaded.path)).css('title').first.text
@@ -1299,18 +1332,6 @@ class Site < Sequel::Model
       end
     end
 
-    if pathname.extname.match HTML_REGEX
-      # SPAM and phishing checking code goes here
-    end
-
-    dirname = pathname.dirname.to_s
-
-    if !File.exists? dirname
-      FileUtils.mkdir_p dirname
-    end
-
-    uploaded_size = uploaded.size
-
     FileUtils.cp uploaded.path, path
     File.chmod 0640, path
 
@@ -1332,6 +1353,7 @@ class Site < Sequel::Model
     elsif pathname.extname.match IMAGE_REGEX
       ThumbnailWorker.perform_async values[:username], relative_path
     end
+
     true
   end
 end
diff --git a/tests/site_file_tests.rb b/tests/site_file_tests.rb
index 7428c417..dc64b744 100644
--- a/tests/site_file_tests.rb
+++ b/tests/site_file_tests.rb
@@ -69,8 +69,30 @@ describe 'site_files' do
         'files[]' => Rack::Test::UploadedFile.new('./tests/files/test.jpg', 'image/jpeg')
       )
       delete_file filename: 'test'
+      @site.site_files.select {|f| f.path == 'test'}.length.must_equal 0
       @site.site_files.select {|f| f.path =~ /^test\//}.length.must_equal 0
-      @site.site_files.select {|f| f.path =~ /^test/}.length.must_equal 1
+      @site.site_files.select {|f| f.path =~ /^test.jpg/}.length.must_equal 1
+    end
+
+    it 'deletes records for nested directories' do
+      upload(
+        'dir' => 'derp/ing/tons',
+        'files[]' => Rack::Test::UploadedFile.new('./tests/files/test.jpg', 'image/jpeg')
+      )
+
+      expected_site_file_paths = ['derp', 'derp/ing', 'derp/ing/tons', 'derp/ing/tons/test.jpg']
+
+      expected_site_file_paths.each do |path|
+        @site.site_files.select {|f| f.path == path}.length.must_equal 1
+      end
+
+      delete_file filename: 'derp'
+
+      @site.reload
+
+      expected_site_file_paths.each do |path|
+        @site.site_files.select {|f| f.path == path}.length.must_equal 0
+      end
     end
 
     it 'goes back to deleting directory' do
@@ -248,6 +270,10 @@ describe 'site_files' do
       ThumbnailWorker.jobs.length.must_equal 1
       ThumbnailWorker.drain
 
+      @site.site_files_dataset.where(path: 'derpie').count.must_equal 1
+      @site.site_files_dataset.where(path: 'derpie/derptest').count.must_equal 1
+      @site.site_files_dataset.where(path: 'derpie/derptest/test.jpg').count.must_equal 1
+
       Site::THUMBNAIL_RESOLUTIONS.each do |resolution|
         File.exists?(@site.thumbnail_path('derpie/derptest/test.jpg', resolution)).must_equal true
         @site.thumbnail_url('derpie/derptest/test.jpg', resolution).must_equal(