Merge configuration properly. Closes #978.

lib/jekyll/configuration.rb

@@ -108,11 +108,10 @@ module Jekyll
     #
     # Returns this configuration, overridden by the values in the file
     def read_config_file(file)
-      configuration = clone
       next_config = YAML.safe_load_file(file)
       raise "Configuration file: (INVALID) #{file}".yellow if !next_config.is_a?(Hash)
       Jekyll::Logger.info "Configuration file:", file
-      configuration.deep_merge(next_config)
+      next_config
     end
 
     # Public: Read in a list of configuration files and merge with this hash
@@ -126,7 +125,8 @@ module Jekyll
 
       begin
         files.each do |config_file|
-          configuration = read_config_file(config_file)
+          new_config = read_config_file(config_file)
+          configuration = configuration.deep_merge(new_config)
         end
       rescue SystemCallError
         # Errno:ENOENT = file not found