```ruby
class JoDoc
  JO_DOC_CLI         = 'jodoc'
  TEMPLATE_DIRECTORY = File.expand_path( File.join( File.dirname(__FILE__), '..', '..', 'template', 'phonegap' ) )
  
  attr_accessor :input_directory
  attr_accessor :output_directory
  
  def initialize(input_directory, output_directory)
    @input_directory  = input_directory
    @output_directory = output_directory
    check_dependencies
  end
  
  def run
    # Copy HTML template assets
    FileUtils.cp_r TEMPLATE_DIRECTORY, @output_directory

    # Run joDoc
    FileUtils.cd @input_directory do
      `jodoc --output #{@output_directory} --title "PhoneGap API Documentation" --template #{TEMPLATE_DIRECTORY}/index.html ./phonegap`
    end
  end
  
  protected
  
  def check_dependencies
    die 'The jodoc script is not in your path' unless command_exists?(JO_DOC_CLI)

    [@input_directory, TEMPLATE_DIRECTORY].each do |directory|
      die "The directory #{directory}/ should exist." unless File.directory? directory
    end
  end
  
  def command_exists?(command)
    system("which #{command} > /dev/null 2>/dev/null")
  end
  
  def die(message)
    raise StandardError, message
  end
end```

Remove __ prefix from generated HTML files.
user
```ruby
class JoDoc
  JO_DOC_CLI         = 'jodoc'
  TEMPLATE_DIRECTORY = File.expand_path( File.join( File.dirname(__FILE__), '..', '..', 'template', 'phonegap' ) )
  
  attr_accessor :input_directory
  attr_accessor :output_directory
  
  def initialize(input_directory, output_directory)
    @input_directory  = input_directory
    @output_directory = output_directory
    check_dependencies
  end
  
  def run
    # Copy HTML template assets
    FileUtils.cp_r TEMPLATE_DIRECTORY, @output_directory

    # Run joDoc
    FileUtils.cd @input_directory do
      `jodoc --output #{@output_directory} --title "PhoneGap API Documentation" --template #{TEMPLATE_DIRECTORY}/index.html .`
    end
  end
  
  protected
  
  def check_dependencies
    die 'The jodoc script is not in your path' unless command_exists?(JO_DOC_CLI)

    [@input_directory, TEMPLATE_DIRECTORY].each do |directory|
      die "The directory #{directory}/ should exist." unless File.directory? directory
    end
  end
  
  def command_exists?(command)
    system("which #{command} > /dev/null 2>/dev/null")
  end
  
  def die(message)
    raise StandardError, message
  end
end```
assistant