I also spent a couple of days writing a solution for this problem. 
Here is a ruby script that you can add to your project's target as a run script build phase. This was tested with XCode 3.2.4 and ruby 1.8.7.
For this to work you will need to install rb-appscript ruby gem. ( eg: sudo gem install rb-appscript )
There is little setup to do:
- First it needs a list of compile targets for added files. 
- Second it expects a project group name which it will synchronize with it's associated disk folder ('objc' in my case) . Obviously this group needs to exist and to point to a real folder.
Here is the script:
require 'rubygems'
require 'appscript'
target_names = ['MinitSample'] # Put your target names here
group_name = 'objc'   # Name of Xcode project group where to add the generated files
project_name = ENV["PROJECT_NAME"]
project_dir = ENV["PROJECT_DIR"]
xcode = Appscript.app('Xcode')
project = xcode.projects[project_name]
group = project.groups[group_name]
group_path =  group.real_path.get
generated_files = Dir.glob(group_path+"/*.m")
missing_files = Array.new(generated_files)
group.item_references.get.each {|item|
  item_path = item.real_path.get
  missing_files.delete(item_path)
  if ! generated_files.include?(item_path) then
    group.file_references[item.name.get].delete
    puts "Deleting #{File.basename(item_path)} from group #{group_name}, as it is not in generated files list"
  end
}
if missing_files.empty? then
  puts "There are no new files to add. "
  exit
end
# holds the compile targets for generated files
targets = []
project.targets.get.each{ |target|
  targets << target if target_names.include?(target.name.get)
}
if targets.empty? then
  puts "Unable to find #{target_names.inspect} in project targets ! Aborting"
  exit
end
missing_files.each{ |path|
  file_name = File.basename(path)
  msg = "Adding #{file_name} to group #{group_name} and to targets: "
  item = xcode.make(:new => :file_reference, 
                    :at => group.item_references.after, 
                    :with_properties => {:full_path => path,
                    :name => file_name})
  targets.each {|target|
      xcode.add(item,{:to=>target})
      msg += target.name.get
    }
    puts msg
}