submodule_strategy.rb

# Usage: 
# 1. Drop this file into lib/capistrano/submodule_strategy.rb
# 2. Add the following to your Capfile:
#   require 'capistrano/git'
#   require './lib/capistrano/submodule_strategy'
# 3. Add the following to your config/deploy.rb
#   set :git_strategy, SubmoduleStrategy
# 4. Add .capignore file and list each file or directory to exclude from deployment on a separate line.  Example:
#  .capignore
#  lib
#  config
#  .git

module SubmoduleStrategy
  # do all the things a normal capistrano git session would do
  include Capistrano::Git::DefaultStrategy
  
  # check for a .git directory
  def test
    test! " [ -d #{repo_path}/.git ] "
  end

  # same as in Capistrano::Git::DefaultStrategy
  def check
    test! :git, :'ls-remote', repo_url
  end

  def clone
    git :clone, '-b', fetch(:branch), '--recursive', repo_url, repo_path
  end

  # same as in Capistrano::Git::DefaultStrategy
  def update
    git :remote, :update
  end

  # put the working tree in a release-branch,
  # make sure the submodules are up-to-date
  # and copy everything to the release path
  def release
    release_branch = fetch(:release_branch, File.basename(release_path))
    git :checkout, '-B', release_branch, 
      fetch(:remote_branch, "origin/#{fetch(:branch)}")
    git :submodule, :update, '--init'
    context.execute "rsync -ar --exclude-from '#{repo_path}/.capignore' #{repo_path}/ #{release_path}"
  end
end

Added option for Capistrano to ignore files when deploying.
OOTB Capistrano 3.1.x uses .gitattributes to accomplish. Due to changes in this fork, that feature was lost.
Can now be replicated by using .capignore file in project root.
List each file or direcotry to ignore on its own line.

.capignore
.git
lib
cap
...