This script walks thru all the files in a Xcode project's groups belong to the target they are supposed to, according to group names found while walking the groups hierarchy.

xcodeproj_check_files_in_proper_targets.rb

#!/usr/bin/env ruby

# This script walks thru all the files in a Xcode project's groups belong to the target they are supposed to
# according to group names found while walking the groups hierarchy.
#
# This example only focuses on test files and groups/targets ending with "...Tests"

require 'xcodeproj'

def check(group, all_targets, walk_path, ctx_target_name = nil, ctx_expected_files_list = nil)
  group_name = group.name || group.path
  walk_path += "/#{group_name}"

  # If folder ends with "...Tests", try to find a target matching its name
  if group_name.end_with?('Tests')
    matching_target = all_targets.find { |t| t.name == group_name }
    unless matching_target.nil?
      ctx_target_name = matching_target.name
      ctx_expected_files_list = matching_target
        .build_phases
        .find { |p| p.is_a? Xcodeproj::Project::Object::PBXSourcesBuildPhase }
        .files_references
    end
  end
  
  # Loop on the group's files and check they are in the ctx_expected_files_list (if matching target has been found)
  if ctx_expected_files_list
    group.files.each do |file_ref|
      next unless file_ref.path.end_with?('.swift')
      unless ctx_expected_files_list.include?(file_ref)
        puts "File #{file_ref.path} in #{walk_path} was expected to be found in #{ctx_target_name}"
      end
    end
  end

  # Recursion: Loop on the group's subgroups
  group.groups.each do |group|
    check(group, all_targets, walk_path, ctx_target_name, ctx_expected_files_list)
  end
end

x = Xcodeproj::Project.open('Babylon.xcodeproj')
x.groups.each do |group|
  check(group, x.targets, File.basename(x.path))
end