diff --git a/grader b/grader
--- a/grader
+++ b/grader
@@ -15,7 +15,7 @@
 
 def clear_stopfile
   if FileTest.exist?(File.dirname(__FILE__) + "/stop.#{Process.pid}")
-    system("rm " + File.dirname(__FILE__) + "/stop.#{Process.pid}")
+    File.delete(File.dirname(__FILE__) + "/stop.#{Process.pid}")
   end
 end
 
diff --git a/grader_id b/grader_id
--- a/grader_id
+++ b/grader_id
@@ -1,18 +1,13 @@
 #!/usr/bin/ruby
 
+require 'fileutils'
+
 def talk(str)
   if TALKATIVE
     puts str
   end
 end
 
-def execute(command, error_message="")
-  if not system(command)
-    puts "ERROR: #{error_message}"
-    exit(127)
-  end
-end
-
 def save_source(submission,dir,fname)
   f = File.open("#{dir}/#{fname}","w")
   f.write(submission.source)
@@ -81,18 +76,6 @@
   save_result(sub,read_result("#{problem_out_dir}/test-result"))
 end
 
-def stop_grader
-  File.open(File.dirname(__FILE__) + '/stop','w')
-end
-
-def check_stopfile
-  FileTest.exist?(File.dirname(__FILE__) + '/stop')
-end
-
-def clear_stopfile
-  system("rm " + File.dirname(__FILE__) + '/stop')
-end
-
 # reading environment and options
 GRADER_ENV = 'exam'
 puts "environment: #{GRADER_ENV}"
@@ -104,7 +87,5 @@
 RAILS_ENV = 'development'
 require RAILS_APP_DIR + '/config/environment'
 
-current_dir = `pwd`
+current_dir = FileUtils.pwd
 grade(ARGV[0].to_i)
-
-
diff --git a/import_problem b/import_problem
--- a/import_problem
+++ b/import_problem
@@ -32,8 +32,8 @@
 end
 
 def copy_testcase(importing_test_dir,fname,dir,i)
-  system("cp #{importing_test_dir}/#{fname}.in #{input_filename(dir,i)}")
-  system("cp #{importing_test_dir}/#{fname}.sol #{answer_filename(dir,i)}")
+  FileUtils.cp("#{importing_test_dir}/#{fname}.in", "#{input_filename(dir,i)}")
+  FileUtils.cp("#{importing_test_dir}/#{fname}.sol", "#{answer_filename(dir,i)}")
 end
 
 def process_options(options)
@@ -100,6 +100,12 @@
   end while true
 end
 
+def create_dir_if_not_exists(dir)
+  if ! FileTest.exists? dir
+    FileUtils.mkdir(dir)
+  end
+end
+
 def import_problem(ev_dir, problem, testcase_dir, num_testruns, raw_prefix, check_script, options)
   testrun_info = build_testrun_info_from_dir(num_testruns, testcase_dir, raw_prefix)
 
@@ -113,9 +119,9 @@
   # start working
   puts "creating directories"
 
-  system("mkdir #{problem_dir}")
-  system("mkdir #{problem_dir}/script")
-  system("mkdir #{problem_dir}/test_cases")
+  create_dir_if_not_exists("#{problem_dir}")
+  create_dir_if_not_exists("#{problem_dir}/script")
+  create_dir_if_not_exists("#{problem_dir}/test_cases")
 
   puts "copying testcases"
 
@@ -132,7 +138,7 @@
       
       puts "copy #{testcase_fname} to #{testcase_num}"
       
-      system("mkdir #{problem_dir}/test_cases/#{testcase_num}")
+      create_dir_if_not_exists("#{problem_dir}/test_cases/#{testcase_num}")
       copy_testcase("#{testcase_dir}",testcase_fname,"#{problem_dir}/test_cases/#{testcase_num}",testcase_num)
       
       num_testcases += 1
@@ -163,14 +169,14 @@
     
     File.chmod(0755,"#{problem_dir}/script/check")
     
-    system("cp #{check_script_fname} #{problem_dir}/script/#{script_name}")
+    FileUtils.cp("#{check_script_fname}", "#{problem_dir}/script/#{script_name}")
   else
     if File.exists?(SCRIPT_DIR + "/templates/check.#{check_script}")
       check_script_fname = SCRIPT_DIR + "/templates/check.#{check_script}"
     else
       check_script_fname = check_script
     end
-    system("cp #{check_script_fname} #{problem_dir}/script/check")
+    FileUtils.cp("#{check_script_fname}", "#{problem_dir}/script/check")
   end
   
   # generating test_request directory
@@ -185,8 +191,10 @@
   cfg_file.puts test_request_all_test_cfg.result
   cfg_file.close
   
-  system("cp #{SCRIPT_DIR}/templates/check_empty #{ev_dir}/test_request/#{problem}/script/check")
-  system("cp #{SCRIPT_DIR}/templates/answer-1.txt #{ev_dir}/test_request/#{problem}/test_cases/1")
+  FileUtils.cp("#{SCRIPT_DIR}/templates/check_empty",
+               "#{ev_dir}/test_request/#{problem}/script/check")
+  FileUtils.cp("#{SCRIPT_DIR}/templates/answer-1.txt",
+               "#{ev_dir}/test_request/#{problem}/test_cases/1")
   
   puts "done"
 end
diff --git a/lib/dir_init.rb b/lib/dir_init.rb
--- a/lib/dir_init.rb
+++ b/lib/dir_init.rb
@@ -25,7 +25,7 @@
     # Check if someone has initialized the dir.  If not, call block.
 
     def setup    # :yields: block
-      dir = File.new(@dir_name)
+      dir = File.new(@dir_name + '/lockfile',"w+")
       dir.flock(File::LOCK_EX)
       begin
         counter_filename = get_counter_filename
diff --git a/lib/engine.rb b/lib/engine.rb
--- a/lib/engine.rb
+++ b/lib/engine.rb
@@ -1,5 +1,4 @@
 require 'fileutils'
-require 'ftools'
 require File.join(File.dirname(__FILE__),'dir_init')
 
 module Grader
@@ -32,7 +31,7 @@
     # takes a submission, asks room_maker to produce grading directories,
     # calls grader scripts, and asks reporter to save the result
     def grade(submission)
-      current_dir = `pwd`.chomp
+      current_dir = FileUtils.pwd
 
       user = submission.user
       problem = submission.problem
@@ -137,9 +136,10 @@
 
       scripts.each do |s|
         fname = File.basename(s)
+        next if FileTest.directory?(s)
         if !FileTest.exist?("#{script_dir}/#{fname}")
           copied << fname
-          system("cp #{s} #{script_dir}")
+          FileUtils.cp(s, "#{script_dir}")
         end
       end
       
@@ -174,7 +174,7 @@
 
     def clear_script(log,problem_home)
       log.each do |s|
-        system("rm #{problem_home}/script/#{s}")
+        FileUtils.rm("#{problem_home}/script/#{s}")
       end
     end
 
diff --git a/lib/test_request_helper.rb b/lib/test_request_helper.rb
--- a/lib/test_request_helper.rb
+++ b/lib/test_request_helper.rb
@@ -5,6 +5,23 @@
 
 module Grader
 
+  def self.link_or_copy(src, des)
+    begin
+      FileUtils.ln_s(src, des)
+    rescue NotImplementedError
+      FileUtils.cp(src,des)
+    end
+  end
+
+  def self.call_and_log(error_message)
+    begin
+      yield
+    rescue
+      msg = "ERROR: #{error_message}"
+      raise msg
+    end
+  end
+   
   #
   # A TestRequestRoomMaker is a helper object for Engine
   # - finds grading room: in user_result_dir/(user)/test_request/ ...
@@ -28,8 +45,8 @@
       #    to the sandbox directory later.  The run script should do it.
       #
       if FileTest.exists?("#{test_request.input_file_name}.files")
-        cmd = "cp #{test_request.input_file_name}.files/* #{grading_room}"
-        system(cmd)
+        FileUtils.cp_r("#{test_request.input_file_name}.files/.",
+                       "#{grading_room}")
       end
 
       grading_room
@@ -82,11 +99,12 @@
     end
     
     def copy_problem_template(template_dir,problem_home)
-      cmd = "cp -R #{template_dir}/* #{problem_home}"
-      system_and_raise_when_fail(cmd,"Test Request: cannot copy problem template")
+      Grader::call_and_log("Test Request: cannot copy problem template") {
+        FileUtils.cp_r("#{template_dir}/.","#{problem_home}")
+      }
     end
-    
-    def link_input_file(test_request,problem_home)
+
+    def link_input_file(test_request, problem_home)
       input_fname = "#{test_request.input_file_name}"
       if !File.exists?(input_fname)
         raise "Test Request: input file not found."
@@ -97,20 +115,14 @@
         FileUtils.rm([input_fname_problem_home], :force => true)
       end
 
-      cmd = "ln -s #{input_fname} #{input_fname_problem_home}" 
-      system_and_raise_when_fail(cmd,"Test Request: cannot link input file")
+      Grader::link_or_copy("#{input_fname}", "#{input_fname_problem_home}")
     end
     
     def remove_data_files(problem_home)
       if File.exists?("#{problem_home}/test_cases/1/input-1.txt")
-        cmd = "rm #{problem_home}/test_cases/1/*"
-        system_and_raise_when_fail(cmd,"Test Request: cannot remove data files")
-      end
-    end
-    
-    def system_and_raise_when_fail(cmd,msg)
-      if !system(cmd)
-        raise msg
+        Grader::call_and_log("Test Request: cannot remove data files") {
+          FileUtils.rm Dir.glob("#{problem_home}/test_cases/1/*")
+        }
       end
     end
     
@@ -221,10 +233,7 @@
       target_file_name = random_output_file_name(test_request.user,
                                                  test_request.problem)
       FileUtils.mkdir_p(File.dirname(target_file_name))
-      cmd = "ln -s #{fname} #{target_file_name}"
-      if !system(cmd)
-        raise "TestRequestReporter: cannot move output file"
-      end
+      Grader::link_or_copy("#{fname}", "#{target_file_name}")
       return target_file_name
     end
 
diff --git a/std-script/.gitignore b/std-script/.gitignore
--- a/std-script/.gitignore
+++ b/std-script/.gitignore
@@ -1,2 +1,2 @@
 box
-
+box.exe
diff --git a/std-script/judge b/std-script/judge
--- a/std-script/judge
+++ b/std-script/judge
@@ -1,5 +1,7 @@
 #!/usr/bin/ruby
 
+require 'fileutils'
+
 def log(str='')
   if ENV['TALKATIVE']!=nil
     puts str
@@ -22,6 +24,21 @@
   end
 end
 
+def call_and_log(error_message)
+  begin
+    yield
+  rescue
+    msg = "ERROR: #{error_message}"
+    log msg
+    raise msg
+  end
+end
+
+def clear_and_create_empty_dir(dir)
+  FileUtils.rm_rf(dir, :secure => true)
+  call_and_log("Cannot make directory #{dir}.") { FileUtils.mkdir(dir) }
+end
+
 # ARGV[0] --- language
 # ARGV[1] --- program source file
 # ARGV[2] --- test result directory
@@ -49,7 +66,7 @@
 
 log "Making test result and sandbox directories..."
 
-current_dir = `pwd`
+current_dir = FileUtils.pwd
 current_dir.strip!
 
 if ARGV.length >= 3
@@ -57,9 +74,9 @@
 else
   test_result_dir = "#{current_dir}/test-result"
 end
+
 log "Test result directory: #{test_result_dir}"
-system("rm -Rf #{test_result_dir}")
-execute("mkdir #{test_result_dir}", "Cannot make directory #{test_result_dir}.")
+clear_and_create_empty_dir(test_result_dir)
 
 if ARGV.length >= 4
   sandbox_dir = ARGV[3]
@@ -67,13 +84,14 @@
   sandbox_dir = "#{current_dir}/sandbox"
 end
 log "Sandbox directory: #{sandbox_dir}"
-system("rm -Rf #{sandbox_dir}")
-execute("mkdir #{sandbox_dir}", "Cannot make directory #{sandbox_dir}")
+clear_and_create_empty_dir(sandbox_dir)
 
 # Compile
 log
 log "Compiling..."
-execute("cp #{source_file} #{sandbox_dir}", "Cannot copy the source file to #{sandbox_dir}")
+call_and_log("Cannot copy the source file to #{sandbox_dir}") { 
+  FileUtils.cp(source_file, sandbox_dir) 
+}
 begin 
   Dir.chdir sandbox_dir
 rescue
@@ -81,15 +99,19 @@
   exit(127)
 end
 execute("#{problem_home}/script/compile #{language} #{source_file}", "Compilation error!")
-compile_message = `cat compiler_message`
+compile_message = open("compiler_message").read
 compile_message.strip!
-execute("mv compiler_message #{test_result_dir}", "Cannot move the compiler message to #{test_result_dir}.")
+call_and_log("Cannot move the compiler message to #{test_result_dir}.") {
+  FileUtils.mv("compiler_message", test_result_dir)
+}
 if !FileTest.exist?("a.out")
   log "Cannot compile the source code. See message in #{test_result_dir}/compile_message"
   exit(127)
 else
-  execute("mv a.out #{test_result_dir}", "Cannot move the compiled program to #{test_result_dir}")
-  system("rm -Rf #{sandbox_dir}/*")
+  call_and_log("Cannot move the compiled program to #{test_result_dir}") {
+    FileUtils.mv("a.out",test_result_dir)
+  }
+  FileUtils.rm_rf("#{sandbox_dir}/.")
 end
 
 require "#{problem_home}/script/test_dsl.rb"
@@ -108,17 +130,29 @@
   $stdout.flush
 
   log "Test number: #{test_num}"
-  execute("cp #{test_result_dir}/a.out #{sandbox_dir}", "Cannot copy the compiled program into #{sandbox_dir}")
+  call_and_log("Cannot copy the compiled program into #{sandbox_dir}") {
+    FileUtils.cp("#{test_result_dir}/a.out", sandbox_dir)
+  }
   begin
     execute("#{problem_home}/script/run #{language} #{test_num}", "Error occured during execution of the run script")
   rescue
     # do nothing
   end
-  execute("mkdir #{test_result_dir}/#{test_num}", "Cannot create directory #{test_result_dir}/#{test_num}")
-  execute("mv #{sandbox_dir}/result #{test_result_dir}/#{test_num}", "Cannot copy the result file into #{test_result_dir}/#{test_num}")
-  execute("mv #{sandbox_dir}/comment #{test_result_dir}/#{test_num}", "Cannot copy the comment file into #{test_result_dir}/#{test_num}")
-  execute("mv #{sandbox_dir}/output.txt #{test_result_dir}/#{test_num}", "Cannot copy the output file into #{test_result_dir}/#{test_num}")
-  execute("rm -Rf #{sandbox_dir}/*", "Cannot clear #{sandbox_dir}")
+  call_and_log("Cannot create directory #{test_result_dir}/#{test_num}") {
+    FileUtils.mkdir "#{test_result_dir}/#{test_num}"
+  }
+  call_and_log("Cannot copy the result file into #{test_result_dir}/#{test_num}") {
+    FileUtils.mv "#{sandbox_dir}/result", "#{test_result_dir}/#{test_num}"
+  }
+  call_and_log("Cannot copy the comment file into #{test_result_dir}/#{test_num}") {
+    FileUtils.mv "#{sandbox_dir}/comment", "#{test_result_dir}/#{test_num}"
+  }
+  call_and_log("Cannot copy the output file into #{test_result_dir}/#{test_num}") {
+    FileUtils.mv "#{sandbox_dir}/output.txt", "#{test_result_dir}/#{test_num}"
+  }
+  call_and_log("Cannot clear #{sandbox_dir}") {
+    FileUtils.rm_rf(Dir.glob("#{sandbox_dir}/*"), :secure => true)
+  }
 end
 
 $stdout.print "[done]\n"
diff --git a/std-script/run b/std-script/run
--- a/std-script/run
+++ b/std-script/run
@@ -111,7 +111,7 @@
   result_file.write run_stat.strip 
   result_file.write "\n"
   result_file.close 
-  `rm run_result`
+  FileUtils.rm "run_result"
   # `rm output.txt`   --- keep the output
 
   comment_file.write comment
diff --git a/test/engine_spec_helper.rb b/test/engine_spec_helper.rb
--- a/test/engine_spec_helper.rb
+++ b/test/engine_spec_helper.rb
@@ -1,17 +1,18 @@
+require 'fileutils'
+
 module GraderEngineHelperMethods
 
   def clear_sandbox
     config = Grader::Configuration.get_instance
-    clear_cmd = "rm -rf #{config.test_sandbox_dir}/*"
-    system(clear_cmd)
+    FileUtils.rm_rf(Dir.glob("#{config.test_sandbox_dir}/*"), 
+                    :secure => true)
   end
 
   def init_sandbox
     config = Grader::Configuration.get_instance
     clear_sandbox
     FileUtils.mkdir_p config.user_result_dir
-    cp_cmd = "cp -R #{config.test_data_dir}/ev #{config.test_sandbox_dir}"
-    system(cp_cmd)
+    FileUtils.cp_r("#{config.test_data_dir}/ev", "#{config.test_sandbox_dir}")
   end
 
   def create_submission_from_file(id, user, problem,