diff --git a/make_autotest.sh b/make_autotest.sh
index dca12c731b..e5af26e552 100755
--- a/make_autotest.sh
+++ b/make_autotest.sh
@@ -35,7 +35,9 @@ AUTOTEST_DEST="/usr/local/autotest"
 echo -n "Installing Autotest... "
 sudo mkdir -p ${AUTOTEST_DEST}
 sudo chmod 777 ${AUTOTEST_DEST}
-cp -rpf ${CHROOT_TRUNK_DIR}/src/third_party/autotest/files/{client,server,tko,utils,global_config.ini,shadow_config.ini} ${AUTOTEST_DEST}
+cd ${CHROOT_TRUNK_DIR}/src/third_party/autotest/files
+cp -fpru {client,conmux,server,tko,utils,global_config.ini,shadow_config.ini} \
+    ${AUTOTEST_DEST}
 
 # Create python package init files for top level test case dirs.
 function touchInitPy() {
diff --git a/run_autotest.sh b/run_autotest.sh
index da785cdd63..a0b133e1ca 100755
--- a/run_autotest.sh
+++ b/run_autotest.sh
@@ -27,7 +27,6 @@ set -e
 
 AUTOTEST_CHROOT_DEST="/usr/local/autotest"
 AUTOTEST_SRC="${GCLIENT_ROOT}/src/third_party/autotest/files"
-echo $AUTOTEST_SRC
 
 CHROOT_AUTHSOCK_PREFIX="/tmp/chromiumos_test_agent"
 
@@ -50,27 +49,29 @@ then
 fi
 
 # Install authkey for testing
-
 chmod 400 $FLAGS_test_key
-/usr/bin/ssh-add $FLAGS_test_key 2> /dev/null
+/usr/bin/ssh-add $FLAGS_test_key 
 
 if [ -n "${FLAGS_machine}" ]
 then
-  CLIENT_CONTROL_FILE=${FLAGS_client_control}
   # run only a specific test/suite if requested
-  if [ ! -n "${CLIENT_CONTROL_FILE}" ]
+  if [ ! -n "${FLAGS_client_control}" ]
   then
     # Generate meta-control file to run all existing site tests.
     CLIENT_CONTROL_FILE=\
-      "${AUTOTEST_CHROOT_DEST}/client/site_tests/AllTests/control"
+      "${AUTOTEST_CHROOT_DEST}/client/site_tests/accept_Suite/control"
     echo "No control file specified. Running all tests."
+  else
+    CLIENT_CONTROL_FILE=${AUTOTEST_CHROOT_DEST}/${FLAGS_client_control}
   fi
   # Kick off autosrv for specified test
   autoserv_cmd="${AUTOTEST_CHROOT_DEST}/server/autoserv \
     -m ${FLAGS_machine} \
     -c ${CLIENT_CONTROL_FILE}"
   echo "running autoserv: " ${autoserv_cmd}
+  pushd ${AUTOTEST_CHROOT_DEST} 1> /dev/null
   ${autoserv_cmd}
+  popd 1> /dev/null
 else
   echo "To execute autotest manually:
   eval \$(ssh-agent)        # start ssh-agent