diff --git a/.ci/docker/docker-compose-system-test.yml b/.ci/docker/docker-compose-system-test.yml
index 37d9366c..0417cd41 100644
--- a/.ci/docker/docker-compose-system-test.yml
+++ b/.ci/docker/docker-compose-system-test.yml
@@ -9,7 +9,7 @@ services:
       ports:
          - "${HIRS_ACA_PORTAL_PORT}:${HIRS_ACA_PORTAL_CONTAINER_PORT}"
       entrypoint: /bin/bash -c
-      command: [HIRS/.ci/setup/setup_aca.sh]
+      command: [HIRS/.ci/setup/container/setup_aca.sh]
       hostname: ${HIRS_ACA_HOSTNAME}
       networks:
          hirs_aca_system_tests:
diff --git a/.ci/setup/setup_aca.sh b/.ci/setup/container/setup_aca.sh
similarity index 100%
rename from .ci/setup/setup_aca.sh
rename to .ci/setup/container/setup_aca.sh
diff --git a/.ci/setup/setup_tpm2provisioner.sh b/.ci/setup/container/setup_tpm2provisioner.sh
similarity index 67%
rename from .ci/setup/setup_tpm2provisioner.sh
rename to .ci/setup/container/setup_tpm2provisioner.sh
index b5508332..3da44cec 100755
--- a/.ci/setup/setup_tpm2provisioner.sh
+++ b/.ci/setup/container/setup_tpm2provisioner.sh
@@ -1,13 +1,15 @@
 #!/bin/bash
 #########################################################################################
-#  Script to setup the TPM 2.0 Provisioner Docker Image for System Tests
-#
+#  Script to setup the TPM 2.0 Provisioner for System Tests
+#  Initial setup only  use resetTpm2Emulator to reset PCR values in subsequent tests
 #########################################################################################
 set -e
 pushd /  > /dev/null
 echo "Setting up TPM emulator for the TPM2 Provisioner"
  
-source /HIRS/.ci/setup/tpm2_common.sh
+source /HIRS/.ci/setup/container/tpm2_common.sh
+mkdir -p /etc/hirs
+touch /etc/hirs/tcg_boot.properties   # work around for install issues with tcg default values 
 
 #Wait for the ACA to spin up, if it hasnt already
 waitForAca
@@ -16,7 +18,7 @@ waitForAca
 installProvisioner
 
 # set location of tcg artifacts
-setTcgProperties
+#setTcgProperties
 #echo "Contents of /etc/hirs is $(ls -al /etc/hirs)";
 
 # Install TPM 2.0 Emulator
@@ -33,4 +35,4 @@ echo "===========HIRS ACA TPM 2.0 Provisioner Setup Complete!==========="
 
 popd > /dev/null
 
-tpm2_pcrlist -g sha256 
+#tpm2_pcrlist -g sha256 
diff --git a/.ci/setup/setup_tpmprovisioner.sh b/.ci/setup/container/setup_tpmprovisioner.sh
similarity index 100%
rename from .ci/setup/setup_tpmprovisioner.sh
rename to .ci/setup/container/setup_tpmprovisioner.sh
diff --git a/.ci/setup/tpm2_common.sh b/.ci/setup/container/tpm2_common.sh
similarity index 98%
rename from .ci/setup/tpm2_common.sh
rename to .ci/setup/container/tpm2_common.sh
index 2d457e96..10c33eaf 100755
--- a/.ci/setup/tpm2_common.sh
+++ b/.ci/setup/container/tpm2_common.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 #########################################################################################
-#  Script to setup the TPM 2.0 Provisioner Docker Image for System Tests
+#  Support scripts for the TPM 2.0 Provisioner System Tests
 #
 #########################################################################################
 
@@ -124,7 +124,7 @@ pkill -f "tpm_server"
 
  pushd /ibmtss/utils  > /dev/null
     ./startup
- popd
+ popd > /dev/null
   tpm2-abrmd -t socket &
 }
 
diff --git a/.ci/system-tests/container/pc_setup.sh b/.ci/system-tests/container/pc_setup.sh
index 6a13a348..d272f93b 100644
--- a/.ci/system-tests/container/pc_setup.sh
+++ b/.ci/system-tests/container/pc_setup.sh
@@ -2,6 +2,7 @@
 #########################################################################################
 #   Setup for platform certificates for testing
 #   Copies platform certs (Base and Delta) to the tcg directory
+#   usage pc_setup.sh <profile> <test>
 #########################################################################################
 
 profile=$1
diff --git a/.ci/system-tests/container/rim_setup.sh b/.ci/system-tests/container/rim_setup.sh
index f6fba8e1..a3f605e8 100644
--- a/.ci/system-tests/container/rim_setup.sh
+++ b/.ci/system-tests/container/rim_setup.sh
@@ -1,7 +1,8 @@
 #!/bin/bash
 #########################################################################################
 #   Setup for PC Client Reference Integrity Manifest (RIM) tests
-#
+#   usage rim_setup.sh <profile> <test> <option>
+#   use "clear" option to clear existing TPM PCR values
 #########################################################################################
 
 profile=$1
@@ -17,7 +18,7 @@ swidDir="$testDir/swidtags"
 rimDir="$testDir/rims"
 pcrScript="$testDir/"$profile"_"$test"_setpcrs.sh"
 
-source /HIRS/.ci/setup/tpm2_common.sh
+source /HIRS/.ci/setup/container/tpm2_common.sh
 
 echo "Test is using RIM files from $profile : $test"
 
@@ -36,7 +37,7 @@ if [[ ! -f "$eventLog" ]]; then
     eventLog="$defaultDir"/"$profile"_default_binary_bios_measurements
 fi    
 sed -i "s:tcg.event.file=.*:tcg.event.file=$eventLog:g" "$propFile"
-echo "eventLog was $eventLog"
+#echo "eventLog used was  $eventLog"
 
 # Step 2: Copy Base RIM files to the TCG folder
 #      a: See if test specific swidtag folder exists, if not use the defualt folder
@@ -63,13 +64,12 @@ pushd $rimDir > /dev/null
   fi
 popd > /dev/null
 
-  echo "Contents of tcg swidtag folder $tcgDir/manifest/swidtag/ : $(ls $tcgDir/manifest/swidtag/)"
-  echo "Contents of tcg rim folder tcgDir/manifest/rim/: $(ls $tcgDir/manifest/rim/)"
+#  echo "Contents of tcg swidtag folder $tcgDir/manifest/swidtag/ : $(ls $tcgDir/manifest/swidtag/)"
+#  echo "Contents of tcg rim folder tcgDir/manifest/rim/: $(ls $tcgDir/manifest/rim/)"
 
 #Step 4, run the setpcr script to make the TPM emulator hold values that correspond the binary_bios_measurement file
 #     a: Clear the TPM PCR registers vi a call to the tss clear 
 #     b: Check if a test specific setpcr.sh file exists. If not use the profiles default script
-echo "Options were $options"
 
 if [[ $options == "clear" ]]; then
    resetTpm2Emulator
@@ -80,6 +80,6 @@ if [[ ! -f $pcrScript ]]; then
 fi
 sh $pcrScript;
 echo "PCR script was $pcrScript"
-tpm2_pcrlist -g sha256 
+#tpm2_pcrlist -g sha256 
 
 # Done with rim_setup
\ No newline at end of file
diff --git a/.ci/system-tests/run_system_tests.sh b/.ci/system-tests/run_system_tests.sh
index 572011e9..5c576b5d 100644
--- a/.ci/system-tests/run_system_tests.sh
+++ b/.ci/system-tests/run_system_tests.sh
@@ -31,14 +31,14 @@ echo "ACA Container info: $(checkContainerStatus $aca_container)";
 echo "TPM2 Provisioner Container info: $(checkContainerStatus $tpm2_container)";
 
 # Install HIRS provioner and setup tpm2 emulator
-docker exec $tpm2_container /HIRS/.ci/setup/setup_tpm2provisioner.sh
+docker exec $tpm2_container /HIRS/.ci/setup/container/setup_tpm2provisioner.sh
 
 # ********* Execute system tests here, add tests as needed ************* 
 echo "******** Setup Complete Begin HIRS System Tests ******** "
 
-source aca_policy_tests.sh
-source platform_cert_tests.sh
-source rim_system_tests.sh
+source tests/aca_policy_tests.sh
+source tests/platform_cert_tests.sh
+source tests/rim_system_tests.sh
 
 
 echo "******** HIRS System Tests Complete ******** "
diff --git a/.ci/system-tests/aca_policy_tests.sh b/.ci/system-tests/tests/aca_policy_tests.sh
similarity index 100%
rename from .ci/system-tests/aca_policy_tests.sh
rename to .ci/system-tests/tests/aca_policy_tests.sh
diff --git a/.ci/system-tests/platform_cert_tests.sh b/.ci/system-tests/tests/platform_cert_tests.sh
similarity index 100%
rename from .ci/system-tests/platform_cert_tests.sh
rename to .ci/system-tests/tests/platform_cert_tests.sh
diff --git a/.ci/system-tests/rim_system_tests.sh b/.ci/system-tests/tests/rim_system_tests.sh
similarity index 100%
rename from .ci/system-tests/rim_system_tests.sh
rename to .ci/system-tests/tests/rim_system_tests.sh