diff --git a/AOloopControl/scripts/cacao-calib-apply b/AOloopControl/scripts/cacao-calib-apply
index 15d68d93..3af7ddd7 100755
--- a/AOloopControl/scripts/cacao-calib-apply
+++ b/AOloopControl/scripts/cacao-calib-apply
@@ -1,5 +1,44 @@
 #!/usr/bin/env bash
 
+#######################################################################################
+# Script to apply a CACAO loop calibration previously saved with cacao-calib-archive. 
+# 
+# Usage: cacao-calib-apply cal_name
+#
+# This script must be run in `loop-name-rootdir`. Here cal_name corresponds to a directory 
+# in `../loop-name-calibs`.  Note this is not the whole path, just the directory name including
+# the timestamp appended by cacao-calib-archive.
+#
+# The following steps are performed:
+# 1. The loop is turned off
+# 2. The loop processes are shutdown, in each case both run and conf:
+#         mvalC2dm
+#         mfilt
+#         wfs2cmodeval
+#         acquWFS
+# 3. The script `./scripts/pre-calib-apply` is run, if it exists.  This is a user script
+#    that can be used for any other desired pre-apply actions on your system. The calib name
+#    and path (relative to rootdir) are passed as arguments.
+# 4. The calibration is loaded into shared memory. This means the files:
+#         CMmodesDM/CMmodesDM.fits
+#         CMmodesWFS/CMmodesWFS.fits
+#         RMmodesWFS/zrespM-H.fits
+#         wfsref.fits
+#         wfsmask.fits
+#         dmmask.fits
+# 5. The loop processes, conf and run, are started in the correct order to be initialized:
+#         acquWFS
+#         wfs2cmodeval
+#         mfilt
+#         mvalC2dm
+# 6. The script `./scripts/post-calib-apply` is run, if it exists.  This is a user script
+#    that can be used for any other desired post-apply actions on your system (e.g. zero all gains).
+#    The calib name and path (relative to rootdir) are passed as arguments.
+# 7. The following files are created:
+#         $MILK_SHM_DIR/aol${CACAO_LOOPNUMBER}_calib_source.txt [contains the directory to calibration files]
+#         $MILK_SHM_DIR/aol${CACAO_LOOPNUMBER}_calib_loaded.txt [contains the time calibration was loaded]
+# 8. A log entry is made.
+############################################################################################################
 
 MSdescr="Apply AO calibration"
 
@@ -39,23 +78,73 @@ echo "Loop ${CACAO_LOOPNUMBER}: Loading calibration from ${ARCHDIR}"
 
 if [[ -d "${ARCHDIR}" ]]; then
 
-# Load CM to shared memory
-milk-FITS2shm "${ARCHDIR}/CMmodesWFS/CMmodesWFS.fits" aol${CACAO_LOOPNUMBER}_modesWFS
-milk-FITS2shm "${ARCHDIR}/CMmodesDM/CMmodesDM.fits" aol${CACAO_LOOPNUMBER}_DMmodes
+#open the loop
+echo "setval mfilt-${CACAO_LOOPNUMBER}.loopON OFF" >> /milk/shm/${CACAO_LOOPNAME}_fpsCTRL.fifo
+
+#Shutdown processes
+echo "runstop mvalC2dm-${CACAO_LOOPNUMBER}" >> /milk/shm/${CACAO_LOOPNAME}_fpsCTRL.fifo
+echo "confstop mvalC2dm-${CACAO_LOOPNUMBER}" >> /milk/shm/${CACAO_LOOPNAME}_fpsCTRL.fifo
 
+echo "runstop mfilt-${CACAO_LOOPNUMBER}" >> /milk/shm/${CACAO_LOOPNAME}_fpsCTRL.fifo
+echo "confstop mfilt-${CACAO_LOOPNUMBER}" >> /milk/shm/${CACAO_LOOPNAME}_fpsCTRL.fifo
 
-milk-FITS2shm "${ARCHDIR}/shmim.aol${CACAO_LOOPNUMBER}_wfsref.fits" aol${CACAO_LOOPNUMBER}_wfsref
-milk-FITS2shm "${ARCHDIR}/shmim.aol${CACAO_LOOPNUMBER}_wfsrefc.fits" aol${CACAO_LOOPNUMBER}_wfsrefc
+echo "runstop wfs2cmodeval-${CACAO_LOOPNUMBER}" >> /milk/shm/${CACAO_LOOPNAME}_fpsCTRL.fifo
+echo "confstop wfs2cmodeval-${CACAO_LOOPNUMBER}" >> /milk/shm/${CACAO_LOOPNAME}_fpsCTRL.fifo
 
-milk-FITS2shm "${ARCHDIR}/shmim.aol${CACAO_LOOPNUMBER}_wfsmask.fits" aol${CACAO_LOOPNUMBER}_wfsmask
-milk-FITS2shm "${ARCHDIR}/shmim.aol${CACAO_LOOPNUMBER}_wfsmap.fits" aol${CACAO_LOOPNUMBER}_wfsmap
+echo "runstop acquWFS-${CACAO_LOOPNUMBER}" >> /milk/shm/${CACAO_LOOPNAME}_fpsCTRL.fifo
+echo "confstop acquWFS-${CACAO_LOOPNUMBER}" >> /milk/shm/${CACAO_LOOPNAME}_fpsCTRL.fifo
 
-milk-FITS2shm "${ARCHDIR}/shmim.aol${CACAO_LOOPNUMBER}_dmmask.fits" aol${CACAO_LOOPNUMBER}_dmmask
-milk-FITS2shm "${ARCHDIR}/shmim.aol${CACAO_LOOPNUMBER}_dmmap.fits" aol${CACAO_LOOPNUMBER}_dmmap
+#run pre-apply script if it exists.
+if [ -d "scripts" ]; then
+    cd scripts
+    if [ -f "pre-calib-apply" ]; then
+        echo "running pre-calib-apply"
+        ./pre-calib-apply ${calib} ${ARCHDIR}
+    fi
+    cd ..
+fi
 
+# Load CM to shared memory
+milk-FITS2shm "${ARCHDIR}/CMmodesWFS/CMmodesWFS.fits" aol${CACAO_LOOPNUMBER}_CMmodesWFS
+milk-FITS2shm "${ARCHDIR}/CMmodesDM/CMmodesDM.fits" aol${CACAO_LOOPNUMBER}_CMmodesDM
+
+milk-FITS2shm "${ARCHDIR}/RMmodesWFS/zrespM-H.fits" aol${CACAO_LOOPNUMBER}_zrespM
+
+milk-FITS2shm "${ARCHDIR}wfsref.fits" aol${CACAO_LOOPNUMBER}_wfsref
+milk-FITS2shm "${ARCHDIR}wfsref.fits" aol${CACAO_LOOPNUMBER}_wfsrefc
+
+milk-FITS2shm "${ARCHDIR}wfsmask.fits" aol${CACAO_LOOPNUMBER}_wfsmask
+
+milk-FITS2shm "${ARCHDIR}dmmask.fits" aol${CACAO_LOOPNUMBER}_dmmask
+
+#Startup processes
+echo "confstart acquWFS-${CACAO_LOOPNUMBER}" >> /milk/shm/${CACAO_LOOPNAME}_fpsCTRL.fifo
+sleep 1
+echo "runstart acquWFS-${CACAO_LOOPNUMBER}" >> /milk/shm/${CACAO_LOOPNAME}_fpsCTRL.fifo
+sleep 1
+echo "confstart wfs2cmodeval-${CACAO_LOOPNUMBER}" >> /milk/shm/${CACAO_LOOPNAME}_fpsCTRL.fifo
+sleep 1
+echo "runstart wfs2cmodeval-${CACAO_LOOPNUMBER}" >> /milk/shm/${CACAO_LOOPNAME}_fpsCTRL.fifo
+sleep 1
+echo "confstart mfilt-${CACAO_LOOPNUMBER}" >> /milk/shm/${CACAO_LOOPNAME}_fpsCTRL.fifo
+sleep 1
+echo "runstart mfilt-${CACAO_LOOPNUMBER}" >> /milk/shm/${CACAO_LOOPNAME}_fpsCTRL.fifo
+sleep 1
+echo "confstart mvalC2dm-${CACAO_LOOPNUMBER}" >> /milk/shm/${CACAO_LOOPNAME}_fpsCTRL.fifo
+sleep 1
+echo "runstart mvalC2dm-${CACAO_LOOPNUMBER}" >> /milk/shm/${CACAO_LOOPNAME}_fpsCTRL.fifo
+
+if [ -d "scripts" ]; then
+    cd scripts
+    if [ -f "post-calib-apply" ]; then
+        echo "running post-calib-apply"
+        ./post-calib-apply ${calib} ${ARCHDIR}
+    fi
+    cd ..
+fi
 
 # record this calib as applied
-echo $(pwd)/../${ARCHDIR} > $MILK_SHM_DIR/aol${CACAO_LOOPNUMBER}_calib_source.txt
+echo $(pwd)/${ARCHDIR} > $MILK_SHM_DIR/aol${CACAO_LOOPNUMBER}_calib_source.txt
 
 DATESTRING="$(date -u --iso-8601=seconds)"
 
diff --git a/AOloopControl/scripts/cacao-calib-archive b/AOloopControl/scripts/cacao-calib-archive
index 5fe0b075..be70f017 100755
--- a/AOloopControl/scripts/cacao-calib-archive
+++ b/AOloopControl/scripts/cacao-calib-archive
@@ -1,5 +1,34 @@
 #!/usr/bin/env bash
 
+#######################################################################################
+# Script to archive a CACAO loop calibration.
+# 
+# Usage: cacao-calib-arhchive cal_name
+#
+# This script must be run in `loop-name-rootdir`. Here cal_name corresponds to a descriptive name
+# of the calibration.  A timestamp will be apended to it, and the result is used to create a directory
+# in ``../loop-name-calibs`.  
+#
+# The time stamp appendage can be suppressed with -u for update.
+#
+# The following files are copied to the cal directory.
+#         conf/CMmodesDM/CMmodesDM.fits
+#         conf/CMmodesWFS/CMmodesWFS.fits
+#         conf/RMmodesWFS/zrespM-H.fits
+#         conf/wfsref.fits
+#         conf/wfsmap.fits
+#         conf/wfsmask.fits
+#         conf/dmmap.fits
+#         conf/dmmask.fits
+#         LOOPNAME
+#
+# Additionally a file named calib_dir.txt is created which holds the directory path (useful for
+# dereferencing symlinks).
+#
+# The file calib_archived.txt is updated with the current time, and a log entry is made.
+#
+##########################################################################################################
+
 MSdescr="Archive AO calibration"
 
 MSextdescr="Copy current filesystem calibration to ../CACAO_LOOPNAME-AOcalibs/<calibname>/ directory
@@ -16,8 +45,6 @@ RequiredFiles=()
 
 RequiredDirs=(conf)
 
-
-
 MSarg+=( "calibname:string:calibration name" )
 MSopt+=( "u:update:setupdate::update existing, do not append timestamp" )
 
@@ -62,6 +89,10 @@ ARCHDIR="${BASEARCHDIR}${calib}/"
 
 
 mkdir -p ${ARCHDIR}
+mkdir -p ${ARCHDIR}/RMmodesDM
+mkdir -p ${ARCHDIR}/RMmodesWFS
+mkdir -p ${ARCHDIR}/CMmodesDM
+mkdir -p ${ARCHDIR}/CMmodesWFS
 
 echo "Saving to DIRECTORY ${ARCHDIR}"
 
@@ -69,30 +100,23 @@ echo "Saving to DIRECTORY ${ARCHDIR}"
 
 CONFDIR="conf"
 
-for f in $CONFDIR
-do
-    if [ -d "$f" ]
-    then
-        for ff in $f/*
-        do
-            #if this is a broken symlink, ignore it
-            if [ -L $ff ] && [ ! -e $ff ]
-            then
-                continue
-            fi
-
-	        cp -L -r $ff ${ARCHDIR}"$(basename $ff)"
-        done
-    else
-        cp -L -r $ff ${ARCHDIR}
-    fi
-done
+cp ${CONFDIR}/RMmodesWFS/zrespM-H.fits ${ARCHDIR}/RMmodesWFS/zrespM-H.fits
+cp ${CONFDIR}/CMmodesDM/CMmodesDM.fits ${ARCHDIR}/CMmodesDM/CMmodesDM.fits
+cp ${CONFDIR}/CMmodesWFS/CMmodesWFS.fits ${ARCHDIR}/CMmodesWFS/CMmodesWFS.fits
+cp ${CONFDIR}/RMmodesDM/RMmodesDM.fits ${ARCHDIR}/RMmodesDM/RMmodesDM.fits
+cp ${CONFDIR}/RMmodesWFS/RMmodesWFS.fits ${ARCHDIR}/RMmodesWFS/RMmodesWFS.fits
+cp ${CONFDIR}/wfsref.fits ${ARCHDIR}/wfsref.fits
+cp ${CONFDIR}/wfsmask.fits ${ARCHDIR}/wfsmask.fits
+cp ${CONFDIR}/wfsmap.fits ${ARCHDIR}/wfsmap.fits
+cp ${CONFDIR}/dmmask.fits ${ARCHDIR}/dmmask.fits 
+cp ${CONFDIR}/dmmap.fits ${ARCHDIR}/dmmap.fits 
 
+cp LOOPNAME ${ARCHDIR}/LOOPNAME
 
 # write out complete path so someone following a symlink can easily track where we are
-echo $(pwd)/${ARCHDIR} > ${ARCHDIR}/aol${CACAO_LOOPNUMBER}_calib_dir.txt
+echo $(pwd)/${ARCHDIR} > ${ARCHDIR}/calib_dir.txt
 
 # append timestamp
-echo ${DATESTRING} >> ${ARCHDIR}/aol${CACAO_LOOPNUMBER}_calib_archived.txt
+echo ${DATESTRING} >> ${ARCHDIR}/calib_archived.txt
 
 echo "${DATESTRING} ARCHIVED ${calib}" >> ${BASEARCHDIR}/aol${CACAO_LOOPNUMBER}_archive-log.txt