diff --git a/folderupgrade b/folderupgrade
new file mode 100644
index 0000000..e48106b
--- /dev/null
+++ b/folderupgrade
@@ -0,0 +1,82 @@
+#!/bin/bash
+#script to remove the submissionDocumentation folder
+#calling mmfunctions
+SCRIPTDIR=$(dirname $(which "${0}"))
+. "${SCRIPTDIR}/mmfunctions" || { echo "Missing '${SCRIPTDIR}/mmfunctions'. Exiting." ; exit 1 ;};
+while [ "${*}" != "" ] ; do
+	echo "removing the submissionsDocumentation folder"
+	INPUTFILE="${1}"
+	echo "The input is ${INPUTFILE}"
+	SUBDOC="${INPUTFILE}/metadata/submissionDocumentation/"
+	METADOC="${INPUTFILE}/metadata/"
+	OBJECTDOC="${INPUTFILE}/objects/Preservation/"
+	shift
+	"${SCRIPTDIR}/removeDSStore" "${INPUTFILE}"
+	#remove unnecessary directory
+	if [ -d "${SUBDOC}" ] ; then
+		mv -v -n "${SUBDOC}"* "${METADOC}"
+		#mv "${SUBDOC}"*
+		echo "going to delete for realsies"
+		rmdir "${SUBDOC}"
+	fi
+	
+	for entry in "${OBJECTDOC}"* ; do
+		echo "here is file $entry"
+		if [ -d "$entry" ] ; then
+			cd "$entry"
+			mv -v -n * .[^.]* "${INPUTFILE}/objects/"
+	
+			echo "deleting unnecessary folders"
+		
+			rmdir "$entry"
+		
+			#moving images folder to metadata and renaming
+			mkdir -p ${METADOC}depictions/ ; mv -n "${INPUTFILE}/objects/Image"* "${METADOC}depictions/object_photos"
+			
+			#removing extra Image folder
+			if [ -d "${METADOC}depictions/object_photos/Image" ] ; then
+				cd "${METADOC}depictions/object_photos/Image"
+				mv -v -n * .[^.]* ..
+				echo "deleting extra Image folder"
+				rmdir "${METADOC}depictions/object_photos/Image"
+			fi
+				
+		
+			#removing Preservation folder
+			mv -n "${INPUTFILE}/objects/Preservation Master/"* "${INPUTFILE}/objects/"
+			echo "removing empty preservation folder"
+			rmdir "${INPUTFILE}/objects/Preservation Master"
+			rmdir "${OBJECTDOC}"
+		
+			#renaming restoration/access folder
+			if [ -d "${INPUTFILE}/objects/Restoration" ] ; then
+				mv -v "${INPUTFILE}/objects/Restoration" "${INPUTFILE}/objects/restoration"
+			fi
+			
+			#renaming access folder
+			if [ -d "${INPUTFILE}/objects/Access/" ] ; then
+				echo "moving to restoration folder"
+				mkdir -p ${INPUTFILE}/objects/restoration/
+				echo "created restoration folder" 
+				for object in "${INPUTFILE}/objects/Access/" ; do
+					echo "here is $object"
+					cd $object
+					mv -n * .[^.]* "${INPUTFILE}/objects/restoration/"
+				done 
+				rmdir "${INPUTFILE}/objects/Access"
+			fi
+		fi
+	done
+done
+#checksum verification
+cd ${INPUTFILE}/objects &&
+for file in *; do
+	if [[ -f "$file" ]] ; then
+		echo "file is $file.md5"
+		NEWMD5="$(md5 -q "$file")"
+		OLDMD5="$(cat ${METADOC}${file}.md5)"
+	fi
+done
+if [[ "${NEWMD5}" =  "${OLDMD5}" ]] ; then
+	echo "checksums match"
+fi
diff --git a/makepdf b/makepdf
index 787f312..4cf33c2 100755
--- a/makepdf
+++ b/makepdf
@@ -50,6 +50,7 @@ while [ "${*}" != "" ] ; do
         OUTPUTDIR="${OUTPUTDIR_FORCED}"
         LOGDIR="${OUTPUTDIR}/logs"
     fi
+	INGESTLOG="${LOGDIR}/capture.log"
     OUTPUTDIRTEXT="${INPUT}/objects/access/txt_1"
     _run mkdir -p "${LOGDIR}"
     exec > >(tee "${LOGDIR}/$(basename "${0}")_$(_get_iso8601_c)_$(basename "${0}")_${VERSION}.txt")
@@ -75,7 +76,7 @@ while [ "${*}" != "" ] ; do
     TMP_JPG_DIR="${TMP_MAKEPDF_DIR}/jpgs"
     _run mkdir -p "${TMP_MAKEPDF_DIR}" "${TMP_JPG_DIR}" "${OUTPUTDIRTEXT}"
 
-    for TIF in $(find "${SOURCEDIR}" -maxdepth 1 -mindepth 1 -iname "*.tif" -type f | sort) ; do
+    for TIF in $(find "${SOURCEDIR}" -maxdepth 1 -mindepth 1 \( -iname "*.tif" -o -iname "*.tiff" \) -type f | sort) ; do
         tifname="$(basename "${TIF}")"
         _report -dt "Working on ${tifname}..."
         pageno="$(echo "${tifname}" | cut -d_ -f2 | cut -d. -f1)"
@@ -95,20 +96,30 @@ while [ "${*}" != "" ] ; do
         if [[ ! -s "${JPG_NAME}" ]] ; then
             ffmpeg -hide_banner -nostdin -i "${TIF}" -pix_fmt yuvj420p -s 1275x1650 "${JPG_NAME}"
         fi
-        TESSERACT_CONFIG=(-c tessedit_char_whitelist="abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789!@#$%^\&*(){}[]\|\"':;?/>.<,~\` " -c textord_min_linesize=2.25 -c preserve_interword_spaces=1)
+		
+		if [[ -f "$INGESTLOG" ]] ; then
+			DOCTYPE=$(_readingestlog "doctype")
+		fi
+		
+		if [[ "${DOCTYPE}" == "t" ]] ; then
+			TESSERACT_CONFIG=(-c tessedit_char_whitelist="abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789!@#$%^\&*(){}[]\|\"':;?/>.<,~\` " -c textord_min_linesize=2.25 -c preserve_interword_spaces=1)
+			_report -dt "ATTENTION: Character whitelist will be used for reading."
+		elif [[ "${DOCTYPE}" == "c" ]] ; then
+			TESSERACT_CONFIG=(-c textord_min_linesize=2.25 -c preserve_interword_spaces=1)
+		fi	
         tesseract "${JPG_NAME}" "${TMP_JPG_DIR}/${TIF_BASE_NAME}" -l eng --psm 4 "${TESSERACT_CONFIG[@]}" pdf
         tesseract "${JPG_NAME}" "${TMP_JPG_DIR}/${TIF_BASE_NAME}" -l eng --psm 4 "${TESSERACT_CONFIG[@]}" txt
     done
 
-    _report -dt "Checking for PBCore data"
-    SCRIPT_TITLE=$(fmpbcore "${MEDIAID}" | xmlstarlet 'select' -N "p=http://www.pbcore.org/PBCore/PBCoreNamespace.html" -t -v "/p:pbcoreCollection/p:pbcoreDescriptionDocument/p:pbcoreTitle[@titleType='Series']" -o ": " -v "/p:pbcoreCollection/p:pbcoreDescriptionDocument/p:pbcoreTitle[@titleType='Episode']")
-    if [[ -n "${SCRIPT_TITLE}" ]] ; then
-        MIDDLE_OPTIONS+=(--pdftitle "${SCRIPT_TITLE}")
-    fi
-    SCRIPT_AUTHOR=$(fmpbcore "${MEDIAID}" | xmlstarlet 'select' -N "p=http://www.pbcore.org/PBCore/PBCoreNamespace.html" -t -m "/p:pbcoreCollection/p:pbcoreDescriptionDocument/p:pbcoreCreator" -v "p:creatorRole" -o ": " -v "p:creator" -o " ; ")
-    if [[ -n "${SCRIPT_AUTHOR}" ]] ; then
-        MIDDLE_OPTIONS+=(--pdfauthor "${SCRIPT_AUTHOR}")
-    fi
+    #_report -dt "Checking for PBCore data"
+    #SCRIPT_TITLE=$(fmpbcore "${MEDIAID}" | xmlstarlet 'select' -N "p=http://www.pbcore.org/PBCore/PBCoreNamespace.html" -t -v "/p:pbcoreCollection/p:pbcoreDescriptionDocument/p:pbcoreTitle[@titleType='Series']" -o ": " -v "/p:pbcoreCollection/p:pbcoreDescriptionDocument/p:pbcoreTitle[@titleType='Episode']")
+    #if [[ -n "${SCRIPT_TITLE}" ]] ; then
+    #    MIDDLE_OPTIONS+=(--pdftitle "${SCRIPT_TITLE}")
+    #fi
+    #SCRIPT_AUTHOR=$(fmpbcore "${MEDIAID}" | xmlstarlet 'select' -N "p=http://www.pbcore.org/PBCore/PBCoreNamespace.html" -t -m "/p:pbcoreCollection/p:pbcoreDescriptionDocument/p:pbcoreCreator" -v "p:creatorRole" -o ": " -v "p:creator" -o " ; ")
+    #if [[ -n "${SCRIPT_AUTHOR}" ]] ; then
+    #    MIDDLE_OPTIONS+=(--pdfauthor "${SCRIPT_AUTHOR}")
+    #fi
 
     pdfjoin "${MIDDLE_OPTIONS[@]}" --pdfkeywords "${MEDIAID}" --fitpaper 'false' --rotateoversize 'false' --paper letter $(find "${TMP_JPG_DIR}" -name "*.pdf" | sort | xargs) --outfile "${OUTPUT}"
 
diff --git a/paperingest b/paperingest
index a09f557..108cb36 100755
--- a/paperingest
+++ b/paperingest
@@ -1,7 +1,7 @@
 #!/bin/bash
 REQUIRECONFIG="Y"
 
-SCRIPTDIR=$(dirname "${0}")
+SCRIPTDIR="$(dirname "${0}")"
 . "${SCRIPTDIR}/mmfunctions" || { echo "Missing '${SCRIPTDIR}/mmfunctions'. Exiting." ; exit 1 ;};
 
 _cleanup(){
@@ -9,6 +9,44 @@ _cleanup(){
     exit 1
 }
 
+_ask_scantype(){
+    if [ -z "${SCANTYPE}" ] ; then
+        _report -qn "Enter 'a' to use ADF or 'f' to use flatbed or 'q' to quit: "
+        read -e SCANTYPE
+        [ -z "${SCANTYPE}" ] && _ask_scantype
+        [[ "${SCANTYPE}" = "q" ]] && exit 0
+    fi
+}
+
+_ask_doubleside(){
+    if [ -z "${DOUBLESIDE}" ] ; then
+        _report -qn "Enter 1 if scanning only front or 2 if scanning both front and back or 'q' to quit: "
+        read -e DOUBLESIDE
+        [ -z "${DOUBLESIDE}" ] && _ask_doubleside
+        [[ "${DOUBLESIDE}" = "q" ]] && exit 0
+    fi
+}
+
+_ask_doctype(){
+    if [ -z "${DOCTYPE_ANSWER}" ] ; then
+        _report -qn "If document is from typewriter, enter 't', if from computer, enter 'c', if handwritten, enter 'h', if other, enter 'o': "
+		read -e DOCTYPE_ANSWER
+        [ -z "${DOCTYPE_ANSWER}" ] && _ask_doctype
+        [[ "${DOCTYPE_ANSWER}" = "q" ]] && exit 0
+		
+		if [[ "${DOCTYPE_ANSWER}" = "t" ]] ; then
+			DOCTYPE="typewriter"
+ 	    elif [[ "${DOCTYPE_ANSWER}" = "c" ]] ; then
+			DOCTYPE="computer"
+		elif [[ "${DOCTYPE_ANSWER}" = "h" ]] ; then
+			DOCTYPE="handwritten"
+		elif [[ "${DOCTYPE_ANSWER}" = "o" ]] ; then
+			DOCTYPE="other"
+		else
+			_report -w "You said ${DOCTYPE_ANSWER} which is not valid."
+		fi
+    fi
+}
 trap _cleanup SIGHUP SIGINT SIGTERM
 _log -b
 
@@ -16,6 +54,23 @@ _ask_operator
 
 _ask_mediaid
 
+_ask_scantype
+_ask_doctype
+
+MIDDLE_OPTIONS+=(--rgb --bits 8 --resolution 600 --auto-length --paper-width 10200 --paper-height 13200 --rotate-n-n --left 0 --width 10200 --top 0 --height 13200 --double-feed n --tiff --no-jpeg --images-per-file 1 --compress zlib)
+
+_scan_page(){
+	echo "Running: fscanx ${MIDDLE_OPTIONS[@]} ${ORIGDIR}/${MEDIAID}_${COUNTER}.tif" >> "${LOGDIR}/fscanx_process.txt"
+	fscanx "${MIDDLE_OPTIONS[@]}" "${ORIGDIR}/${MEDIAID}_${COUNTER}.tif" | tee -a "${LOGDIR}/fscanx_process.txt"
+=======
+COMMAND_OPTIONS+=(--rgb --bits 8 --resolution 600 --auto-length --paper-width 10200 --paper-height 13200 --rotate-n-n --left 0 --width 10200 --top 0 --height 13200 --double-feed n --tiff --no-jpeg --images-per-file 1 --compress zlib)
+
+_scan_page(){
+	echo "Running: fscanx ${MIDDLE_OPTIONS[@]} ${COMMAND_OPTIONS[@]} ${ORIGDIR}/${MEDIAID}_scan${COUNTER}_${SCANTYPE_ANSWER}_.tif" >> "${LOGDIR}/fscanx_process.txt"
+	fscanx "${MIDDLE_OPTIONS[@]}" "${COMMAND_OPTIONS[@]}" "${ORIGDIR}/${MEDIAID}_scan${COUNTER}_${SCANTYPE_ANSWER}_.tif" | tee -a "${LOGDIR}/fscanx_process.txt"
+>>>>>>> Stashed changes
+
+}
 if [ -d "${OUTDIR_PAPER}/${MEDIAID}" ] ; then
     _report -wdt "It looks like this ${MEDIAID} was already scanned. If you want to overwrite the existing one please delete ${MEDIAID} first and then try again."
 exit
@@ -29,20 +84,127 @@ LOGDIR="${OUTDIR_PAPER}/${MEDIAID}/metadata/logs"
 mkdir -p "${ORIGDIR}"
 mkdir -p "${LOGDIR}"
 
+_file_rename_flatbed(){
+	for file in ${ORIGDIR}/*1.tif ; do mv -v -n "${file}" "${file//1.tif/.tiff}" ; done
+	for file in ${ORIGDIR}/*1.tif ; do mv -v -n "${file}" "${file//1.tif/${COUNTER}.tiff}" ; done
+
+}
+
+_file_rename_adf(){
+	for file in ${ORIGDIR}/*.tif ; do mv -v -n "${file}" "${file//.tif/.tiff}" ; done
+
+}
 START=$(date -u "+%Y%m%dT%H%M%SZ")
 
-COMMAND="fscanx  --adf --rgb --bits 8 --resolution 600 --paper-width 10200 --paper-height 13200 --rotate-n-n --left 0 --width 10200 --top 0 --height 13200 --double-feed n --tiff --no-jpeg --images-per-file 1 --compress zlib '${ORIGDIR}/${MEDIAID}_.tif'"
-exec &> "${LOGDIR}/fscanx_process.txt"
-eval "${COMMAND}"
+if [[ "${SCANTYPE}" == "a" ]] ; then
+	MIDDLE_OPTIONS+=(--adf)
+	SCANTYPE_ANSWER="ADF"
+_scan_page_adf() {
+	MIDDLE_OPTIONS=(--adf)
+	SCANTYPE_ANSWER="ADF"
+	_ask_doctype
+	_ask_doubleside
+	if [[ "${DOUBLESIDE}" == 2 ]] ; then
+		MIDDLE_OPTIONS+=(--duplex)
+	elif [[ "${DOUBLESIDE}" == 1 ]] ; then
+		break
+		:
+>>>>>>> Stashed changes
+	else
+		_report -w "You said ${DOUBLESIDE} for the number of pages which is not valid, use 1 or 2."
+	fi
+	_scan_page
+	_file_rename_adf
+<<<<<<< Updated upstream
+elif [[ "${SCANTYPE}" == "f" ]] ; then
+	MIDDLE_OPTIONS+=(--flatbed)
+	SCANTYPE_ANSWER="flatbed"
+	COUNTER=1
+	_report -d -n "Hit enter to scan a page or q to stop scanning pages: "
+	read PAGE_ANSWER
+	
+	while [[ ! "${PAGE_ANSWER}" = "q" ]] ; do
+		_scan_page
+		_file_rename_flatbed
+		((COUNTER++))
+		_report -d -n "Hit enter to scan a page or q to stop scanning pages (next page is ${COUNTER}): "
+		read PAGE_ANSWER
+	done
+		
+else
+	_report -w "You said ${SCANTYPE} for the scantype which is not valid, use 'a' or 'f'."
+	exit 1
+fi
+=======
+	DOUBLESIDE=""
+	DOCTYPE_ANSWER=""
+}
+
+_scan_page_flatbed(){
+	MIDDLE_OPTIONS=(--flatbed)
+	SCANTYPE_ANSWER="flatbed"
+	#((COUNTER++))
+	_report -d -n "Hit enter to scan a page or q to stop scanning pages: "
+		read PAGE_ANSWER
+		
+		while [[ "${PAGE_ANSWER}" != "q" && "${PAGE_ANSWER}" != "a" ]] ; do
+			_ask_doctype
+			_scan_page
+			_file_rename_flatbed
+			((COUNTER++))
+			_report -d -n "Hit enter to scan a page, a to change the scanner or q to stop scanning pages (next page is ${COUNTER}): "
+			read PAGE_ANSWER
+			if [[ "${PAGE_ANSWER}" == "a" ]] ; then
+				SCANTYPE="a"
+				echo "scantype is ${SCANTYPE} now."
+			fi
+			DOCTYPE_ANSWER=""
+			#echo "doctype is ${DOCTYPE_ANSWER}"
+			#_ask_doctype
+		done
+}
+
+
+
+COUNTER=1
+if [[ "${SCANTYPE}" == "f" ]] ; then
+	_scan_page_flatbed
+fi
+
+if [[ "${SCANTYPE}" == "a" ]] ; then
+	#((COUNTER++))
+	while [[ "${PAGE_ANSWER}" != "q" ]] ; do
+		_scan_page_adf
+		#echo "duplex is ${DOUBLESIDE}"
+		((COUNTER++))
+		_report -d -n "Hit a to continue scanning, f to change the scanner or q to stop scanning pages: "
+		read PAGE_ANSWER
+		if [[ "${PAGE_ANSWER}" == "f" ]] ; then
+			SCANTYPE="f"
+			echo "scantype is ${SCANTYPE} now."
+			_scan_page_flatbed
+		fi
+	done
+fi
+	
+if [[ "${SCANTYPE}" != "a" && "${SCANTYPE}" != "f" && "${SCANTYPE}" != "q" ]] ; then
+	_report -w "You said ${SCANTYPE} for the scantype which is not valid, use 'a' or 'f'."
+	exit 1
+fi
+	
+
+
+>>>>>>> Stashed changes
+
 FIRST=$(find "${ORIGDIR}" -type f -mindepth 1 -maxdepth 1 ! -name ".*" -exec ls -1rt '{}' \; | head -n 1)
 LAST=$(ls -1t "${ORIGDIR}" | head -n 1)
-open -a /Applications/Preview.app/ "${FIRST}" "${ORIGDIR}/${LAST}"
+open "${FIRST}" "${ORIGDIR}/${LAST}"
 END=$(date -u "+%Y%m%dT%H%M%SZ")
 SYSTEM_DATA=$(system_profiler SPHardwareDataType)
 #These retrieved the right info on the Mac I'm using, but I don't know how standard the output is
-SERIAL_NUMBER=$(echo "${SYSTEM_DATA}" | grep "Serial Number" | awk '{ print $4 }')
-MODEL=$(echo "${SYSTEM_DATA}" | grep "Model Identifier" | awk '{ print $3; }')
-OS=$(system_profiler SPSoftwareDataType | grep "System Version" | awk '{ print substr(${0}, index(${0},$3)); }')
+SERIAL_NUMBER="$(echo "${SYSTEM_DATA}" | grep "Serial Number" | awk '{ print $4 }')"
+MODEL="$(echo "${SYSTEM_DATA}" | grep "Model Identifier" | awk '{ print $3; }')"
+OS="$(system_profiler SPSoftwareDataType | grep "System Version" | cut -d ":" -f 2- | awk '{$1=$1;print}')"
 echo "datetime_start: ${START}" >> "${LOGDIR}/capture.log"
 echo "datetime_end: ${END}" >> "${LOGDIR}/capture.log"
 echo "serial number: ${SERIAL_NUMBER}" >> "${LOGDIR}/capture.log"
@@ -50,7 +212,10 @@ echo "model id: ${MODEL}" >> "${LOGDIR}/capture.log"
 echo "os: ${OS}" >> "${LOGDIR}/capture.log"
 echo "identifier: ${MEDIAID}" >> "${LOGDIR}/capture.log"
 echo "operator: ${OP}" >> "${LOGDIR}/capture.log"
-echo "command: ${COMMAND}"  >> "${LOGDIR}/capture.log"
+echo "scantype: ${SCANTYPE_ANSWER}" >> "${LOGDIR}/capture.log"
+echo "doctype: ${DOCTYPE}" >> "${LOGDIR}/capture.log"
+echo "fscanx_options: ${MIDDLE_OPTIONS[@]}"  >> "${LOGDIR}/capture.log"
+echo "fscanx_options: ${MIDDLE_OPTIONS[@]} ${COMMAND_OPTIONS[@]}"  >> "${LOGDIR}/capture.log"
 
 echo done scanning "${MEDIAID}"