pdf processing script, for personal use. with some adaptation it could suit other people as well.

pdeffer

#!/bin/bash
# pdf scanning script
# 1/13/2015

bold='\033[01m' #bold
red='\033[01;31m' #error color 
NC='\033[0m' # No Color

if [ $# == 0 ]; then
    #tell em whats up
    echo -e "pdeffer ${bold}[ -q ] [ -i | -I${NC} input_location${bold} ] [ -o | -O${NC} output_location${bold} ] [ -f${NC} filename ${bold} ] [ -t ${NC}datestring ${bold}| -T ] [ -N ] [ -u | -U ]${NC}"
    echo -e "${bold} -d${NC}\tdefault"
    echo -e "${bold} -q${NC}\treally quiet. no terminal output at all."
    echo -e "${bold} -i${NC}\tspecify #, defaults to /run/media/${USER}/AV_SCAN/200DOC"
    echo -e "${bold} -I${NC}\tspecify an explicit input path"
    echo -e "${bold} -o${NC}\tspecify Dropbox directory, defaults to ~/Dropbox/UNSORTED"
    echo -e "${bold} -O${NC}\tspecify an explicit output path"
    echo -e "${bold} -f${NC}\tspecify string to append to files (after datestamp)"
    echo -e "${bold} -t${NC}\tspecify date string format (see ${bold}man date${NC}) be cautious of special characters. defaults to ${bold}%Y-%m-%d_%H.%M.%S${NC}"
    echo -e "${bold} -T${NC}\tno date stamping"
    echo -e "${bold} -N${NC}\tno processing (pdfsandwich). move and apply name if applicable"
    echo -e "${bold} -u${NC}\tunite all pdfs in input directory before processing. defaults to no datestamp. uses ${bold}pdfunite${NC}"
    echo -e "${bold} -U\t-u ${NC}with a date stamp."

else
    #make it happen
    while getopts "i:I:o:O:f:t:TvdqNuU" OPTNAME
    do
        case "$OPTNAME" in
            "i")
                INPUT="/run/media/$USER/AV_SCAN-$OPTARG/DCIM/200DOC"
                ;;
            "I")
                INPUT="$OPTARG"
                ;;
            "o")
                OUTPUT="$HOME/Dropbox/$OPTARG/"
                ;;
            "O")
                OUTPUT="$OPTARG"
                ;;
            "f")
                #echo "filename is ${OPTARG}"
                FILENAME="${OPTARG}.PDF"
                ;;
            "t")
                DATESTRING="$OPTARG"
                ;;
            "T")
                NODATE=1
                ;;
            "q")
                QUIET=1
                ;;
            "N")
                NOPROC=1
                ;;
            "u")
                UNITE=1
                NODATE=1
                ;;
            "U")
                UNITE=1
                ;;
            "d")
                ;;
        esac
    done

    #set defaults
    ############
    if [ -z $INPUT ]; then INPUT="/run/media/$USER/AV_SCAN/DCIM/200DOC"; fi
    if [ -z $OUTPUT ]; then OUTPUT="$HOME/Dropbox/UNSORTED/"; fi
    if [ -z $DATESTRING ]; then DATESTRING="%Y-%m-%d_%H.%M.%S"; fi

    ############

    FILEES=$(find "$INPUT" -maxdepth 1 -name '*.PDF' -printf '%f\n' | sort)
    if [ ! -z $UNITE ]; then 
        if [ -z $QUIET ]; then
            UNITECOUNT=0
            for z in $FILEES; do let "UNITECOUNT += 1"; done
            echo -e "${bold}>>>>>Uniting $UNITECOUNT pdfs...${NC}"
        fi
            PDFUNITEFILES=$(find "$INPUT" -maxdepth 1 -name '*.PDF' -print0 | sort | sed -e 's/\x0/ /g')
            if [ "$QUIET" = 1 ]; then
                pdfunite ${PDFUNITEFILES} "$INPUT/UNITED.PDF" &> /dev/null
            else
                pdfunite ${PDFUNITEFILES} "$INPUT/UNITED.PDF"
            fi
            ORIGFILES=$FILEES
            FILEES="UNITED.PDF"
    fi

    if [ -z $QUIET ]; then echo -e "${bold}>>>>>Copying pdfs to ~/pdfs..${NC}"; fi

    for z in $FILEES
    do
        if [ -z $FILENAME ]; then FILENAME="$z"; fi
        if [ -z $NODATE ]; then
            TIMESTAMP="$(stat ${INPUT}/${z} --printf %y | sed 's/\([0-9]*-[0-9]*-[0-9]*\) \([0-9]*\):\([0-9]*\):\([0-9]*\).*/\1_\2.\3.\4/')_"
        else
            TIMESTAMP=""
        fi
        ORIGINALNAME="$z"
        if [ "$QUIET" = 1 ]; then
            cp --preserve=timestamps "${INPUT}/${ORIGINALNAME}"  "$HOME/pdfs/${TIMESTAMP}${FILENAME}" &> /dev/null
        else
            cp -v --preserve=timestamps "${INPUT}/${ORIGINALNAME}" "$HOME/pdfs/${TIMESTAMP}${FILENAME}"
        fi
    done

    if [ -z $NOPROC ]; then

        if [ -z $QUIET ]; then echo -e "${bold}>>>>>pdfsandwiching them..${NC}"; fi

        FILES=$(find "$HOME"/pdfs -maxdepth 1 -name '*.PDF' | sort)
        PDFCOUNT=0
        PDFTOT=0
        for z in $FILES; do let "PDFTOT += 1"; done

        for f in $FILES
        do
            let "PDFCOUNT += 1"
            echo -e "${bold}>>>>>Processing $PDFCOUNT of $PDFTOT - $f${NC}"
            if [ "$QUIET" = 1 ]; then
                pdfsandwich -quiet -coo "-black-threshold 70% -enhance" $f &> /dev/null
                PDFSTATUS="$?"
            else
                pdfsandwich -coo "-black-threshold 70% -enhance" $f
                PDFSTATUS="$?"
            fi
        done
    else
        PDFSTATUS=0
    fi

    if [ "$PDFSTATUS" = 0 ]; then
        
        if [ -z $QUIET ]; then echo -e "${bold}>>>>>Moving processed PDFs to ${OUTPUT}...${NC}"; fi
        if [ "$QUIET" = 1 ]; then
            mv "$HOME"/pdfs/*.PDF "$OUTPUT" &> /dev/null
        else
            mv -v "$HOME"/pdfs/*.PDF "$OUTPUT"
        fi

        if [ -z $QUIET ]; then echo -e "${bold}>>>>>moving PDFs to completed directory on scanner...${NC}"; fi
        if [ "$QUIET" = 1 ]; then
            for z in $FILEES
            do
                mv ${INPUT}/${z} ${INPUT}/OCRdone &> /dev/null
            done

            if [ ! -z "$ORIGFILES" ]; then 
                for z in $ORIGFILES
                do
                    mv ${INPUT}/${z} ${INPUT}/OCRdone &> /dev/null
                done
            fi
        else
            for z in $FILEES
            do
                mv -v ${INPUT}/${z} ${INPUT}/OCRdone
            done

            if [ ! -z "$ORIGFILES" ]; then 
                for z in $ORIGFILES
                do
                    mv -v ${INPUT}/${z} ${INPUT}/OCRdone
                done
            fi
        fi
        if [ -z $QUIET ]; then echo -e "${bold}>>>>completed, please check for errors${NC}"; fi
        exit 0
    else
        echo -e "${red}>>>>>>pdfsandwich encountered an error, aborting...${NC}"
        exit 2
    fi
fi

updated to move original files as well as united files to completed dir after processing
also a file count / total count for progess

eliminated verbose, made it fully verbose by default. specify -q for totally silent.