Es posible pedir carpetas en AppleScript, aquí hay un ejemplo:
set theInputFolder to choose folder with prompt "Please select input folder:"
set theInputFolderPOSIX to POSIX path of theInputFolder -- POSIX path that is used in shell scripts
set quotedInputFolder to quoted form of theInputFolderPOSIX -- quoted form to handle spaces in path
set theOutputFolder to choose folder with prompt "Please select output folder:"
set theOutputFolderPOSIX to POSIX path of theOutputFolder -- POSIX path that is used in shell scripts
set quotedOutputFolder to quoted form of theOutputFolderPOSIX -- quoted form to handle spaces in path
set theResponse to display dialog "Output filename" default answer "merged" with icon note buttons {"Cancel", "Continue"} default button "Continue"
do shell script "find " & quotedInputFolder & " -iname '*.pdf' |tr '\n' '\\0' |xargs -0 /Users/xxxxx/Downloads/cpdf-binaries-master/OSX-Intel/cpdf -o " & quotedOutputFolder & "/" & (text returned of theResponse) & ".pdf"
Nota: Es más seguro utilizar formas entrecomilladas, debido a los posibles espacios en la ruta de la carpeta.