AppleScript to output notes from all PDFs in a directory as "Notes as Markdown", using my template for the Skim PDF editor.

Export All Skim.scpt

set this_folder to ""
set export_folder to ""
	set these_files to every file of folder this_folder whose name extension is "pdf"
end tell
repeat with i from 1 to the count of these_files
	set this_file to (item i of these_files as alias)
	set fileName to name of item i of these_files
	set savePath to export_folder & ":" & fileName & ".md"
	tell application "Skim"
		open this_file
		try
			convert notes document 1 with waiting
		end try
		if (count of notes in document 1) > 0 then
			save document 1 in savePath as "Notes as Markdown"
		end if
		close document 1 saving no
	end tell
	log i
end repeat