makemetadata: fix output of metadata reports

using _run function printed messages into the output
makemetadata: only mkdir if needed
makemetadata: report on action
makemetadata: cleanup options and usage
makemetadata: remove unused code
makemetadata: bracket all arguments
makemetadata: use variables for filepaths of metadata outputs
makepdf: fixes to handle underscore in paths
makepdf: sort filenames before join pdfs
maketmp: comment out temp file removal