app: handle output on MSWin32; docs for '--incoming'

- Added more comments in the code where --incoming is checked; the
  --incoming check can't be placed in the same block as --dotfiles,
  because --dotfiles needs a file object, and --incoming does not;
  Since the file is reported prior to the --dotfiles check, it's too
  late to prevent output if --incoming is not used and the
  file/directory is in --incoming