Continuing the discussion from MetaPDF offline:
MetaPDF has been so helpful that I have been using it for PDF annotations on PDFs that are not academic papers, and thus not in paperpile. Recently, the metapdf.com website has been consistently unreachable, but the pdf annotations built-in to Paperpile continue to work fine.
I hope this is a temporary glitch, rather than an indication that the stand-alone MetaPDF is no longer supported.