We, me and a schoolmate of mine, Gaetano Catalli, have developed a patch for xpdf which let the user create select and delete freehand annotations; the best thing is that you can even save the file.
To apply the patch you have to download xpdf sources and apply the two pl patches ([1] [2]); after that you can safely apply our patch.
Remember: we need some feedback yet, thus it’s better for you to MAKE backup copies.
Remember1: let’s suppose we open foo.pdf, and we add an annotations; foo.pdf.temp is created during the operation, and deleted when closing the document! For this reason it’s better that you don’t use file .temp, because they gonna be deleted!
You can take the patched version of xpdf from the repository: xpdf is the name of the project.
[1] ftp://ftp.foolabs.com/pub/xpdf/xpdf-3.02pl1.patch
[2] ftp://ftp.foolabs.com/pub/xpdf/xpdf-3.02pl2.patch