At least in principle it is possible to annotate a PDF file while leaving the original file as a prefix of the end result. The directory of objects is at the en

At least in principle it is possible to annotate a PDF file while leaving the original file as a prefix of the end result. The directory of objects is at the end of the file, so the annotation software can build a new tree of objects, referencing any unchanged parts of the original, and append its own directory which the reader software will find. I don't know of any PDF editors that do this, though.