I use QPDF too. Specifically its QDF mode. Essentially it tries to make the document as human-editable as possible. There's also a fix-qdf utility that fixes the values of offsets at the end of the file, so that you need not be careful not to change file size while editing.
The reference is well Adobe's official PDF reference downloadable from its website.
The reference is well Adobe's official PDF reference downloadable from its website.