xournal is a complement to that, since it allows to easily annotate pdf files. Unfortunately, it cannot do those rearrangements to pdf files.

Here is a naturalistic example of what you can do with the presently available instruments:

1) I received a fax in my email, in the form of a long multipage tiff attachment;
2) browsed the multipage tiff in evince, and saw there were several forms to compile and resend;
3) converted the multipage tiff in pdf format. How? Use tiff2pdf om your IT. To get it you must install libtiff-tools (you must be in red pill mode);
4) took from the pdf only the pages to annotate, with pypdf, and joined in a new, shorter, pdf file;
5) fired xournal to annotate the pdf file, and finally...
6) resent the pdf with my internet fax service.

All on the IT.
Now I only wish I could open directly pdf files from the file manager with evince...