Manipulate PDFs from the command line
To join, shuffle, select, etc. pdftk is a great tool:
$ pdftk *.pdf cat output all.pdf # Join PDFs together
$ pdftk A=in.pdf cat A5 output out.pdf # Extract page from PDF
You can also manipulate the content with cpdf:
$cpdf -draft in.pdf -o out.pdf # Remove images
$cpdf -blacktext in.pdf -o out.pdf # Convert all text to black color