Qpdf is a command line PDF manipulation tool.
Examples
These join the 6x6 Hard Inky puzzles, removing the answer sheet, if you're wondering what this command does.
qpdf --empty --pages INKY_v2_6H_b001_1pp.pdf 1-8 INKY_v2_6H_b002_1pp.pdf 1-8 INKY_v2_6H_b003_1pp.pdf 1-8 INKY_v2_6H_b004_1pp.pdf 1-8 INKY_v2_6H_b005_1pp.pdf 1-8 -- combined/InkyKenken_6H_1pp_B1-5.pdf
Or put this in e.g. catlist
--empty
--pages
INKY_v2_6H_b001_1pp.pdf
1-8
INKY_v2_6H_b002_1pp.pdf
1-8
INKY_v2_6H_b003_1pp.pdf
1-8
INKY_v2_6H_b004_1pp.pdf
1-8
INKY_v2_6H_b005_1pp.pdf
1-8
--
combined/InkyKenken_6H_1pp_B1-5.pdf
and then
qpdf @catlist
Rotate
Rotate only pages 1 and 3:
qpdf in.pdf --rotate=180:1,3 out.pdf