@njoseph I have been using PDF arranger for years, it is good. The most sophisticated PDF tool I know for viewing and making notes is okular. To change resolution, I use ghostscript in command line.

@njoseph I used to use PDFTK regularly when I was a student, to split and concatenate class notes. Ah, nostalgia!

@njoseph I usually use poppler-utils, which includes commands like "pdfunite" and "pdfseparate" to do that stuff from command line. Also handy to have pdftotext to grab some text out of a pdf (when cutting/pasting results in weird formatting and garbage). I don't think there's anything in poppler-utils to rotate, but I do that from GUIs.

@njoseph @neil i use qpdf a lot as a command line tool. It does lack a couple of features pdftk use to have, e.g. the pdf repair facility, but i haven't had to use that in a while.