How to "save" a rotated pdf file

Another great and tiny program for this is PDF-Shuffler.

merge or split pdf documents and rotate, crop and rearrange their pages using an interactive and intuitive graphical interface

Installation

You can install it from the software center, or through the command-line:

sudo apt-get install pdfshuffler

Screenshot

Rotate a page

1. open a PDF (click the + button) ;
2. select the page you want to rotate ;
3. click the rotate icon ↺ or ↻ (or use the menu) ;

Rotate several pages

If you want to rotate all pages, click on one, then press Ctrl+a to select all.

Or you can select as many as you want individually by holding down Ctrl as you select.

To clarify, this is what you use to rotate 180 degrees:

   pdftk input.pdf cat 1-endsouth output output.pdf
#        \_______/     \___/\___/        \________/
#        input file    range  |          output file
#                           direction

Where direction can be any of these:

• north
• south
• east
• west
• left
• right
• down

According to the man page for pdftk, one of the operations is rotate and you can save the rotated file:

The page rotation setting can cause pdftk to rotate pages and
documents. Each option sets the page rotation as follows (in
degrees): north: 0, east: 90, south: 180, west: 270, left:
-90, right: +90, down: +180. left, right, and down make
relative adjustments to a page's rotation.

Example (will rotate pages 1 to 5 +180 degrees, i.e. vertically / upside down):

pdftk original.pdf rotate 1-5south output new-rotated.pdf

However, pdftk is quite powerful and it's better that you read the man pages and use pdftk --help to meet your exact needs.

If you want to take a look at man pdftk without installing it, here's a link for 13.10: http://manpages.ubuntu.com/manpages/saucy/en/man1/pdftk.1.html