In principle evince can be controlled through its dbus api. An example of its application is the SyncTeX plugin for gedit, which allows easier editing and browsing of latex source files in combination with evince. On the other hand, the dbus api itself has been found to change sensibly from gnome 2 to 3 and it's somewhat hidden so you'll have to dig into the evince source to find the exposed methods.
Concerning annotations: as of version 2.31 evince supports adding (but not deleting) annotations. This feature is currently broken in evince 3.2 (the version shipped with Ubuntu 12.04) due to a regression but a fix has been released upstream.
Congrats on starting your adventure with Ubuntu. You'll be hooked in no time! My answer uses shell commands, which on a *nix OS is a good thing to become familiar with. You can access the shell by pressing the key combination CtrlAltT. The shell/terminal will pop up; then you can cd to the file location, e.g. if it's in your Documents directory, type cd ~/Documents. You can type ls to make sure your pdf is there.
You are correct, this is very typical of a document viewer to make the rotation a display property. In order to truly rotate the pdf, try using
pdftk temp.pdf cat 1-endR output tempR.pdf
which means, given a file temp.pdf, rotate 90° pages 1 to the end of the document and write out to the file tempR.pdf.
For details, see man pdftk and search for rotation, e.g.:
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.
Best Answer
Look at the toolbar from left, then locate the rightmost icon.
Click the icon (pencil icon in your screenshot), then another toolbar will appear and will show two more icons for adding "text annotation" and "highlight annotation".
Evince Document Viewer has slightly different user interface, depending on which available package of Evince in use. The annotation icon is located either in the toolbar menu (newer version, above) or the sidebar menu (older version, below).
I have tested and confirmed the annotated PDF file that has been created in the newer version can be opened and seen similarly in the older version. However:
text that has been added to any highlight annotation will neither be viewable nor editable
older version of Evince allows to add and modify "text annotation", but can't remove it
the "highlight annotation" feature is unavailable for older version of Evince, which is
3.10.3-0ubuntu10in Xubuntu Trusty (14.04)Compare above screenshots and notice some differences.
TL;DR The annotation icon is already there. Similarly noted in this canonical answer.