Question: The PDF viewer Okular (part of KDE desktop) has lots of nice features and supports lots of file formats.
One of the things I like about it is the comments and annotations.
Unfortunately, all of the comments and metadata (like last viewed page) get stored locally in:
**~/.kde/share/apps/okular/docdata**

Is there any way to make Okular store them in the PDF itself?

Answer: 
After making any annotation using Okular, 

Go the the Print option (in File Menu or Ctrl+P) and then in the **Name** option change the value to Print to File(PDF) and in the **Output file** option give the path of the output file you need. 

Voila, your annotations are now a part of your new PDF.
Just use `file > print > printer name: print to file (PDF)`. Output file goes to your home by default. Your annotation should be there.