Download Zotero standalone, unzip to
Place the following in
#!/usr/bin/env xdg-open [Desktop Entry] Type=Application Name=Zotero GenericName=Bibliography Manager Icon=/opt/Zotero_linux-x86_64/chrome/icons/default/default48.png Exec= /opt/Zotero_linux-x86_64/zotero %f Categories=Office Terminal=false
By default zotero will place all its data in
~/.zotero. Knowing this you can save any highlighting and comments into the PDF document as long as its in the same location and name, zotero will sync it up.
This was written for zotero version 4, they have since updated to version 5. Which will focus on the standalone application. The new location for data by default will be
~/Zotero, but if you are migrating from the firefox add-on it will be in
~/.mozilla/firefox*. They promised to tidy up the data folder.