There is a handy guide with steps for updating the FP2 when you are using an alternative recovery rom: ✏ How to update a rooted FP2 with TWRP?
The only difference in the steps I take is that I sideload the update. Since I’m lazy I created a small script that downloads and sideloads the latest version and a second script for downloading and flashing the rooted boot image. So for the linux user here I thought I should share the scripts. You’ll need to have lynx installed and the android framework.
Disclaimer: use this at you own risk. Please don’t use the script if you don’t know what you are doing. If any of the used terminology doesn’t mean anything to you: please don’t use the scripts.
Any additions or improvements are welcome 
Update: Find the latest version on github
Sideloading the update:
#!/bin/sh
function error_exit {
local parent_lineno="$1"
local message="$2"
local code="${3:-1}"
if [[ -n "$message" ]] ; then
echo "Error on or near line ${parent_lineno}: ${message}; exiting with status ${code}"
else
echo "Error on or near line ${parent_lineno}; exiting with status ${code}"
fi
exit "${code}"
}
trap 'error_exit ${LINENO}' ERR
echo "Connect phone in recovery mode with sideload option on!"
echo "Press <enter> to continue"
read
# Get newest firmware downloadlink=$(lynx --dump $1 'https://fairphone.zendesk.com/hc/en-us/articles/213290023-Fairphone-OS-downloads-for-Fairphone-2’|awk ‘/http/{print $2}’|grep ‘.zip’|head -n1)
echo "-= Downloading update =-"
wget $link
fileName=$(echo $link|rev|cut -d/ -f1|rev)
androiddir=$(locate platform-tools|head -n1)
echo "-= Sideloading update =-"
sudo $androiddir/adb sideload $fileName
echo "-= Removing update =-"
sudo rm -f $fileName
echo "-= Done! Reboot the phone =-"
Flashing the rooted boot image
#!/bin/sh
function error_exit {
local parent_lineno="$1"
local message="$2"
local code="${3:-1}"
if [[ -n "$message" ]] ; then
echo "Error on or near line ${parent_lineno}: ${message}; exiting with status ${code}"
else
echo "Error on or near line ${parent_lineno}; exiting with status ${code}"
fi
exit "${code}"
}
trap 'error_exit ${LINENO}' ERR
echo "Connect phone with usb debugging on!"
echo "Press <enter> to continue"
read
# Get newest bootimage download
link=$(lynx --dump $1 'https://fairphone.zendesk.com/hc/en-us/articles/213290023-Fairphone-OS-downloads-for-Fairphone-2'|awk '/http/{print $2}'|grep '.zip'|head -n1)
fileName=$(echo $link|rev|cut -d/ -f1|rev)
version=$(echo $fileName|cut -d- -f3)
linkImage=$(lynx --dump $1 'https://fp2.retsifp.de/'|awk '/http/{print $2}'|grep "$version/"|head -n1)
linkImage=$(lynx --dump $1 "$linkImage"|awk '/http/{print $2}'|grep '.img'|grep '-eng-'|head -n1)
echo "-= Downloading root image =-"
wget $linkImage
fileName=$(echo $linkImage|rev|cut -d/ -f1|rev)
androiddir=$(locate platform-tools|head -n1)
echo "-= Reboot phone =-"
sudo $androiddir/adb reboot bootloader
sleep 30
echo "-= Push boot.img =-"
sudo $androiddir/fastboot flash boot $fileName
sleep 10
echo "-= Reboot phone =-"
sudo $androiddir/fastboot reboot
echo "-= Removing file =-"
sudo rm -f $fileName
). I like the adb wait-for-device. I’ll change that when I get the chance. It is far better.