when we install / deinstall apps using apt or dpkg (debian app installer, on which "app manager" is based), there may be old files no more necessary.
So

1/ become root in the terminal

2/ backup /etc/apt/sources.list and /etc/apt/sources.list.d/* files :
#cp /etc/apt/sources.list /home/user/MyDocs/.documents/
#cp -r /etc/apt/sources.list.d/ /home/user/MyDocs/.documents/
3/ backup the file obtained thanks to :
#dpkg --get-selections > /home/user/MyDocs/.documents/installed.list

4/ You should then backup using "backup/restore" utility

5/ reflash

6/enable "extras" repository in order to install bash, gainroot and sudser

7/ Restore your personnal settings thanks to "backup/restore" utility

7/ become root in a terminal

8/ restore apt repositories :
#cp /home/user/MyDocs/.documents/sources.list /etc/apt/sources.list
#cp -rv /home/user/MyDocs/.documents/sources.list.d /etc/apt/
#apt-get update

9/ reinstall before-flashing installed apps/libs :
#dpkg --set-selections < /home/user/MyDocs/.documents/installed.list
#apt-get -f install