How do your apt config folders look like?

$ ls -la /etc/apt/apt.conf.d/
00aptitude             01autoremove-kernels   15update-stamp         70debconf
00trustcdrom           01-vendor-ubuntu       20archive              
01autoremove           10periodic             50unattended-upgrades  

$ ls -la /etc/apt/preferences.d/
total 8
drwxr-xr-x 2 root root 4096 Apr 14  2016 .
drwxr-xr-x 6 root root 4096 Mar  6 03:45 ..

Do you have special (maybe unwanted) files (for example for pinning) in

Do you notice a difference if using apt instead of apt-get?
sudo apt update
apt list --upgradable
and then maybe:
sudo apt upgrade
sudo apt full-upgrade

Btw. In your sources.list you have lot's of deb-src lines active - in
case you don't do development based on the package sources you should
consider to disable them (comment out).

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  apt-get update doesn't get new packages

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