This thread is getting long, if someone else all ready suggested this, forgive me,
I don't agree , on "synaptic" is utterly useless", it is a tool, I use it quite a bit, but like any "tool" or "tools", each one has it's purpose.
But H_0_A_S, says:
Head_on_a_Stick » 2016-01-10 15:16
Stop using Synaptic for repository management, it is utterly useless for that purpose.
He is clear, on "for that purpose". Synaptic, is not the tool to use , for example to modify or edit your sources.list, the sources.list is what "manages" or determines which repos will be used.
Understanding what tools are available, and what each one is intended for is the key to using any given tool succesfully.
The OP should read this, carefully:
https://www.debian.org/doc/manuals/debi ... ls.en.html
by krita »But just curios, anybody knowns why Synaptic keep adding the "jessie"-lines by itself and lists "standard"-lines in sources.list as Other software in the Synaptic GUI?
It shouldn't be doing anything ,"by itself", and not sure exactly what you mean here, but
One thing about synaptic, you need to run edit>Reload Package Information
After YOU, make any changes in your sources.list file, other wise :
the checkboxes for main, contrib and non-free are all empty. Before they were all checked. And when I check them again, Synaptic adds the rows I just removed again. Why?
Like wise, if you use
or
you still need to run:
To update the package information, after you make any changes in your sources.list file, and before you try to install new updates.
More on sources.list:
There is, manuals in your computer:
If you look at the "apt-get" manual, in the link posted by H_O_A_S,
or
Look for the -s option, this is safe way to check what will be updated,upgraded and installed or removed.
The links to online manuals on apt, and aptitude all ready were posted, but also they are available using the "man" command.
Postby krita »
@Head_on_a_Stick
Your system is already broken
How do you know that? As far as I can tell it runs perfectly well!
It may run perfectly well, for quite some time, but as all ready mentioned, you can not safely do any updates or upgrades, until if and when you get all of the mixed packages sorted out,etc.
Probably, as long as you don't do any upadates,or install any new packages, or upgrades , it will keep running just fine. Making a "backup" will give you a safe way to save important data, but a "back up" would not be of any use, to restore the system, you would be simply re-installing a back up of the same "broken" system.
The main cause of the problem, not reading very much documentation, as you can see, just trying to explain a little, about "package management" on Debian, makes a very long, to long of a post/thread. This just "scratches" the surface, read the documentation, to get the "Full Picture" or a more complete understanding.
Below , covers most everything, lots of good info, not just package management:
https://www.debian.org/doc/manuals/debian-handbook/
Well, this post is way to long, I know it is redundant, but the same questions all the time are redundant as well, many problems could be avoided if documentation is read ahead of time, and using the "man" command to check and see what exactly the commands issued will do, and how they work.
Now, I just added testing to get some lib or just search for something - don't remember - but I don't use any package (including dependencies) from it as far as I can tell. (Is there a handy way to list packages from testing easily b.t.w.? I compared output from apt list --installed to check).
At least in the past. Not for everything, sure, but for common tasks. Do I need "visual aids"? Well, perhaps not, but a functional graphical interface is quite nice don't you think. Many applications use it nowadays... 
