Debian Sources.List.D Versus Sources.List

what is the function of /etc/apt/sources.list.d?

The function of the /etc/apt/sources.list.d directory is as follows:

Using the directory you can easily add new repositories without the need to edit the central /etc/apt/sources.list file. I.e. you can just put a file with a unique name and the same format as /etc/apt/sources.list into this folder and it is used by apt.

In order to remove this source again you can just remove that specific file without the need for handling side effects, parsing or mangling with /etc/apt/sources.list. It's mainly for scripts or other packages to put their repositories there automatically - if you manually add repositories you could add them to /etc/apt/sources.list manually.

This answers your question, however, it won't solve your problem. APT is complaining about a missing GPG key which you have to manually import before you can use your newly added repository (GPG verifies all data cryptographically and needs the public keys of the owners for this).

This can be done calling sudo apt-key add public-key-file or wget -qO - http://example.com/archive.key | sudo apt-key add - where http://example.com/archive.keyis the URL for the public key (which you should verify before using).

In case of llvm, you could issue wget -O - http://llvm.org/apt/llvm-snapshot.gpg.key|sudo apt-key add - (according to http://llvm.org/apt/)

Fore more details see

How to add a GPG key to the apt sources keyring?

Get package source from sources.list.d

This line:

Get:1 http://us.archive.ubuntu.com/ubuntu bionic/universe suricata 3.2-2ubuntu3 (dsc) [2,768 B]

will tell you from where the package has been downloaded, it is from universe repository.

You need to enable the source package for the added PPA:

echo "deb-src http://ppa.launchpad.net/oisf/suricata-stable/ubuntu bionic main" |
sudo tee -a /etc/apt/sources.list.d/oisf-suricata-stable-bionic.list
sudo apt update
apt source suricata

Repositories in sources.list (Debian)

You can sort out the error by comment out all the repolist except as follow in the sources.list.

deb http://ftp.us.debian.org/debian stable main
deb http://ftp.de.debian.org/debian squeeze main non-free 
deb http://security.debian.org/ squeeze/updates main contrib

E: Malformed entry 1 in list file /etc/apt/sources.list.d/docker.list (Component)

To make sure that /etc/apt/sources.list.d/docker.list is formatted correctly use the following command (tee without -a to override the source):

On debian Buster:

printf "%s\n" "deb [arch=amd64] https://download.docker.com/linux/debian buster stable" |\
sudo tee /etc/apt/sources.list.d/docker.list

On debian Stretch:

printf "%s\n" "deb [arch=amd64] https://download.docker.com/linux/debian stretch stable" |\
sudo tee /etc/apt/sources.list.d/docker.list

(You can use $(lsb_release -cs) instead of debian codename which require lsb-release package to be installed.)

An alternative way to add docker-ce repository: You have already installed software-properties-common, you can use add-apt-repository to add the repository:

sudo add-apt-repository \
   "deb [arch=amd64] https://download.docker.com/linux/debian \
   $(lsb_release -cs) \
   stable"

Docker-ce docs

add debian repository with sed command

sed -i '$ a\\ndeb http://packages.dotdeb.org wheezy all\ndeb-src http://packages.dotdeb.org wheezy all' /etc/apt/sources.list