I know most of the information I use in my daily basis is stored in the home folder, however, I want to be sure nothing important is left out of the backup.
Edit: Which command I use to copy these files into an external HD?
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The only files that are important for you to backup are the user data in de home folders of the different users of the system. All the other folders contain system files.
Do not put efforts in backing up these. Operating systems come for free and are installed in less than 30 minutes. Personal user data, however, is unique and can be lost forever if not good backup exists.
I already made a backup following the instructions on this post: backup - How to back up my entire system?. This link also leads to another forum where you can find the complete information: Howto: Backup and restore your system! by Heliode
If you were searching the same thing as I did some days ago, I recommend you to follow the instructions on the links above.