I am not quite new to Debian but it was my first major version upgrade. I didn't know what to do and I might have messed up with apt sources.
I upgraded by replacing jessie by strecth in /etc/apt/sources.list by running:
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sed -i 's|jessie|stretch|' /etc/apt/sources.list
apt update
apt full-upgrade
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Ign:2 http://ftp.us.debian.org/debian stretch InRelease
Get:3 http://ftp.us.debian.org/debian stretch-updates InRelease [88.5 kB]
Err:4 http://ftp.us.debian.org/debian stretch Release
Bad header line Bad header data [IP: 64.50.233.100 80]
Get:5 http://security.debian.org stretch/updates InRelease [62.9 kB]
0% [Working]
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amichaut@debian:/var/lib/apt/lists$ ll
total 108848
drwxr-xr-x 3 root root 4096 Jun 19 18:23 .
drwxr-xr-x 5 root root 4096 Jun 20 10:20 ..
-rw-r--r-- 1 root root 996 Jun 12 05:28 desktop-download.mendeley.com_download_apt_dists_stable_main_binary-amd64_Packages
-rw-r--r-- 1 root root 1934 Jun 12 05:28 desktop-download.mendeley.com_download_apt_dists_stable_Release
-rw-r--r-- 1 root root 490 Jun 12 05:28 desktop-download.mendeley.com_download_apt_dists_stable_Release.gpg
-rw-r--r-- 1 root root 38880082 Jun 17 04:23 ftp.us.debian.org_debian_dists_stretch_main_binary-amd64_Packages
-rw-r--r-- 1 root root 4723194 Jun 16 10:33 ftp.us.debian.org_debian_dists_stretch_main_dep11_Components-amd64.yml.gz
-rw-r--r-- 1 root root 6804014 Jun 16 10:32 ftp.us.debian.org_debian_dists_stretch_main_dep11_icons-64x64.tar.gz
-rw-r--r-- 1 root root 26436445 Jun 18 04:11 ftp.us.debian.org_debian_dists_stretch_main_i18n_Translation-en
-rw-r--r-- 1 root root 33712242 Jun 17 04:23 ftp.us.debian.org_debian_dists_stretch_main_source_Sources
-rw-r--r-- 1 root root 113425 Jun 17 04:46 ftp.us.debian.org_debian_dists_stretch_Release
-rw-r--r-- 1 root root 3108 Jun 17 05:45 ftp.us.debian.org_debian_dists_stretch_Release.gpg
-rw-r--r-- 1 root root 88481 Jun 19 16:48 ftp.us.debian.org_debian_dists_stretch-updates_InRelease
-rw-r----- 1 root root 0 Nov 4 2015 lock
-rw-r--r-- 1 root root 23521 Jun 7 20:13 packagecloud.io_slacktechnologies_slack_debian_dists_jessie_InRelease
-rw-r--r-- 1 root root 29879 Jun 7 20:13 packagecloud.io_slacktechnologies_slack_debian_dists_jessie_main_binary-amd64_Packages
drwx------ 2 _apt root 4096 Jun 20 19:05 partial
-rw-r--r-- 1 root root 62912 Jun 19 18:01 security.debian.org_dists_stretch_updates_InRelease
-rw-r--r-- 1 root root 213998 Jun 19 11:30 security.debian.org_dists_stretch_updates_main_binary-amd64_Packages
-rw-r--r-- 1 root root 119814 Jun 19 11:30 security.debian.org_dists_stretch_updates_main_i18n_Translation-en
-rw-r--r-- 1 root root 187277 Jun 19 11:30 security.debian.org_dists_stretch_updates_main_source_Sources
Thanks for your help!