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So I'm trying to upgrade from Debian Jessie to Stretch and following the official guide from the wiki.

I came across this section

The upgrade process described in this chapter has been designed for upgrades from “pure” jessie systems without third-party packages. For the greatest reliability of the upgrade process, you may wish to remove third-party packages from your system before you begin upgrading.

Running $ apt-forktracer | sort reveals I have quite a number of packages from third party sources as well as packages from Jessie-Backport. Most appear to be harmless applications that aren't system dependent but there's also some Java RE in there. I've checked and these packages are supported in Stretch.

Can I safely ignore these third party packages for the upgrade ?

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    My experience has not been stellar doing upgrades with backports or 3rd party repos. You would better spin up test VMs rather than trusting what we say. – Rui F Ribeiro Jul 8 '18 at 21:40
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The main issues are addressed in the section on “unofficial sources”:

  • third-party packages may be removed, if they have dependencies which conflict with the upgrade;
  • unofficial backports (which doesn’t include packages from Jessie backports) may cause file conflict issues.

In the first case, the package manager will tell you about the issue during the upgrade, before it actually starts, and the conflicts shouldn’t prevent the upgrade from completing. The second case is trickier to handle: it will only be detected when the conflicting packages are unpacked, during the upgrade, and dealing with it then will be messier (because your system will be half-upgraded), albeit not insurmountable. See the section on file conflicts for details.

All this is why the documentation recommends identifying all such packages before starting the upgrade process.

To answer your specific question, in your specific case it seems the only suspect package is the JRE. If it comes from Jessie backports (OpenJDK 8, by any chance?), you’ll be fine. Otherwise, you might want to remove it (and anything depending on it) before the upgrade, and re-install anything you care about afterwards.

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