If you require greater stability please wait for Byzantium to become stable. Since Byzantium is a rolling release you will face the occasional issue, like this one.
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I can confirm issue on my machine and am working on finding a fix.
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I was also hit by this issue over the weekend. I tried installing xfce and kde Plasma with no luck. Since I have most of my data backed up and stored separately from my OS, my quickest solution was to start over with a different distro, since the version of GNOME in Pure OS Amber is older than I like. But if I had not already isolated by data, I could have been screwed.
I was under the impression that while PureOS Byzantium was less tested than Amber and more likely to have bugs, that there was still someone checking the updates before they went out to users (as in the system may crash more than usual, but it will at least boot). Was that an inaccurate assumption?
Byzantium is less tested. Updates from Debian are imported directly as binaries for a couple of reasons, not least our effort towards convergence. Since they are binaries imported directly from Debian testing they are not manually checked and a GNOME transition has snuck in causing a bit of havoc. I think it is resolvable but Iām hoping to provide a quick way to fix the system in lieu of having to wait for automatic updates.
Iām running both Amber and Byzantium here on two different Librem. Byzantium is broken for me too, trying to find a fix. This should not affect Amber.
Here is our naming scheme;
Amber = Stable = Security fixes and other updates from Debian Stable
Byzantium = rolling release = New software, new updates, new bugs
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Getting this output on apt dist-upgrade now:
Reading package lists... Done
Building dependency tree
Reading state information... Done
Calculating upgrade... Done
The following packages were automatically installed and are no longer required:
apg apt-file cups-pk-helper flatpak gir1.2-appstream-1.0 gir1.2-packagekitglib-1.0
gnome-control-center-data gnome-getting-started-docs gnome-online-accounts gnome-software-common
libappstream-glib8 libapt-pkg-perl libcolord-gtk1 libexporter-tiny-perl libflatpak0
libgoa-backend-1.0-1 libgspell-1-1 liblist-moreutils-perl libnss-myhostname libostree-1-1
libpipewire-0.2-1 libpython3.7 libregexp-assemble-perl librygel-core-2.6-2 librygel-db-2.6-2
librygel-renderer-2.6-2 librygel-server-2.6-2 pureos-init-disk-crypto python-apt-common python3-cups
python3-cupshelpers python3-distro-info python3-pycurl python3-smbc realmd rygel
system-config-printer-common system-config-printer-udev xdg-desktop-portal xdg-desktop-portal-gtk
Use 'sudo apt autoremove' to remove them.
The following packages will be REMOVED:
command-not-found gnome-contacts gnome-control-center gnome-initial-setup gnome-software
gnome-software-plugin-flatpak isenkram-cli libgnome-desktop-3-18 libmutter-5-0 libphobos2-ldc-shared88
pureos-gnome python3-apt python3-software-properties software-properties-common
software-properties-gtk unattended-upgrades
The following NEW packages will be installed:
liborcus-parser-0.15-0 libphobos2-ldc-shared90 linux-image-5.6.0-1-amd64
The following packages have been kept back:
fwupd-amd64-signed
Iā¦ think Iāll hold off the upgrade for now. Auto-removing some of those things doesnāt sound too great.
I got such a small dependency hell as well, and, always using aptitude, selected manually a bunch of packages pureos-gnome and pureos-desktop implied as dependencies and that I wanted to keep, as I wanted to see if these updates could help avoid frequent libreoffice crashes I had and also some printing issues.
Fortunately, GDM and Gnome shell issues reported a couple of weeks ago are solved now, even if some non-core Gnome packages cannot be updated yet because of conflicts or missing dependencies.
I will also still hold back with upgrading back to byzantium until all issues are resolved.
It says āno longer required.ā If, for instance, you updated gnome, all the old gnome stuff would no longer be required.
Iām missing the context of your upgrade situation, though, so I canāt say for sure what you should do.
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you can make a snapshot if youāre worried before commiting to auto-remove ā¦
It looks like the reason that fwupd-amd64-signed is held back is that libflashrom1, a dependency of fwupd is missing from the repository.
Thatās correct. However itās not old stuff itās removing in this case, but half my system.
I suppose you didnāt disabled Amber from sources list (including amber-proposed-updates main as well) which I find all right. Next, you wrote you added Byzantium as @jeremiah described. But second step: sudo apt update && sudo apt full-upgrade is not an option for you, for your system. How about: sudo apt update && sudo apt upgrade as apt man page defines: upgrade is used to install available upgrades of all packages currently installed on the system from the sources configured via sources.list. New packages will be installed if required to satisfy dependencies, but existing packages will never be removed. If an upgrade for a package requires the removal of an installed package the upgrade for this package isnāt performed.
After running sudo apt upgrade command and if choosing: Yes, reboot and run: sudo apt autoremove --purge just to proof if above satisfies your expectations from Byzantium repository.
I moved to Byzantium a few months ago, and I didnāt leave anything of Amber in apt sources lists, but I had the same problem as @vmedea. I think this results from an incompatibility or conflict in current Byzantium repositories between versions of dependencies of some packages, which lead apt to propose deleting base meta-packages. I didnāt want to remove āhalf my systemā either, but I definitely wanted to upgrade certain packages, so I chose to remove those base packages and manually select packages to keep for a working OS; this may require more massaging of package selections in updates until these conflicts are solved.
After recent Gnome updates in Byzantium, I still experience frequent crashes of gnome-shell, especially after unlocking the screen; I suspect the extensions set I use (a mix of a dozen of Gnome extensions installed from either Byzantium repositories or extensions.gnome.org web site) to contribute to this instability, so I started using KDE Plasma.
Yes, Iāll stay out of this, as after sudo apt upgrade very same question will be asked: Yes or No. And even, at the moment, PureOS offers only /byzantium/plasma/2020-05-05/ .iso and not Gnome, which I prefer. Byzantium Gnome .iso is probably for some good reason(s) not ready yet to be published as standalone, but still testing edition. It is up to @vmedea to decide or even up to someone else to share here if already having some personal experience (not being one as not using PureOS) with using both Amber and Byzantium repositories, without executing sudo apt full-upgrade.
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FWIW I donāt have both amber and byzantium apt sources configured, only byzantium (I donāt think having both configured is useful). This worked great until about two weeks ago. Then the GNOME problem happened, and now since two days there seems to be a new conflict.
I hope there will be an official message or at least a forum post by @jeremiah once gnome shell works again in byzantium.
Knowing if you are doing sudo apt upgrade on top of Amber or on top of Byzantium repository. Either you never mentioned this fact or I skipped this unintentionally. If you are not upgrading some of Amber related packages that are not part of Byzantium any more this is not my problem either.
But I do (think), as unexpected things might happen:
I donāt understand why you think this: packages versions in Byzantium have definitely diverged way too much from Amber for making it useful to install packages from Amber in a Byzantium system, except maybe some non-essential packages with low-demanding dependencies.
If you are currently in trouble with Byzantium updates, Iād recommend to either not apt-upgrading core packages until conflicts are solved in the repository (if your system works well enough), or selectively upgrading packages including core ones trying to minimize breakage and maximizing updates (which I did with moderate success), or move completely back to Amber. 
It seems that not all Byzantium users, especially Gnome users, were prepared to bear this testing period of Gnome 3.36 (I wasnāt), but it is understandable for a testing distribution! 
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