I have no idea about your packages, et al. But if you say its been a long time between updates … sure ? Note the actual size difference is the last line - its adding 1721 MB in total to the running system.
PS:
Maybe you would also be interested in clearing most of the cache afterwards:
Clear all but the last 2 caches of installed packages:
paccache -rvk2
Clear cache of all uninstalled packages:
paccache -rvuk0
Ok, thanks, I gave it Yes, so now I guess it’s gonna download it for a while. I’ll let you know if there are problems. Thanks a lot for the help and for the command for clearing the cache - it would come handy as I have only 41GB on my hard free. Should I try to update the kernel afterwards? Maybe when the system is up to date it would be happier to upgrade it.
If I were you I would probably hop on 6.6 as long as the hardware is happy with it, as the interwebs inform me it is expected to be the next Long Term Support kernel. (I am in fact running 6.6 now)
sudo mhwd-kernel -i linux66
Once booted into 6.6, making sure everything works, then you can remove 6.5.
sudo mhwd-kernel -r linux65
The following will rebuild initramfs and update grub.
mhwd-kernel should already do these things, but here they are anyways:
sudo mkinitcpio -P
sudo update-grub
For now it makes sense to keep 6.1 as its a ‘known-working’ LTS you can have around as a back-up of sorts.
Those cache commands could be helpful then.
If you use the AUR you might have your helpers cache as well; ex, for paru:
paru -Sccd
You might also go looking in your ~/.cache directory, as most everything in there can be wiped out safely but can accrue cruft over time.
Ill leave this here for you as well:
https://wiki.archlinux.org/title/System_maintenance
This is a huge problem.
You should do upgrades, and you should use snapshots as your safety net - not avoidance of updates.
Using BTRFS with snapshots means that, should anything displease me about an update, I can reboot to my previous state and nothing is lost… because a fresh snapshot is created with the update… I like BTRFS because it restores snapshots instantly, as opposed to the Ext4 I had before where it would spend time parsing and restoring the system (up to 15 minutes with snapshots stored on my external drive - I was using it as a kind of backup).
Nah, it’s fine now. See you in a year. 
Well, make fun of me as much as you like, but my laptop is a work station. I don’t reboot unless it crashes. On average I reboot every 2 months. How exactly does this work with constant updates? Not everyone works all in the cloud. As a whole I really don’t appreciate the gloating. My collaborations don’t care about random update breaking gfortran or jupyter or all the 100 libraries I need.
Right now, jupyter is “working” with the password bug I fixed months ago, that requests a token every 5 minutes and packages give and error due to some kind of mismatch it glibc that anaconda froze to some old version (because this is what anaconda does) and now "GLIBCXX_3.4.32’ is not there anymore and nothing works. Some of us require a stable environment, not one that breaks or has to debugged every 2 weeks. And now, off to my favorite sport, debugging.
P.S. Also, I don’t know why I have no slider for the screen brightness and as a whole, I have the feeling the computer is working more sloppy than before. Awesome. It’s not fault of Manjaro that scientific computing sucks, but also, don’t gloat. We all have different requirements for our systems.
That works just fine if you know your system. But since you had (among other things) a plethora of packages installed that don’t exist anymore even in AUR, that suggests you don’t.
And in general… for a critical system as you present it, you show a total lack of ability to maintain it – trying to put things in “IgnorePackage” [sic], trying to use pacman -Rcsn, etc.
And then you go on and say
which is baffling to me.
No one is forcing you to be on a rolling distro and I don’t understand why you’re making your life harder by using one – for critical stuff that is.
Hi. I think the underlying message is simple. If you want relative stability in a Linux distribution which uses a rolling release model, you must be prepared to update it regularly (maybe weekly) and attend to issues as they happen.
As evidenced by your comments above, this does not describe your working environment. You clearly will not perform the necessary updates until something breaks; this reactionary approach is not conducive to achieving this stable environment you say you want. Period.
A rolling release distribution; Manjaro; is not for you.
I suggest the standard release model of a distribution such as Debian would be best suited for your usage. Debian is rock solid, and has the greatest availability of applications within the Linux ecosystem.
We’d be sorry to see you go, but, at the end of the day it comes down to the age-old adage: ‘The right tool for the job’.
Cheers.
A lot is going on with Plasma as the February 2024 closes in.
There will be some leg-work and you should follow the guidance provided by pacman - replace the suggested files with the *5 counterparts.
You may have to temporarily remove packages while syncing the changes to make the system sync.
Especially remove packages build using custom scripts - make notes - you can rebuild later.
Make notes along the way - be warned - there will be more going forward until Plasma 6 is rolled out.
When you are using the Plasma desktop - you will need to be more upfront and keep yourself updated on what is going on.
If you know what you are doing you can condense that into once every 3, 4, 6 months if you want. People think that things will just degrade on their own if they don’t update regularly. They won’t.
Instead, there will just be more of y/n key presses and perhaps some manual intervention to do. Nothing scary at all, if you know what has to be done.
You may need to look at some pacnew-files 
It doesn’t. And I fully understand your concerns, albeit that I would add that a laptop in and of itself, by virtue of its hardware, is unsuitable as a workstation. I would recommend a desktop machine — and if you have the money, even one that qualifies as a professional workstation, with ECC RAM.
But the bottom line is either way that Manjaro is not the right distribution for your needs, nor for that matter, any other rolling-release distribution. Rolling-release means being on the cutting edge — if not bleeding edge — and this in turn means frequent updates. Even the Stable branch of Manjaro sees about two to three major updates per month.
And being Arch-based, Manjaro is high-maintenance, from package updates over merging .pacnew files — which you have apparently not done either — over to actively monitoring the forum, and in particular, the Announcements threads. Every bundled update comes with a dedicated announcement thread that details all the changes, the gotchas, and how to deal with them, all in the first two posts of the thread.
All of the above is — understandably — why Manjaro and other Arch-based distributions are not the right choice for your use case. Now, there used to be a distribution called Scientific Linux, which was put together by the people at CERN and Fermilab, and which was (initially) based upon CentOS, the “free beer” version of RedHat Linux. But it was discontinued in favor of CentOS proper, which in turn has now been discontinued — or at least, as a more settled and stable version — since RedHat was taken over by IBM. CentOS is now called CentOS Stream, and it now sits somewhere in between the stable (and commercial-only) RedHat, and the cutting-edge Fedora.
There is however an alternative, called AlmaLinux. It is rock-solid, and it is what CERN and Fermilab themselves are using now. 
Another option — as others have said — would be to go with Debian, which also has a very good reputation in terms of stability. Even Debian Testing is relatively stable for normal production use — it’s what Ubuntu and Mint are based upon, although I would personally recommend against Ubuntu because of its insistence on using Snaps instead of integrated packages.
And while we’re mentioning RHEL byte-for-byte clones, here’s yet another contender – Rocky Balboa Linux:
No one is making fun of you. You asked for help, so you are receiving it.
It seems you had expectations without fully understanding what you were getting into installing Manjaro. That’s fine, we all do things like that and then learn from the experience. You’d be better off using a point release like Fedora or Debian from what you’ve explained about your workflow.
They aren’t anymore.
Up to the point that respective branding is included, Rocky Linux is (and presumably AlmaLinux also; I’ve yet to take that for a spin).
And, speaking of spins, there is also a Rocky Linux KDE version, which obviously does diverge from RHEL proper, greatly.
Rocky apparently still is although I don’t know how they do it, but Alma isn’t: https://www.phoronix.com/news/AlmaLinux-No-1-1-RHEL
I have a zabbix server running on Alma and well… it’s running. 
Plus, there’s the plausible deniability factor;
if anything goes wrong, they can just blame that dude in the red hat.
Thanks to everyone for the concern and for the help. I do scientific computing, so it’s not a server grade stability, yet I require the system to work for months, because otherwise I keep on losing stuff (yes, I’m a messy person in general, it applies to everything I do).
I like Manjaro, I have Mint on my smaller laptop and I’m not a fan. It was stable forever, true, but the moment I needed to install something, it managed to brick itself and required a full reinstall. Very not fun experience.
I’m sorry I bothered you with something that was already mentioned in the Forum but I hadn’t updated for so long that it never crossed my mind that my problem is trivial. And I didn’t notice it when I checked quickly trough the forum. I promise next time, I’ll check out the mentioned thread before asking. For now, updating every 3-6 months works for me. It requires 2 days of debugging but usually it’s fine in the end. So again, thank you for the help, I didn’t expect to fix the problem so quickly and everyone was very helpful.
What got me away from Mint was the Ubuntu base - but that not being current, so PPA’s were a real PITA.
If I were to fancy another fling with Debian, I’d go with the Debian edition or a completely different distribution which would be 100% compatible with Ubuntu PPA repos.