[SOLVED] Pacman leaving system in inconsistent state

Question

Today I made an update to my system and wanted to reboot. Since then I am having issues to no end.
To begin with, I had a custom kernel but it became hard to maintain it so I wanted to drop it in favor of a much newer default kernel. So I removed my kernel with pacman and updated the default one. Then I made sure that all traces of the custom kernel were removed and re-ran mkinitcpio and grub-mkconfig.
Afterwards, I rebooted but gut stuck entering by LUKS passphrase, because it would not accept any input. Here you have to know I was using Plymouth which already fell back to its text-mode (so I assume, the nice lock and GUI were gone). I booted from a CD, chrooted and removed plymouth and its hooks and re-installed the encrypt hook. Upon regenerating the image, it complained libgcrypt.20.so or something was missing. I checked and while pacman -Ql libgcrypt said there should be such a file, there actually wasn't (only in lib32 there was this file, and in lib there was an older version).
So I reinstalled the package and the file was there. Then I wanted to start vim and it complained some libraries were missing. I checked and again same behavior. So reinstalled all packages. This did not help. Again, manual install of those packages. Now I rebooted.
The system started, I could enter my passphrase and was automatically logged in. However, my window manager displayed several errors (among others, ACPI problems) and the screen froze. Reboot, start X as root, screen freezes as well (no WM set up here). I checked /var/log/Xorg.0.log and it is empty as is my .xlog which logs the stdout in case of my user.
I then reinstalled my graphics- and input-drivers. I also removed some packages where pacman claimed they were no longer needed (I know, risky). Now I couldn't even log in to a shell, even as root, login just said something about an Incorrect Login oder something?
So I booted from CD again, chrooted and reinstalled those packages I removed. And here comes the major suprise: My stdout gets overwhelmed with "exists in filesystem". It literally took several seconds to run through. So it seems pacman never removed those files properly.
I checked pacman.log, dmesg, journalctl and anything else I could think of but I only found possible symptoms (like VBox not finding modules), no cause.
Some additional info:
The system is a laptop with an SSD that is encrypted and uses LVM with an ext4 filesystem on all partitions (root, home, usr, var). I know usr is not such a good idea, but I learned that too late...
The installed graphics card is a generic intel card with an additional nVidia card accessible via Optimus (if that's relevant).
I have no idea what could possibly have gone wrong and would love if anyone could provide any suggestion on how to fix it or find the cause of it.
Last note: The initial problem was that it always took multiple seconds to connect to something via network. However I assumed that is because of my outdated kernel but updated libraries that require a newer kernel. Seems I was wrong...
Regards,
javex
Last edited by javex (2014-03-17 16:52:54)

Answer 1

Sorry for my late reply. Since the problem had to be fixed fast, I just reinstalled arch. I created a backup and so it was much quicker to reinstall than to unwrap this issue.
Still, concerning the kernel version: It was just some patches to add real multi-threading to luks/dm-crypt.
And during installation, I found that my usr directory had a lot of packages directories (possibly w/ content) even when the actual usr partition was not mounted. I found that I did not have the usr hook in mkinitcpio and must say, I possibly broke it myself by mounting it for my chroot environ. So this may be the cause of the extended issues.
So what likely happened here was that I broke my system by sometimes exeuting pacman with separately mounted /usr and sometimes without. This still doesn't explain the original issue but maybe a simple live CD boot & update/upgrade would have solved that. Thank you all for your responses and your effort and sorry this thread wasn't of much use to anyone.