System a bit broken pacman -Syu exists in filesystem

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Hi,

My system has two hard drive, one SSD with / and /home/user on two
partitions and a HDD mounted on /opt and /var.

The HDD failed, and the system works with only the SSD as it was installed
like this and then extended to the HDD.

Only 3 or 4 weeks of update make a difference between the content of /var
and /opt on the SSD and the HDD.

Now I'm performing an upgrade of the whole system to get back to normal but
all files in /usr are making conflict as the /opt and /var are older and
trying to install files that are already there.

So I could - but it seems really painful - rename all the conflicting files
(they are a lot), if anyone as an idea how to automatize this. Or maybe I
would love some kind of option in pacman that would overwrite or ignore
those conflicts, I know that's against how pacman is build so I'm asking
here.

Hope I make sens.

thx
Laurent


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