when I installed debian 12.7 I created a separated /var directory, along other 2 separated directories (names forgotten).

I also use flatpak and this program is installed in this directory. Executing ‘flatpack update’ I discovered this directory is 95% full, meaning I cannot update anything, because /var is 95% full (only 400 MiB free)

Ideas to solve this?

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In the future, you should look into using LVMs for your partitions. I ran into a similar problem recently where my /var needed to be increased - I was able to run a simple lvextend -L+4G /dev/myvg/var --resizefs to grow my /var by 4 gigabytes.

Before I was using LVMs though I used a gparted live disk a lot

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