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OK, I found the culprit, it's an internal Groovy system script we wrote. It recreates some view every 15min, and only calls jenkins.save() at the end, but it seems Jenkins is saving the complete configuration on every manipulation of the view (which also explains why it is so slow). And so the process of creating the view is recorded by the plugin, although the end product doesn't change very often.
I have disabled that script, and now it looks fine.
So if no one else has hit that file system limit so far, I assume it's safe to close this.