My LAMP server got a virus. (I think.) The root partition started to fill up. But there is no clue as to what it filled up with (no logs). After restart, the used space of the root went back to 4% (as normal). I reinstalled the server, but I saved the old root files to preserve the configuration.
Afterwards, I tried to delete the saved files, it started to disappear only one files I could not delete with root and then something started to build up the whole "old" root file structure again. All the deleted folders came back. I needed to format the drive to get rid of it. Unfortunately I have another copy from this. Do I have to do some kind of security action?
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. This SO-question may give you help in finding what uses disk space.