While looking at Tool Labs homedir sizes I noticed that /home/whym is quite a bit larger than at typical user's homedir. It looks like there is a complete copy of dumps.wikimedia.org from December 2015 stored in /home/whym/data that could possibly be removed.
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Thanks for notifying me. It was a (probably incomplete) copy of dumps.wikimedia.org/other. The largest subdirectory was /other/diffdb/ which I have deleted. I was particularly interested in https://dumps.wikimedia.org/other/slow-parse/ - I hope the remaining 600MB is okay to stay.
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Usage now is ~2G. Thanks a lot for the quick response @whym. It is very much appreciated.