If you are talking about the traffic data imported via CSV that is stored under the PATH you defined for TEMPORARY DATA STRUCTURE FOLDER, and you can remove it from the same place you set it up. Let us know if you ask for other kind of data...
all the data related to configs is stored in /home/userSpace
Each project has its own database and stored in /var/lib/mysql by default. Try to keep the number of projects the lower you can
You can clean the /var/log/ folder like in any other linux distribution there are stored the mysql , apache2 and system logs and its a good practice to clean them from time to time
Hope that helps
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