The weird thing about revision control technologies is that deleting an object (file/folder) from one of the branches (master, HEAD, etc) does not necessarily delete it physically from the file system.
Most revision control systems just mark those objects as deleted as it needs to keep them in the repository's history. You will need to perform some intervention to delete it physically from the file system.
One of the most frequently asked questions is on how to reduce a user's XP-Dev.com space usage to below its allowed limit, and the steps taken to reduce it depends heavily on which version control system it is.
If you're a free account holder, you will have project quotas too, and as such you may need to delete projects as well.
Feel free to contact us if you need any assistance.
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