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You'd probably best off setting up quota's. There is also setting the max size of files (since a directory is simply a file) on your system using ulimit but that would also limit the size of all files, unless you set it for that particular user, etc.
What you actually want to do is to limit maximum amount of data owned by user "user" in /home partition.
You can do this by quota. How to do it depends on your distribution.
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