Hi. The issue is that foo.com/bar/ is not a separate domain from foo.com/ but rather a subdirectory of that domain. Spidering can now be limited to subdirectories, but the domain is still the domain. On the other hand, the bar.foo.com/ subdomain, while it can point to the foo.com/bar/ subdirectory, it is a third level domain and can also be treated as a separate site on a separate server. The database storage scheme is domain based, and that is why subdirectories are not stored separately but subdomains are separately stored.
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