The File Server and the Provisioning Data Store are separate entities.
"BMC Server Automation uses the file server to store the contents of files included in snapshots, Network Shell scripts, BLPackages, software packages, and other types of information that is not easily stored in the database. In addition, the file server stores registry, COM+, and metabase values longer than 255 characters."
"where you store sets of installation files that are used for provisioning operating systems."
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the pxe/tftp server contains the boot images for the OSes you are provisioning - eg WinPE, RHEL, SLES, and the gentoo pre-boot image. the DataStore is also typically located on the PXE/TFTP server, though it does not have to be.