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MSDOS.SYS is a hidden, system, read-only, text configuration file and not an executable program in the root directory of your boot drive. This file contains paths that contain information about the location for other Windows files like Registry. 
This file determines whether the computer boots into DOS or into Windows 95/98. In DOS, it works with IO.SYS to start the boot process but in Windows 9x, it is a configuration-based file.
