This article describes how to run a dos command as a run command in a Deployment Manager package
In the "What is the run command?" field of a run command for a package, it is normally expecting the location of a .exe, .bat, .sh or a vb script file. It is not expecting a direct dos command.
So if a direct dos command is put in this field (eg. rmdir), you would see an error like "File Not Found:rmdir xxxx" in the client installation log.
To overcome this issue, you can put "cmd/c" in front of the dos command line to force the installation agent to realize it is a dos command rather than a file location.
eg. you can put "cmd/c rmdir xxxx" in the field "What is the run command?" of a run command, and this command will run successfully on the client machines.