There is a way to execute server commands in Unix, and there is one for the windows environment too. The SXPG_COMMAND_EXECUTE function module.
The setup is not as simple as the Unix command call, an example where a file is moved from server location ..\in to server location ..\completed involves the windows MOVE command. Run the function module with MOVE and it will simply state that the command is not recognized. That's because commands are controlled. In table SXPGCOSTAB a line needs to be added to support the MOVE command for our very own Z_MOVE command. This table can be edited through transaction SM69 - External commands for the operating system. Add the following lines (as example):
NAME OPSYSTEM OPCOMMAND Z_MKDIR Windows NT mkdir Z_MOVE Windows NT cmd /c move
Commands to make a directory and to execute a Z_MOVE.