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You can replace explorer.exe in Windows XP by changing the key
HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows NT\CurrentVersion\Winlogon\Shell
to e.g. c:\pf\totalcmd\totalcmd.exe or something like c:\startup.bat.
A basic problem of replacing Windows Explorer is that the System Tray is inaccesible. Use a program
like AM Productions TrayModule to
emulate the System Tray.
You might have to start stuff manually to get e.g. WLAN working.
Run msconfig and check the 'Startup' tab for any essential programs.
Alternatively, you could install a replacement like the Emerge Desktop
You can replace explorer.exe in Windows 98 by editing C:\Windows\system.ini:
[boot] shell=c:\programmer\totalcmd\totalcmd.exe
How's that for a 'totally commanded' machine?