Код:

@Echo Off
Set "Source=Z:\Box_In\Source"
Set "Include=Z:\Box_In\Source\Include"
Set "PSource=C:\Programming\Source"
Set "PInclude=C:\Programming\Include"
Set "Mask=*.cpp"
Set "Prg=Z:\Programming\compile.exe"
MD "%PSource%" 2>nul
MD "%PInclude%" 2>nul
Copy "%Include%\*.*" "%PInclude%\" >nul
Copy "%Source%\%Mask%" "%PSource%\" >nul
Call :PrgPushd "%Prg%"
FOR %%f IN ("%PSource%\%Mask%") DO "%Prg%" "%%f"
Popd
GoTo :Eof
:PrgPushd
Pushd "%~dp1%
GoTo :Eof