How to use if – else structure in a batch file?

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Your syntax is incorrect. You can’t use ELSE IF. It appears that you don’t really need it anyway. Simply use multiple IF statements:

IF %F%==1 IF %C%==1 (
    ::copying the file c to d
    copy "%sourceFile%" "%destinationFile%"
    )

IF %F%==1 IF %C%==0 (
    ::moving the file c to d
    move "%sourceFile%" "%destinationFile%"
    )

IF %F%==0 IF %C%==1 (
    ::copying a directory c from d, /s:  boş olanlar hariç, /e:boş olanlar dahil
    xcopy "%sourceCopyDirectory%" "%destinationCopyDirectory%" /s/e
    )

IF %F%==0 IF %C%==0 (
    ::moving a directory
    xcopy /E "%sourceMoveDirectory%" "%destinationMoveDirectory%"
    rd /s /q "%sourceMoveDirectory%"
    )

Great batch file reference: http://ss64.com/nt/if.html

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