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chroot is not what you want, it changes the / path to be the named dir, so any subsequent calls will have that as their / path - not a good idea

chdir() is what you need
man 2 chdir will give you...

tar always preserves paths, so the only way to do what you want is to change to the directory where the files are, and add them from there using just thier name not path/name

system("tar -cf...