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When calling the copyFileWithFlags function with the preserveSrc flag set, file permissions must be set after creating the destination file and setting the file owner. This is necessary because umask can prevent newly created files from acquiring the source file's permissions and file ownership changes can impact the setuid/setgid permissions. Similarly directory permissions are set after creating the directory to avoid unexpected permission behavior caused by umask. Signed-off-by: John Akre <john.w.akre@intel.com>