You can use server-root/permissions.properties to specify permissions you want to apply to files copied to the server root.
The permissions.properties file, located in the server-root directory, is an optional file that specifies the permissions to apply to files that are copied to the server root. These permissions are represented in octal notation. By default, server root files maintain their permissions when copied.
The following example shows the contents of a typical permissions.properties file.
default=700 file-with-special-permissions.txt=600 new-subdirectory/file-with-special-permissions.txt=644 bin/example-script.sh=760