This file is indexed.

/usr/lib/ubuntu-mate/ubuntu-mate-settings-overlay is in ubuntu-mate-default-settings 16.04.5.

This file is owned by root:root, with mode 0o755.

The actual contents of the file can be viewed below.

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#!/usr/bin/env bash

function overlay_file() {
    local SYSTEM_FILE="/usr/share/ubuntu-mate/settings-overlay/${1}"
    local USER_FILE="${HOME}/.${1}"
    local USER_DIR=$(dirname "${USER_FILE}")
    if [ ! -f "${USER_FILE}" ]; then
        mkdir -p "${USER_DIR}"
        cp "${SYSTEM_FILE}" "${USER_FILE}"
    fi
}

# If the 'xim' input method is set, probably by gnome-language-selector,
# this causes all manner of compatibility issues. This is a work around
# for pre-existing configurations, a patch has been submitted upstream.
#  - https://bugs.launchpad.net/language-selector/+bug/1550325
function correct_xinputrc() {
    DETECT_XIM=$(grep xim ${HOME}/.xinputrc)
    if [ $? -eq 0 ]; then
        AUTO=$(im-config -m | sed '3q;d')
        /usr/bin/im-config -n ${AUTO}
    fi
}

if [ ! -d "${HOME}/.config/plank/dock1" ]; then
    overlay_file config/plank/dock1/launchers/clock.dockitem
    overlay_file config/plank/dock1/launchers/desktop.dockitem
    overlay_file config/plank/dock1/launchers/firefox.dockitem
    overlay_file config/plank/dock1/launchers/matecc.dockitem
fi
overlay_file config/folder-color/hide_donation
overlay_file config/libreoffice/4/user/registrymodifications.xcu
overlay_file config/synapse/config.json
overlay_file config/Trolltech.conf
correct_xinputrc