dts: renesas_ra: Referencing clocks change to DeviceTree's standard.

DeviceTree typically references the clock source using the `clocks`
property defined in `base.yaml`, so we'll change it to this.

Also delete the custom clock source definitions in
`renesas,ra-cgc-pclk-block.yaml`, `renesas,ra-cgc-pclk.yaml`, and
`renesas,ra-cgc-pll.yaml`.

Signed-off-by: TOKITA Hiroshi <tokita.hiroshi@gmail.com>