PCI: imx6: Assert ref_clk_en after reference clock stabilizes on i.MX95

According to the PHY Databook Common Block Signals section, the
ref_clk_en signal must remain de-asserted until the reference clock is
running at the appropriate frequency. Once the clock is stable,
ref_clk_en can be asserted. For lower power states where the reference
clock to the PHY is disabled, ref_clk_en should also be de-asserted.

Move the ref_clk_en bit manipulation into imx95_pcie_enable_ref_clk()
to ensure the reference clock stabilizes before ref_clk_en is asserted
and before the PHY reset is de-asserted. This aligns with the timing
requirements specified in the PHY documentation.

Fixes: d8574ce57d76 ("PCI: imx6: Add external reference clock input mode support")
Signed-off-by: Richard Zhu <hongxing.zhu@nxp.com>
Signed-off-by: Manivannan Sadhasivam <mani@kernel.org>
Reviewed-by: Frank Li <Frank.Li@nxp.com>
Cc: stable@vger.kernel.org
Link: https://patch.msgid.link/20260518072715.3166514-3-hongxing.zhu@nxp.com

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