PCI: imx6: Fix bugs in PCIe startup code

LTSSM shouldn't be set once in assert_core_reset().  Move peripheral reset
just before LTSSM start.

Signed-off-by: Richard Zhu <r65037@freescale.com>
Signed-off-by: Bjorn Helgaas <bhelgaas@google.com>
Acked-by: Shawn Guo <shawn.guo@linaro.org>
Cc: Frank Li <lznuaa@gmail.com>
Cc: Harro Haan <hrhaan@gmail.com>
Cc: Jingoo Han <jg1.han@samsung.com>
Cc: Mohit KUMAR <Mohit.KUMAR@st.com>
Cc: Pratyush Anand <pratyush.anand@st.com>
Cc: Richard Zhu <r65037@freescale.com>
Cc: Sascha Hauer <s.hauer@pengutronix.de>
Cc: Sean Cross <xobs@kosagi.com>
Cc: Siva Reddy Kallam <siva.kallam@samsung.com>
Cc: Srikanth T Shivanand <ts.srikanth@samsung.com>
Cc: Tim Harvey <tharvey@gateworks.com>
Cc: Troy Kisky <troy.kisky@boundarydevices.com>
Cc: Yinghai Lu <yinghai@kernel.org>