arm: dts: marvell: clearfog-gtr: add missing pinctrl for all used gpios

Various control signals such as sfp module-absence, pci-e reset or led
gpios were missing pinctrl nodes, leaving any u-boot choices in place.

Since U-Boot is shared between multiple board variants, i.e. a388
clearfog pro / base, clearfog gtr l8 / s4, it is better to explicitly
configure functions.
Add explicit pinctrl entries for all gpios currently in use.

Additionally the loss-of-signal gpio specified is invalid, in fact los
only has a pull-up on the board but no gpio connection to the cpu.
Remove this stray reference.

Signed-off-by: Josua Mayer <josua@solid-run.com>
Signed-off-by: Gregory CLEMENT <gregory.clement@bootlin.com>