arty/nexys: Rework reset with litedram

arty/nexys: Rework reset with litedram

When using litedram, request a much longer PLL reset. This seems to
help get rid of all the grabled output after config.

Also use the clean system_rst out of litedram as our source of reset
for the rest of the SoC (it is synchronized with system_clk and takes
pll_locked into account already)