OpenWRT trunk has support of Linux 4.1 for MVEBU platform. And it also maintains 4.4 as well. In order to use 4.4 in ClearFog board and PCIe bus, you should not only switch to 4.4 kernel but also enable i2c bus driver and gpio-pca9655 driver.
[ 0.849089] i2c /dev entries driver [ 0.854577] GPIO line 496 (pcie1.0-clkreq) hogged as input [ 0.860688] GPIO line 499 (pcie1.0-w-disable) hogged as output/low [ 0.867199] GPIO line 500 (pcie2.0-clkreq) hogged as input [ 0.873317] GPIO line 503 (pcie2.0-w-disable) hogged as output/low [ 0.879812] GPIO line 501 (usb3-current-limit) hogged as input [ 0.886278] GPIO line 502 (usb3-power) hogged as output/high [ 0.892570] GPIO line 507 (m.2 devslp) hogged as output/low [ 0.898453] GPIO line 508 (sfp-los) hogged as input [ 0.903655] GPIO line 509 (sfp-tx-fault) hogged as input [ 0.909590] GPIO line 510 (sfp-tx-disable) hogged as output/low [ 0.915832] GPIO line 511 (sfp-mod-def0) hogged as input
From the output of dmesg, we know that the i2c GPIO expander chip controls the enable of PCIe bus.
