Prevent stack overflow when flashing px4io

Large local variable causing stack overflow when attempting to flash
IO!!!
Read the full buffer

sizeof wont work here since file_buf is now a pointer
Merge pull request #1158 from jean-m-cyr/master

Prevent stack overflow when flashing px4io
Fixed the submodule check logic
mavlink: use all outputs in HIL mode
Merge pull request #1162 from PX4/hil_outs_fix

mavlink: use all outputs in HIL mode