I've compiled and uploaded firmware versus v1.2.9 on apm2.5 but I've not added #define GPS_PROTOCOL GPS_PROTOCOL_UBLOX in apm_conf.h so in my opinion it uses the default protocol MTK (as defined).
But in terminal it says ublox OK:so it seems to accept my ublox gps.
Mission planner has also no functionality to choose between MTK and UBLOX.
Does mission planner firmware upload accept UBLOX gps?
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the apm auto detects, and uses the correct driver for the gps