When I try to connect to my apm 2.6 board with terminal in mission planner it shows a bunch of continuous letters numbers and symbols. The specs on the apm 2.6 does say it has the ATMEGA2560 and ATMEGA32U-2 chips
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If you want to download a log file you can do it on the "graphs" page now.
If you want to change what is logged you can do it in config/tuning (search for "mask" among parameters).
That is correct. The CLI is disabled on APM2.x HW to save firmware space. http://copter.ardupilot.com for more help