Adding obstacle avoiding in AUTO mode, or any such alternative to the issue

I want to plan a mission on my mission planner, and my quadcopter must avoid the obstacles which come in path, and should also reach the checkpoints. Can anyone please help me come up with a solution ?

Update to ArduCopter master, it does what you want. 3.5.x is very outdated.

Can APM 2.8 flight controller be used with Arducopter Master .

No, APM 2.8 hardware only supports ArduCopter firmware up-to 3.2.1.
So you can either change the source code and implement that feature yourself (not easy) or buy one of the newer hardware boards (for around 22€) that support master: