How to set up a development environment?

Install your favorite development environment, eg. Eclipse (Oxygen) on GNU/Linux: sudo apt install eclipse eclipse-cdt

Start Eclipse and go to the Eclipse Marketplace → Help → Eclipse Marketplace

Search for AVR Eclipse Plugin and install it.

Setting up your Project with the AVR Plugin

Project→Properties AVR tab on the left? - so you can change the target hardware to atxmega32a4u and rebuild the index.

If not so, you can change the target hardware within C/C++ Build → Environment.

Here change the value of AVRTARGETMCU to atxmega32a4u.

C/C++ Build → Tool Chain Editor: AVR-GCC Toolchain

Maybe you need to check out C/C++ General → Paths and Symbols too:

__AVR_DEVICE_NAME__ = atxmega32a4u

After all changes rebuild the index.