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Setting up the Programming Environment
6443 likes to use IntelliJ as the goto IDE. (insert reason). Unfortunately WPI doesn't offer official support for programming with IntelliJ. This guide will go through all of the necessary steps to begin programming and building code.
Install IntelliJ, use community edition if you don't have a license. As of 2018, you need 2017.3 or higher for the plugin below to work.
Follow this plugin's wiki which is found here but it may move. This wiki is well written and provides examples for generating code, using with an existing project, building, etc. So far 0.7 is the only known version to work, no others have been tested on the team, so that is the safest option.
You will have to add a jdk to your project. This step is necessary because install paths are different computer to computer. On the bottom right, a green bubble should appear prompting you to attach libraries. This is for the wpilib and is part of the FRC plugin.
Since the navX is used on the robot, the navX library will need to be installed. 6443's guide can be found here and the official website can be found here.
The .idea folder contains the iml file which lets IntelliJ know how to setup the project. This is possibly also the file responsible for automatically setting up source.