CLIJ2 uses the maven build system. In order to develop CLIJ2, use git to get the recent version and maven to build it:
Clone the clij2 repository
git clone https://github.com/clij/clij2
Open pom.xml and enter the path of your Fiji installation in the line containing
Go to the source dir and install it to your Fiji.app
cd clij2 mvn install
For development it is recommended to use an integrated development environment such as IntelliJ or Eclipse.