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