The goal of Fiji's build system is to make it extremely simple to define the tasks that are needed for Fiji.
If you want to build Fiji completely, just clone git://github.com/fiji/fiji, change the directory to the cloned one, and launch:
You can add individual targets (versions in versioned file names are ignored), e.g.:
If you want to force a rebuild, just attach the suffix --rebuild to the file name:
The special clean target deletes all artifacts and intermediate build products:
There used to be a custom build system for Fiji called "Fiji Build", but it became unmaintainable and always had the rather big shortcoming of not integrating well with integrated development environments such as Netbeans, Eclipse, IntelliJ, etc. It has been deprecated in January 2013.