The best way to work with the Agis source code is to have it as a project in Eclipse, a Java IDE. You can also find the AGIS index here for reference to the code: http://www.atavismonline.com/docs/api/
You can download eclipse from https://www.eclipse.org/downloads/. You only need Eclipse Standard.
Note: Eclipse is not installed, but rather you just run it after extracting the files you downloaded.
Follow the steps below to set up the AGIS Project in Eclipse
1) Extract the AGIS source file rar contents to a location of your choice. Make sure the full path is extracted (the root folder should be called 'src').
2) Choose File > New > Java Project
3) Un-tick the Use default location checkbox, then click Browse and find the src folder you extracted from the rar. You may want to rename the project.
4) Click Next.
5) Click on the Libraries tab and click on Add External JARs…
6) Find the atavism.jar file in the dist/lib folder of the atavism server files.
7) Click Finish. Your project will now be set up.