You need to make sure your java code is in a java project. If the git source is created from ant, there is a project called "File> New> Other ..> Java from the ant build file."
Otherwise, you need to create a java project in eclipse, and then 1) import the source code into the proj / src directory or 2) create a linked folder in the eclipse that points to the original location on the file system.
Then you need to configure the class path (add all the jars needed for compilation).
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