The project uses Maven for builds. Eclipse supports Maven builds directly, so therefore supports Eclipse. (Or if there are any problems, it is in the Eclipse integration with Maven.) I use IntelliJ and recommend it, but, there is nothing additional to say here about working with Eclipse. It just works, because the Maven build works, and Eclipse uses Maven builds.
Have you modified the build? You say for example that you had to add the avro plugin to pluginManagement, but it is certainly already there in the parent POM: https://github.com/cloudera/oryx/blob/master/pom.xml#L671
You say there is a compile error, but the dependencies you seem to be missing are correctly specified in the POM already.
That is: you can verify that the build is correct with "mvn compile".
You need to clarify what you are doing because I don't think you are building the project as-is.