Thanks for your interest in contributing some code to JabRef! That sounds great!
Regarding your problem: We are using the build system gradle that downloads all necessary libraries and is also able to create preconfigured eclipse projects for you.
To build JabRef from source you can execute the so called gradle wrapper by the command
gradlew build in the root path of the downloaded JabRef repository. Then everything is downloaded, compiled and built automatically. To create a eclipse project just run
gradlew eclipse. More on this topic can be found here.
If you are looking for some tasks checkout the Issue tracker at GitHub - especially those issues tagged with “beginner” might be a good start: https://github.com/JabRef/jabref/issues?q=is%3Aopen+is%3Aissue+label%3Abeginner
To get newbies started we also have a Contribution guide here: https://github.com/JabRef/jabref/blob/master/CONTRIBUTING.md
And there is also a Wiki with some more information: https://github.com/JabRef/jabref/wiki
Don’t hesitate to ask if you need further assistance!