In Eclipse create a project in the base directory of the git repo. Use a general Java project. Unless you use ant or maven to build to build the code, in which case importing the ant or maven build script would be best. In either case identify the git repo base directory as the Eclipse project's base dirctory.
BTW, the git plugin for Eclipse is fairly handy for managing a git repo, but I sympathize with your desire to continue using git from the command line.