The preferred way to set up the Eclipse IDE work with OSCMT projects is to clone the OSCMT git repository, create an empty Eclipse workspace, and then import Maven projects from git repository to the Eclipse workspace.
This directory structure keeps the git repository separate from the Eclipse workspace, which makes it easier to maintain each separately.
After you've imported the OSCMT projects into your workspace, a few additional customization steps will make it much easier to work the projects. First of all, there are a lot of OSCMT projects. In general, one seldom has to work with all the projects simultaneously. Instead, one tends to work with certain subsets depending on the kind of task that one is performing.
These working sets generally follow the Maven project hierarchy and the directory structure in the git repository. The working sets may be created manually through the Eclipse IDE, but they may also be imported from a configuration file that is available in the top-level eclipse_config directory of the git repository.