Here's what I've tried. I have to confess that I have not used Java and Eclipse to develop real world apps for a decade, so this might not be optimal way.
Install JDK SE 1.6 and Apache ANT
Install Eclipse (I tried both Helios and Indigo, either of them is fine)
Use svn or git to pull down the source to disk, say src/sfntly
In Eclipse
1. File->New->Java Project, type sfntly as Project Name, uncheck Use default location, Browse... to src/sfntly/trunk/java, click Next, click Finish
2. To run programs, there's a drop down next to the Run button, click it, select Run Configurations...,
2a. select JUnit, click the New button, select Run all tests in the selected project, package or source folder, and Test Runner is JUnit4. This enables all unit tests.
2b. select Java Application, click the New button, then click Search.... You shall see different classes (e.g. SFLint, SfntDump). Create a Run Configuration for each runnable class.
3. Now in the Debug button drop down, there will be multiple targets to be run. Select the one you want to debug, and start debugging from there.