In order to build the command line utilities, IlMerge mus be run, as they depend on QuickGraph.
First, run the RebuildAllExceptSetup.cmd batch file in the solution root, then run ILMExpSqlCE.cmd in the lib folder.
You may have to modify the paths to suit your environment.
I am currently developing using SSMS 2008 R2 SP1.
To debug the add-in, configure your project as shown:
The command line for SSMS on my computer is:
C:\Program Files\Microsoft SQL Server\100\Tools\Binn\VSShell\Common7\IDE\Ssms.exe
Then build the solution, and right click the Setup project, and select Install.
Then press F5 to debug, and you can set breakpoints etc.