MechJeb2/ReentrySimulation.cs(35,9): error CS0246: The type or namespace name SimulatedVessel' could not be found. Are you missing a using directive or an assembly reference? MechJeb2/ReentrySimulation.cs(80,108): error CS0246: The type or namespace nameSimulatedVessel' could not be found. Are you missing a using directive or an assembly reference?
MechJeb2/MechJebModuleStageStats.cs(7,7): error CS0246: The type or namespace name KerbalEngineer' could not be found. Are you missing a using directive or an assembly reference? MechJeb2/MechJebModuleStageStats.cs(26,16): error CS0246: The type or namespace nameStage' could not be found. Are you missing a using directive or an assembly reference?
MechJeb2/MechJebModuleStageStats.cs(22,16): error CS0246: The type or namespace name Stage' could not be found. Are you missing a using directive or an assembly reference? MechJeb2/MechJebModuleStageStats.cs(23,16): error CS0246: The type or namespace nameStage' could not be found. Are you missing a using directive or an assembly reference?

Am I missing some undocumented dependancy ?

Make sure you use the newest makefile
https://github.com/MuMech/MechJeb2/blob/dev/Makefile

Are you going to update the makefile in the "stable" branch?