In mitkToolFactoryMacro.h there is a macro that generates a code that uses the mitk namespace. Therefore, if you want to put your custom tool in your own namespace, the compilation will fail. The simple fix is to remove the 'mitk::' namespace qualifier from the macro. Since the macro is used within a namespace, anyway, this will not case any problem. I rebuilt the current MITK master with this change, successfully.
Pull request follows.