BaseTools: Add Multiple Workspaces support for custom Makefiles.
    
    This patch makes sure the MODULE_DIR variable points to the correct
    location when multiple workspaces are used. Currently, it is
    always prefixed with $(WORKSPACE), which only works as long as the
    package is in the Workspace.
    Code modules were not effected because the required paths were valid,
    but for custom Makefiles, the MODULE_DIR variable is used.
    
    Contributed-under: TianoCore Contribution Agreement 1.0
    Signed-off-by: Marvin Haeuser <Marvin.Haeuser@outlook.com>
    Reviewed-by: Yonghong Zhu <yonghong.zhu@intel.com>