BaseTools: Add Multiple Workspaces support for custom Makefiles.

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>