BaseTools: Fix a bug Build directory should relative to WORKSPACE

BaseTools: Fix a bug Build directory should relative to WORKSPACE

The bug is for build output files it still use mws.join function, it
cause maybe we will get the build output files in the PACKAGES_PATH
because mws.join will try WORKSPACE first, if the file doesn't exist
then try PACKAGES_PATH. But for build output, we expected it should
relative to WORKSPACE.

Cc: Liming Gao <liming.gao@intel.com>
Contributed-under: TianoCore Contribution Agreement 1.1
Signed-off-by: Yonghong Zhu <yonghong.zhu@intel.com>
Reviewed-by: Liming Gao <liming.gao@intel.com>