BaseTools: Remove the duplicate Pcd items

BaseTools: Remove the duplicate Pcd items

The case is the Pcd item both used in 1 module inf and 1 lib inf, and
in the DSC component section, it override the Pcd value.
In the module, the pcd value is the override value, but in the lib inf
the pcd value is the value that in the DSC PCD section's value, then it
cause the Pcd value is different in the module and lib. but actually we
only need use the Pcd value in the module to decide whether it use the
same value.

Contributed-under: TianoCore Contribution Agreement 1.0
Signed-off-by: Yonghong Zhu <yonghong.zhu@intel.com>
Reviewed-by: Liming Gao <liming.gao@intel.com>