BaseTools: Fix a bug when apply patches to SEC use the FILE_GUID override

BaseTools: Fix a bug when apply patches to SEC use the FILE_GUID override

Fix a bug when applying patches to SEC modules that use the FILE_GUID
override. Since a temp dir is used when FILE_GUID override is used, the
INF file path comparisons fail. The fix is to capture the real INF file
path comparisons instead of using the temp dir path to the INF.

Contributed-under: TianoCore Contribution Agreement 1.0
Signed-off-by: Yonghong Zhu <yonghong.zhu@intel.com>
Reviewed-by: Liming Gao <liming.gao@intel.com>
git-svn-id: https://svn.code.sf.net/p/edk2/code/trunk/edk2@19142 6f19259b-4bc3-4df7-8a09-765794883524