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Creating PCH file (/Yc option) works in usual way as any other object, except that it will produce meta info (stdafx.pch.clcache file) contains it's cache key as identification of headers files and it's contents. Using PCH file (/Yu option) affects /showIncludes - it not contains PCH includes, so for generating manifest hash additionally used PCH cache key. So when PCH headers or it's content changed but no changes in source file or it's headers then it will produce different cache entry.
As PCH supported, we no more need this stats.
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The main difference of using PCH is that /showIncludes will produce no output for precompiled headers, it will only show it's own includes.
To handle such case it is possible to use cache key of PCH object as additional info for computing manifest hash.