What is the relationship between winmd files in different directories

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I'm working on Windows Store Apps development, and I found winmd files in different directories of Windows.

When developing a Windows Store App, the App is referencing Windows.winmd file under:

C:\Program Files (x86)\Windows Kits\8.0\References\CommonConfiguration\Neutral

But I could also find several different winmd files under:

C:\windows\system32\WinMetadata

My question is what's the relationship between winmd files under these two different directories?

I guess the big Windows.winmd file is used at compile time to build appx package, and the separated winmd files under C:\windows\system32\WinMetadata is used at runtime?

Also, why not having one big Windows.winmd file under C:\windows\system32\WinMetadata too ?

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