To cleanup WinSxS you have to manually uninstall old updates. The Windows Update Cleanup is only available for Windows Server 2008 R2 (Windows 7 counterpart) after installing this update, you use the the counterpart of Windows Vista which never gets this feature. Those files need to be there in order for your system to work as intended. Just don't touch anything there, even if it takes up some space. If you remove files from there, next time you try to repair, modify or uninstall an application you will be asked to provide its Windows Installer package, which you will probably not have anymore, or which could be quite difficult to extract from the original installation media or setup files. The second folder stores the Windows Installer files for installed applications, so that they are available if you (or the system) need to repair, modify or uninstall an application. But manually deleting anything from there can and will harm your system, possibly to the point of rendering it unusable. Unfortunately, this has the side effect of the folder contents growing in size each time any update is installed. The first one contains multiple versions of system files and DLLs, so that any program can find the exact version it requires, thus solving the long-dreaded "DLL hell" problem. Don't ever manually delete anything in those folders.
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