Downloaded assembly saved in two places on disk. gacutil.exe ?

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Hi
I have made a Hello World application and used On-Touch deplyment thru a shared network path and from out Intranet. Now I have found the HelloWorld assembly in both C:\WINNT\assembly\download and C:\Documents and Settings\[User]\Local Settings\Application Data\assembly. Why is it saved in two places and what is the differance between the two?
I have used gacutil.exe to clear the downloaded cache, but when I installed version 1.1 I did not get a new gacutil. Does this mean that their is a new way to work with the downloaded cache or is the old gacutil is still beeing used?
Regards
/Niklas

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