.NET 4.0 has a new GAC, why?

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Yes since there are 2 distinct Global Assembly Cache (GAC), you will have to manage each of them individually.

In .NET Framework 4.0, the GAC went through a few changes. The GAC was split into two, one for each CLR.

The CLR version used for both .NET Framework 2.0 and .NET Framework 3.5 is CLR 2.0. There was no need in the previous two framework releases to split GAC. The problem of breaking older applications in Net Framework 4.0.

To avoid issues between CLR 2.0 and CLR 4.0 , the GAC is now split into private GAC’s for each runtime.The main change is that CLR v2.0 applications now cannot see CLR v4.0 assemblies in the GAC.

Source

Why?

It seems to be because there was a CLR change in .NET 4.0 but not in 2.0 to 3.5. The same thing happened with 1.1 to 2.0 CLR. It seems that the GAC has the ability to store different versions of assemblies as long as they are from the same CLR. They do not want to break old applications.

See the following information in MSDN about the GAC changes in 4.0.

For example, if both .NET 1.1 and .NET 2.0 shared the same GAC, then a .NET 1.1 application, loading an assembly from this shared GAC, could get .NET 2.0 assemblies, thereby breaking the .NET 1.1 application

The CLR version used for both .NET
Framework 2.0 and .NET Framework 3.5
is CLR 2.0. As a result of this, there
was no need in the previous two
framework releases to split the GAC.
The problem of breaking older (in this
case, .NET 2.0) applications
resurfaces in Net Framework 4.0 at
which point CLR 4.0 released. Hence,
to avoid interference issues between
CLR 2.0 and CLR 4.0, the GAC is now
split into private GACs for each
runtime.

As the CLR is updated in future versions you can expect the same thing. If only the language changes then you can use the same GAC.

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