The point you're missing is that the CLR doesn't convert code to MSIL.
The CLR loads, verifies, JIT compiles MSIL and runs native code in a
particular app-domain.
The compilers csc.exe and vbc.exe compile source files to msil.
Reflection.Emit can create assemblies and run them dynamically. This
runs on top of the CLR as does any other application.
Source code in codebehind files is compiled on-demand by the ASP.NET
runtime during server requests. This also runs on top of the CLR as an
application.
Instead of just repeating your incorrect assumption, why not explain
exactly what it is you're unclear about and we'll try to answer in the
right way.
--
Bob Powell [MVP]
Visual C#, System.Drawing
Ramuseco Limited .NET consulting
http://www.ramuseco.com
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