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You can use something like Mono.Cecil to rewrite parts of the file and then save the changed file. Check out Mono.Cecil here:
http://www.mono-project.com/docs/tools+libraries/libraries/Mono.Cecil/
dnlib is another similar library:
https://github.com/0xd4d/dnlib
You should be able to alter the attributes of classes and such to your needs to make it work as desired.
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