I'm looking for a open source tool to merge multiple .NET assemblies into a single assembly.
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Check ILRepack, which allows merge of symbol files, xml documentation, App.config and more. It's open-source and based on Cecil. There is also NAnt and MSBuild integration for it in a project called ILRepack-BuildTasks .

Gluck
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mkbundle and monolinker: http://www.mono-project.com/Linker
You can also make your own linker tool using Cecil: https://github.com/jbevain/cecil/wiki

RamC
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Zac Bowling
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1Unforunately, that project was never completed and is no longer active. – tgiphil Sep 20 '10 at 22:16