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Most uses of it either contain a fat or thin lto module. Only WorkItem::LTO could contain both, but splitting that enum variant doesn't complicate things much.
The codegen crate contains the code to convert from MIR into LLVM IR,
and then from LLVM IR into machine code. In general it contains code
that runs towards the end of the compilation process.
For more information about how codegen works, see the rustc dev guide.