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This is currently handled automatically by the fact that codegen doesn't visit coverage statements in unused functions, but that will no longer be the case when unused IDs are identified by a separate query instead.
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.