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Suppose the linker is invoked on a sequence of object files, some with with LTO information, some without, all interspersed. Suppose some symbols are defined in multiple .o files, through the use of common symbols, weak symbols, and/or section groups. The LLVM interface simply passes each object file to the plugin.
No, the native linker handles all the native .o files.
llvm-gcc a.c -O4 -o a.o -c llvm-g++ b.cpp -O4 -o b.o -c llvm-gcc c.m -O4 -o c.o -c gcc d.m -O3 -o d.o -c g++ a.o b.o c.o d.o -o a.out
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