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This cleans up how the CLI parses and handles -E, -S, and -c. Compilation explicitly acknowledges when it is being used to do C preprocessing. -S is properly translated to -fno-emit-bin -femit-asm but Compilation does not yet handle -femit-asm. There is not yet a mechanism for skipping the linking step when there is only a single object file, and so to make this work we have to do a file copy in link.flush() to copy the file from zig-cache into the output directory.