[LinkerWrapper] Make ThinLTO work inside the linker wrapper

Summary:
Previous assumptions held that the LTO stage would only have a single
output. This is incorrect when using thinLTO which outputs multiple
files. Additionally there were some bugs with how we hanlded input that
cause problems when performing thinLTO. This patch addresses these
issues.

The performance of Thin-LTO is currently pretty bad. But I am content to
leave it that way as long as it compiles.