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This looks to be related to ThinLTO specifically, which emits multiple .ll files in this situation.
Some workarounds (that are probably unsatisfying since you're likely trying to understand compile times in the actual config
you ship) to avoid that issue/warning:
using fat LTO
turning off LTO
Otherwise, with ThinLTO, using a single CGU would also give a bit more information (though I'm locally getting more than the 3 lines mentioned in the OP) in the range of 350K lines of IR, but I'm not sure how accurate that is.
This appears to be a re-occurrence of the issue reported in #4.
To reproduce:
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