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llama-imatrix supports --in-file combination, but requires the user to also still process at least one chunk during that final step of combination. (otherwise, we get output like this:
This is rather silly, so I've written a quick "please consider" pull request to indicate the desired behavior.
I believe this simple change is all that is needed because the prompt is pre-filled from arg.cpp, but not yet padded with control tokens until compute_imatrix calls the tokenize downstream