[clang-tools-extra] [clang-apply-replacements] Apply format only if --format is specified (PR #70801)

pepsiman wrote: `createReplacementsForHeaders()` is applying a cleanup without checking the `Cleanup` flag. But clang-apply-replacements always sets `Cleanup` to `true` anyway. The change looks good to me, but it might be working around a bug elsewhere.

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