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When, after patching, `configure.ac` is newer than `configure`, the Makefile will try to regenerate `configure` from `configure.ac`. While that might usually be desirable, in this case we want to keep bootstrapping simple and directly use the `configure` from the package so we can avoid a dependency on automake. Previously, we used the `-T` parameter to automake to make sure the timestamps were okay. However, this is brittle when we update: when the timestamp of the original file changes, and no longer matches the timestamp of the original file in the patch, `patch` will show a warning but otherwise continue without updating the timestamp. This PR changes things so we only patch `configure`, so that will always have a newer timestamp. Refs https://github.com/NixOS/nixpkgs/issues/115177