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
3f4ad3d37d