Fix 'Unchanged files with check annotations' spam (#338)

On every PR GitHub helpfully complains about 'Unchanged files with check
annotations'. So here we silence most of that, to make all our PRs
easier to review. Either by outright fixing the issue, or by flagging it
to the compiler as a known problem.

This should make it easier for me to review eg
#335 (or any other PR).

gkr/src/circuit.rs

@@ -42,6 +42,8 @@ where
         in_eq_vec: &[E],
         challenges: &HashMap<ChallengeConst, Vec<E::BaseField>>,
     ) -> E;
+    // TODO(Matthias, by 2024-11-01): review whether we need this function after all.
+    #[allow(dead_code)]
     fn fix_out_variables(
         &self,
         in_size: usize,

gkr/src/gadgets/keccak256.rs

@@ -13,8 +13,7 @@ use ff::Field;
 use ff_ext::ExtensionField;
 use itertools::{izip, Itertools};
 use multilinear_extensions::{
-    mle::{DenseMultilinearExtension, IntoMLE},
-    virtual_poly_v2::ArcMultilinearExtension,
+    mle::DenseMultilinearExtension, virtual_poly_v2::ArcMultilinearExtension,
 };
 use simple_frontend::structs::CircuitBuilder;
 use std::iter;
@@ -467,6 +466,7 @@ pub fn prove_keccak256<'a, E: ExtensionField>(
     #[cfg(test)]
     {
         use crate::structs::CircuitWitness;
+        use multilinear_extensions::mle::IntoMLE;
         let all_zero: Vec<DenseMultilinearExtension<E>> = vec![
             vec![E::BaseField::ZERO; 25 * 64],
             vec![E::BaseField::ZERO; 17 * 64],

gkr/src/prover.rs

@@ -12,8 +12,8 @@ use transcript::Transcript;
 use crate::{
     entered_span, exit_span,
     structs::{
-        Circuit, CircuitWitness, GKRInputClaims, IOPProof, IOPProverState, IOPProverStepMessage,
-        PointAndEval, SumcheckStepType,
+        Circuit, CircuitWitness, GKRInputClaims, IOPProof, IOPProverState, PointAndEval,
+        SumcheckStepType,
     },
     tracing_span,
 };

gkr/src/prover/phase1_output.rs

@@ -3,7 +3,6 @@ use ff::Field;
 use ff_ext::ExtensionField;
 use itertools::{izip, Itertools};
 use multilinear_extensions::{
-    commutative_op_mle_pair,
     mle::{
         DenseMultilinearExtension, InstanceIntoIteratorMut, IntoInstanceIter, IntoInstanceIterMut,
     },

gkr/src/prover/phase2.rs

@@ -102,6 +102,8 @@ impl<E: ExtensionField> IOPProverState<E> {
                 < lo_in_num_vars
             {
                 Arc::new(
+                    // TODO(Matthias, by 2024-11-01): review whether we can redesign this API to avoid the deprecated resize_ranged
+                    #[allow(deprecated)]
                     circuit_witness.layers_ref()[layer_id as usize + 1].resize_ranged(
                         1 << hi_num_vars,
                         1 << lo_in_num_vars,

gkr/src/prover/phase2_input.rs

@@ -127,6 +127,7 @@ impl<E: ExtensionField> IOPProverState<E> {
             virtual_poly.merge(&tmp);
         }
 
+        #[allow(deprecated)]
         let (sumcheck_proofs, prover_state) =
             SumcheckStateV2::prove_parallel(virtual_poly, transcript);
         let eval_point = sumcheck_proofs.point.clone();

gkr/src/prover/phase2_linear.rs

@@ -128,6 +128,8 @@ impl<E: ExtensionField> IOPProverState<E> {
             virtual_poly_1.merge(&tmp);
         }
 
+        // TODO(Matthias, by 2024-11-01): review whether we can replace this function.
+        #[allow(deprecated)]
         let (sumcheck_proof_1, prover_state) =
             SumcheckStateV2::prove_parallel(virtual_poly_1, transcript);
         let eval_point_1 = sumcheck_proof_1.point.clone();

gkr/src/structs.rs

@@ -5,9 +5,7 @@ use std::{
 
 use ff_ext::ExtensionField;
 use goldilocks::SmallField;
-use multilinear_extensions::{
-    mle::ArcDenseMultilinearExtension, virtual_poly_v2::ArcMultilinearExtension,
-};
+use multilinear_extensions::virtual_poly_v2::ArcMultilinearExtension;
 use serde::{Deserialize, Serialize, Serializer};
 use simple_frontend::structs::{CellId, ChallengeConst, ConstantType, LayerId};