fix: Write diagnostics to stderr (vs stdout)

Before this change (even when logging was not enabled) SP1 was writing diagnostic messages to stdout, breaking the implicit contract that only the application logic should decide what gets written to stdout.
This contract is important, e.g. for passing the output for further processing in shell-driven use cases:

```sh
cat ./input-data.json | my-app | another-app
```

This change aims to fix this issue, and to safeguard against it (to a reasonable extent) in the future.

I've left alone tests, examples and build scripts, and tried to make the change as narrow as possible and to affect only the production code paths.

crates/core/executor/src/executor.rs

@@ -271,12 +271,12 @@ impl<'a> Executor<'a> {
             });
 
             if let Some(trace_buf) = trace_buf {
-                println!("Profiling enabled");
+                eprintln!("Profiling enabled");
 
                 let sample_rate = std::env::var("TRACE_SAMPLE_RATE")
                     .ok()
                     .and_then(|rate| {
-                        println!("Profiling sample rate: {rate}");
+                        eprintln!("Profiling sample rate: {rate}");
                         rate.parse::<u32>().ok()
                     })
                     .unwrap_or(1);
@@ -1341,7 +1341,7 @@ impl<'a> Executor<'a> {
             // See https://github.com/riscv-non-isa/riscv-asm-manual/blob/master/riscv-asm.md#instruction-aliases
             return Err(ExecutionError::Unimplemented());
         } else {
-            println!("unreachable: {:?}", instruction.opcode);
+            eprintln!("unreachable: {:?}", instruction.opcode);
             unreachable!()
         }
 
@@ -2000,10 +2000,10 @@ impl<'a> Executor<'a> {
             if !buf.is_empty() {
                 match fd {
                     1 => {
-                        println!("stdout: {buf}");
+                        eprintln!("stdout: {buf}");
                     }
                     2 => {
-                        println!("stderr: {buf}");
+                        eprintln!("stderr: {buf}");
                     }
                     _ => {}
                 }

crates/core/executor/src/hook.rs

@@ -537,6 +537,8 @@ fn pad_to_be(val: &BigUint, len: usize) -> Vec<u8> {
 
 #[cfg(test)]
 mod tests {
+    #![allow(clippy::print_stdout)]
+
     use super::*;
 
     #[test]

crates/core/executor/src/lib.rs

@@ -18,6 +18,7 @@
 #![allow(clippy::missing_errors_doc)]
 #![allow(clippy::explicit_iter_loop)]
 #![allow(clippy::struct_excessive_bools)]
+#![warn(clippy::print_stdout)]
 #![warn(missing_docs)]
 
 mod air;

crates/core/executor/src/profiler.rs

@@ -189,9 +189,9 @@ impl Profiler {
 
         pb.finish();
 
-        println!("Writing profile, this can take awhile");
+        eprintln!("Writing profile, this can take awhile");
         serde_json::to_writer(writer, &profile_builder.to_serializable())?;
-        println!("Profile written successfully");
+        eprintln!("Profile written successfully");
 
         Ok(())
     }

crates/core/executor/src/syscalls/write.rs

@@ -51,15 +51,15 @@ impl Syscall for WriteSyscall {
                     // If the string does not match any known command, print it to stdout.
                     let flush_s = update_io_buf(ctx, fd, s);
                     if !flush_s.is_empty() {
-                        flush_s.into_iter().for_each(|line| println!("stdout: {}", line));
+                        flush_s.into_iter().for_each(|line| eprintln!("stdout: {}", line));
                     }
                 }
             }
         } else if fd == 2 {
             let s = core::str::from_utf8(slice).unwrap();
             let flush_s = update_io_buf(ctx, fd, s);
             if !flush_s.is_empty() {
-                flush_s.into_iter().for_each(|line| println!("stderr: {}", line));
+                flush_s.into_iter().for_each(|line| eprintln!("stderr: {}", line));
             }
         } else if fd <= LOWEST_ALLOWED_FD {
             if std::env::var("SP1_ALLOW_DEPRECATED_HOOKS")

crates/core/machine/src/alu/add_sub/mod.rs

@@ -273,6 +273,8 @@ where
 
 #[cfg(test)]
 mod tests {
+    #![allow(clippy::print_stdout)]
+
     use p3_baby_bear::BabyBear;
     use p3_matrix::dense::RowMajorMatrix;
     use rand::{thread_rng, Rng};

crates/core/machine/src/alu/bitwise/mod.rs

@@ -241,6 +241,8 @@ where
 
 #[cfg(test)]
 mod tests {
+    #![allow(clippy::print_stdout)]
+
     use p3_baby_bear::BabyBear;
     use p3_matrix::dense::RowMajorMatrix;
     use rand::{thread_rng, Rng};

crates/core/machine/src/alu/divrem/mod.rs

@@ -833,6 +833,7 @@ where
 
 #[cfg(test)]
 mod tests {
+    #![allow(clippy::print_stdout)]
 
     use crate::{
         io::SP1Stdin,

crates/core/machine/src/alu/lt/mod.rs

@@ -467,6 +467,7 @@ where
 
 #[cfg(test)]
 mod tests {
+    #![allow(clippy::print_stdout)]
 
     use std::borrow::BorrowMut;
 

crates/core/machine/src/alu/sll/mod.rs

@@ -419,6 +419,7 @@ where
 
 #[cfg(test)]
 mod tests {
+    #![allow(clippy::print_stdout)]
 
     use std::borrow::BorrowMut;
 

crates/core/machine/src/alu/sr/mod.rs

@@ -542,6 +542,8 @@ where
 
 #[cfg(test)]
 mod tests {
+    #![allow(clippy::print_stdout)]
+
     use std::borrow::BorrowMut;
 
     use crate::{

crates/core/machine/src/bytes/mod.rs

@@ -109,6 +109,8 @@ impl<F: Field> ByteChip<F> {
 
 #[cfg(test)]
 mod tests {
+    #![allow(clippy::print_stdout)]
+
     use p3_baby_bear::BabyBear;
     use std::time::Instant;
 

crates/core/machine/src/bytes/utils.rs

@@ -12,6 +12,8 @@ pub const fn shr_carry(input: u8, rotation: u8) -> (u8, u8) {
 
 #[cfg(test)]
 mod tests {
+    #![allow(clippy::print_stdout)]
+
     use super::*;
 
     /// Tests the `shr_carry` function.

crates/core/machine/src/global/mod.rs

@@ -262,6 +262,8 @@ where
 
 #[cfg(test)]
 mod tests {
+    #![allow(clippy::print_stdout)]
+
     use super::*;
     use crate::programs::tests::*;
     use p3_baby_bear::BabyBear;

crates/core/machine/src/lib.rs

@@ -12,6 +12,7 @@
     deprecated,
     incomplete_features
 )]
+#![warn(clippy::print_stdout)]
 #![warn(unused_extern_crates)]
 
 pub mod air;

crates/core/machine/src/memory/global.rs

@@ -433,6 +433,7 @@ where
 
 #[cfg(test)]
 mod tests {
+    #![allow(clippy::print_stdout)]
 
     use super::*;
     use crate::programs::tests::*;

crates/core/machine/src/memory/local.rs

@@ -271,6 +271,8 @@ where
 
 #[cfg(test)]
 mod tests {
+    #![allow(clippy::print_stdout)]
+
     use crate::programs::tests::*;
     use crate::{
         memory::MemoryLocalChip, riscv::RiscvAir,

crates/core/machine/src/operations/field/field_den.rs

@@ -141,6 +141,8 @@ where
 
 #[cfg(test)]
 mod tests {
+    #![allow(clippy::print_stdout)]
+
     use num::BigUint;
     use p3_air::BaseAir;
     use p3_field::{Field, PrimeField32};

crates/core/machine/src/operations/field/field_inner_product.rs

@@ -133,6 +133,8 @@ where
 
 #[cfg(test)]
 mod tests {
+    #![allow(clippy::print_stdout)]
+
     use num::BigUint;
     use p3_air::BaseAir;
     use p3_field::{Field, PrimeField32};

crates/core/machine/src/operations/field/field_op.rs

@@ -375,6 +375,8 @@ impl<V: Copy, P: FieldParameters> FieldOpCols<V, P> {
 
 #[cfg(test)]
 mod tests {
+    #![allow(clippy::print_stdout)]
+
     use num::BigUint;
     use p3_air::BaseAir;
     use p3_field::{Field, PrimeField32};

crates/core/machine/src/program/mod.rs

@@ -172,6 +172,7 @@ where
 
 #[cfg(test)]
 mod tests {
+    #![allow(clippy::print_stdout)]
 
     use std::sync::Arc;
 

crates/core/machine/src/riscv/mod.rs

@@ -634,6 +634,7 @@ impl<F: PrimeField32> fmt::Debug for RiscvAir<F> {
 
 #[cfg(test)]
 #[allow(non_snake_case)]
+#[allow(clippy::print_stdout)]
 pub mod tests {
 
     use crate::{

crates/core/machine/src/shape/mod.rs

@@ -633,6 +633,7 @@ pub fn create_dummy_record(shape: &Shape<RiscvAirId>) -> ExecutionRecord {
 
 #[cfg(test)]
 pub mod tests {
+    #![allow(clippy::print_stdout)]
 
     use hashbrown::HashSet;
     use sp1_stark::{Dom, MachineProver, StarkGenericConfig};

crates/core/machine/src/syscall/precompiles/sha256/extend/mod.rs

@@ -29,6 +29,7 @@ pub fn sha_extend(w: &mut [u32]) {
 
 #[cfg(test)]
 pub mod extend_tests {
+    #![allow(clippy::print_stdout)]
 
     use p3_baby_bear::BabyBear;
 

crates/core/machine/src/utils/logger.rs

@@ -37,6 +37,7 @@ pub fn setup_logger() {
                     .with_thread_names(false)
                     .with_env_filter(env_filter)
                     .with_span_events(FmtSpan::CLOSE)
+                    .with_writer(std::io::stderr)
                     .finish()
                     .init();
             }

crates/cuda/src/lib.rs

@@ -1,3 +1,5 @@
+#![warn(clippy::print_stdout)]
+
 use std::{
     error::Error as StdError,
     future::Future,

crates/curves/src/lib.rs

@@ -1,3 +1,5 @@
+#![warn(clippy::print_stdout)]
+
 pub mod edwards;
 pub mod params;
 // pub mod polynomial;

crates/curves/src/weierstrass/secp256k1.rs

@@ -113,6 +113,7 @@ pub fn secp256k1_sqrt(n: &BigUint) -> BigUint {
 
 #[cfg(test)]
 mod tests {
+    #![allow(clippy::print_stdout)]
 
     use super::*;
     use crate::utils::biguint_from_limbs;

crates/derive/src/lib.rs

@@ -22,6 +22,8 @@
 // OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 // THE SOFTWARE.
 
+#![warn(clippy::print_stdout)]
+
 extern crate proc_macro;
 
 use proc_macro::TokenStream;
@@ -322,9 +324,9 @@ pub fn cycle_tracker(_attr: TokenStream, item: TokenStream) -> TokenStream {
 
     let result = quote! {
         #visibility fn #name #generics (#inputs) #output #where_clause {
-            println!("cycle-tracker-start: {}", stringify!(#name));
+            eprintln!("cycle-tracker-start: {}", stringify!(#name));
             let result = (|| #block)();
-            println!("cycle-tracker-end: {}", stringify!(#name));
+            eprintln!("cycle-tracker-end: {}", stringify!(#name));
             result
         }
     };

crates/primitives/src/lib.rs

@@ -1,6 +1,8 @@
 //! sp1-primitives contains types and functions that are used in both sp1-core and sp1-zkvm.
 //! Because it is imported in the zkvm entrypoint, it should be kept minimal.
 
+#![warn(clippy::print_stdout)]
+
 use lazy_static::lazy_static;
 use p3_baby_bear::{BabyBear, DiffusionMatrixBabyBear};
 use p3_field::AbstractField;

crates/prover/src/build.rs

@@ -1,3 +1,5 @@
+#![allow(clippy::print_stdout)] // okay to print to stdout: this is a build script
+
 use std::{borrow::Borrow, path::PathBuf};
 
 use p3_baby_bear::BabyBear;

crates/prover/src/lib.rs

@@ -10,6 +10,7 @@
 #![allow(clippy::too_many_arguments)]
 #![allow(clippy::new_without_default)]
 #![allow(clippy::collapsible_else_if)]
+#![warn(clippy::print_stdout)]
 
 pub mod build;
 pub mod components;
@@ -1316,6 +1317,7 @@ pub fn compress_program_from_input<C: SP1ProverComponents>(
 
 #[cfg(test)]
 pub mod tests {
+    #![allow(clippy::print_stdout)]
 
     use std::{
         collections::BTreeSet,

crates/prover/src/shapes.rs

@@ -204,7 +204,7 @@ pub fn build_vk_map<C: SP1ProverComponents + 'static>(
                 let panic_tx = panic_tx.clone();
                 s.spawn(move || {
                     while let Ok((i, shape)) = shape_rx.lock().unwrap().recv() {
-                        println!("shape: {:?}", shape);
+                        eprintln!("shape: {:?}", shape);
                         let is_shrink = matches!(shape, SP1CompressProgramShape::Shrink(_));
                         let prover = prover.clone();
                         let shape_clone = shape.clone();
@@ -466,6 +466,7 @@ impl<C: SP1ProverComponents> SP1Prover<C> {
 
 #[cfg(test)]
 mod tests {
+    #![allow(clippy::print_stdout)]
 
     use super::*;
 

crates/recursion/circuit/src/challenger.rs

@@ -425,6 +425,8 @@ pub fn split_32<C: Config>(builder: &mut Builder<C>, val: Var<C::N>, n: usize) -
 
 #[cfg(test)]
 pub(crate) mod tests {
+    #![allow(clippy::print_stdout)]
+
     use std::iter::zip;
 
     use crate::{

crates/recursion/circuit/src/lib.rs

@@ -1,5 +1,7 @@
 //! Copied from [`sp1_recursion_program`].
 
+#![warn(clippy::print_stdout)]
+
 use challenger::{
     CanCopyChallenger, CanObserveVariable, DuplexChallengerVariable, FieldChallengerVariable,
     MultiField32ChallengerVariable, SpongeChallengerShape,

crates/recursion/compiler/src/circuit/compiler.rs

@@ -886,6 +886,8 @@ impl<C: Config<F: PrimeField64>> Reg<C> for Address<C::F> {
 
 #[cfg(test)]
 mod tests {
+    #![allow(clippy::print_stdout)]
+
     use std::{collections::VecDeque, io::BufRead, iter::zip, sync::Arc};
 
     use p3_baby_bear::DiffusionMatrixBabyBear;

crates/recursion/compiler/src/lib.rs

@@ -1,5 +1,6 @@
 #![allow(clippy::type_complexity)]
 #![allow(clippy::needless_range_loop)]
+#![warn(clippy::print_stdout)]
 
 extern crate alloc;
 

crates/recursion/core/src/chips/batch_fri.rs

@@ -171,7 +171,7 @@ impl<F: PrimeField32, const DEGREE: usize> MachineAir<F> for BatchFRIChip<DEGREE
         );
 
         #[cfg(debug_assertions)]
-        println!(
+        eprintln!(
             "batch fri trace dims is width: {:?}, height: {:?}",
             trace.width(),
             trace.height()