Fix: Update noir-r1cs with Skyscraper v2

[shreyas-londhe]

This PR:

• Refactors the code by moving block_multiplier, block_multiplier_codegen, fp_rounding and hla into /skyscraper and moves /skyscraper to /skyscraper/core.
• Updates /noir-r1cs/skyscraper to be compatible with Skyscraper v2.

Impact:

• No behavior change expected; Merkle, sponge, and proofs continue to work via externalized Skyscraper
• Clear separation of concerns: generic performance code in skyscraper/, noir-r1cs keeps only protocol glue
• Easier maintenance and reuse of skyscraper/ components across projects

[Copilot]

Pull Request Overview

This PR refactors the codebase to align with Skyscraper v2 by moving core components into a centralized skyscraper/ directory structure and updating noir-r1cs to be compatible with the new version. The refactoring maintains behavioral compatibility while improving code organization.

• Moves block_multiplier, block_multiplier_codegen, fp_rounding, and hla into skyscraper/ subdirectory
• Migrates existing /skyscraper to /skyscraper/core for better organization
• Updates noir-r1cs/skyscraper implementation to use Skyscraper v2 APIs

Reviewed Changes

Copilot reviewed 23 out of 88 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
noir-r1cs/src/skyscraper/whir.rs	Updates type aliases from Field256 to FieldElement and replaces local compress function with v2 API
noir-r1cs/src/skyscraper/sponge.rs	New sponge implementation using FieldElement and skyscraper::reference::permute
noir-r1cs/src/skyscraper/skyscraper_impl.rs	Removes old implementation file (171 lines deleted)
noir-r1cs/src/skyscraper/mod.rs	Updates module structure to match new organization
noir-r1cs/Cargo.toml	Adds ark-bn254 dependency for field element conversions
gnark-whir/whir_utilities.go	Updates function calls from Compress to CompressV2
gnark-whir/go.mod	Updates dependency versions for gnark-nimue and gnark-skyscraper
Cargo.toml	Restructures workspace members to use new skyscraper/ directory layout
cm31_ntt/*	Code style improvements including import organization and formatting consistency
.github/workflows/benchmark.yml	Enhances benchmark workflow to automatically discover packages with benchmarks

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[codspeed-hq]

CodSpeed WallTime Performance Report

Merging #142 will improve performances by ×52

_{Comparing sl/skyscraper-refactor (c0a5084) with main (490264f)}

⚠️ Unknown Walltime execution environment detected

Using the Walltime instrument on standard Hosted Runners will lead to inconsistent data.

For the most accurate results, we recommend using CodSpeed Macro Runners: bare-metal machines fine-tuned for performance measurement consistency.

Summary

⚡ 1 improvements
✅ 3 untouched benchmarks
🆕 31 new benchmarks
⁉️ 31 dropped benchmarks

⚠️ Please fix the performance issues or acknowledge them on CodSpeed.

Benchmarks breakdown

	Benchmark	BASE	HEAD	Change
⁉️	ark_ff	98 ns	N/A	N/A
⁉️	block_mul	127 ns	N/A	N/A
⁉️	montgomery_interleaved_3	113 ns	N/A	N/A
⁉️	montgomery_interleaved_4	192 ns	N/A	N/A
⁉️	scalar_mul	95 ns	N/A	N/A
⁉️	simd_mul	112 ns	N/A	N/A
⁉️	ark_ff	81 ns	N/A	N/A
⁉️	block_sqr	91 ns	N/A	N/A
⁉️	montgomery_square_interleaved_3	97 ns	N/A	N/A
⁉️	montgomery_square_interleaved_4	157 ns	N/A	N/A
⁉️	montgomery_square_log_interleaved_3	97 ns	N/A	N/A
⁉️	montgomery_square_log_interleaved_4	157 ns	N/A	N/A
⁉️	scalar_sqr	78 ns	N/A	N/A
⁉️	simd_sqr	85 ns	N/A	N/A
⁉️	wrm_overhead	14 ns	N/A	N/A
⚡	verify_poseidon_1000	118.8 ms	2.3 ms	×52
⁉️	block3	162.5 µs	N/A	N/A
⁉️	block4	196.6 µs	N/A	N/A
⁉️	reference	1.3 ms	N/A	N/A
⁉️	simple	381.5 µs	N/A	N/A
...	...	...	...	...

ℹ️ Only the first 20 benchmarks are displayed. Go to the app to view all benchmarks.

[xrvdg]

These crates are not skyscraper specific. Grouping them separate from skyscraper under montgomery would be better. It will be used by the NTT as well.