refactor: move Cargo.toml from root to core workspace (#3456)

## What ❔

Move `Cargo.toml` from repository root to `core` workspace.

<!-- What are the changes this PR brings about? -->
<!-- Example: This PR adds a PR template to the repo. -->
<!-- (For bigger PRs adding more context is appreciated) -->

## Why ❔

It is mandatory for proper separation of workspaces and setting up a
`release-please` CI that requires all files of a component to be inside
the component directory.

## CI failures

Currently, the following tests are failing:
* `protobuf_compatibility` - the workflow is using base version and will
be fixed with the next PRs after merge to `main`.

<!-- Why are these changes done? What goal do they contribute to? What
are the principles behind them? -->
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iterators are in context about the evolution of repos. -->

## Checklist

<!-- Check your PR fulfills the following items. -->
<!-- For draft PRs check the boxes as you complete them. -->

- [x] PR title corresponds to the body of PR (we generate changelog
entries from PRs).
- [x] Tests for the changes have been added / updated.
- [x] Documentation comments have been added / updated.
- [x] Code has been formatted via `zkstack dev fmt` and `zkstack dev
lint`.

.dockerignore

@@ -20,8 +20,8 @@ keys/setup
 !prover/
 !yarn.lock
 !package.json
-!Cargo.lock
-!Cargo.toml
+!core/Cargo.lock
+!core/Cargo.toml
 !contracts/
 !setup_2\^26.key
 !setup_2\^24.key

.githooks/pre-commit

@@ -15,8 +15,6 @@ check_fmt () {
     fi
 }
 
-check_fmt
-
-cd prover/
-
-check_fmt
+( cd core/ && check_fmt )
+( cd prover/ && check_fmt )
+( cd zkstack_cli/ && check_fmt )

.github/workflows/cargo-license.yaml

@@ -7,5 +7,6 @@ jobs:
     - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
     - uses: EmbarkStudios/cargo-deny-action@8371184bd11e21dcf8ac82ebf8c9c9f74ebf7268 # v2.0.1
       with:
+        manifest-path: "./core/Cargo.toml"
         command: check
         command-arguments: "--hide-inclusion-graph"

.github/workflows/ci-core-reusable.yml

@@ -79,7 +79,7 @@ jobs:
           ci_run zkstack dev test rust
           # Benchmarks are not tested by `cargo nextest` unless specified explicitly, and even then `criterion` harness is incompatible
           # with how `cargo nextest` runs tests. Thus, we run criterion-based benchmark tests manually.
-          ci_run cargo test --release -p vm-benchmark --bench oneshot --bench batch
+          ci_run cargo test --manifest-path ./core/Cargo.toml --release -p vm-benchmark --bench oneshot --bench batch
 
   loadtest:
     runs-on: [ matterlabs-ci-runner-high-performance ]

.github/workflows/ci.yml

@@ -57,8 +57,8 @@ jobs:
               - '.github/workflows/build-contract-verifier-template.yml'
               - '.github/workflows/ci-core-reusable.yml'
               - '.github/workflows/ci-core-lint-reusable.yml'
-              - 'Cargo.toml'
-              - 'Cargo.lock'
+              - './core/Cargo.toml'
+              - './core/Cargo.lock'
               - 'zkstack_cli/**'
               - '!**/*.md'
               - '!**/*.MD'

.github/workflows/protobuf.yaml

@@ -47,13 +47,13 @@ jobs:
           git checkout $(git merge-base $BASE $HEAD) --recurse-submodules
         working-directory: ./before
       - name: compile before
-        run: cargo check --all-targets
-        working-directory: ./before/
+        run: cargo check --manifest-path ./core/Cargo.toml --all-targets
+        working-directory: ./before
       - name: build before.binpb
         run: >
           perl -ne 'print "$1\n" if /PROTOBUF_DESCRIPTOR="(.*)"/'
-          `find ./before/target/debug/build/*/output`
-          | xargs cat > ./before.binpb
+          `find ./before/core/target/debug/build/*/output`
+          | xargs cat > ./before/.binpb
 
       # after
       - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4
@@ -62,19 +62,21 @@ jobs:
           path: after
           submodules: recursive
       - name: compile after
-        run: cargo check --all-targets
+        run: cargo check --manifest-path ./core/Cargo.toml --all-targets
         working-directory: ./after
       - name: build after.binpb
         run: >
           perl -ne 'print "$1\n" if /PROTOBUF_DESCRIPTOR="(.*)"/'
-          `find ./after/target/debug/build/*/output`
+          `find ./after/core/target/debug/build/*/output`
           | xargs cat > ./after.binpb
 
       # compare
       - uses: bufbuild/buf-setup-action@54abbed4fe8d8d45173eca4798b0c39a53a7b658 # v1.39.0
         with:
           github_token: ${{ github.token }}
       - name: buf breaking
-        run: >
-          buf breaking './after.binpb' --against './before.binpb' --exclude-path 'zksync/config/experimental.proto'
-          --config '{"version":"v1","breaking":{"use":["WIRE_JSON","WIRE"]}}' --error-format 'github-actions'
+        run: |
+          pwd
+          ls -la
+          buf breaking './after.binpb' --against './before.binpb' --exclude-path 'zksync/config/experimental.proto' \
+            --config '{"version":"v1","breaking":{"use":["WIRE_JSON","WIRE"]}}' --error-format 'github-actions'

.github/workflows/vm-perf-comparison.yml

@@ -53,8 +53,10 @@ jobs:
         run: |
           ci_run zkstackup -g --local
           ci_run zkstack dev contracts
-          ci_run cargo bench --package vm-benchmark --bench instructions -- --verbose || echo "Instructions benchmark is missing"
-          ci_run cargo run --package vm-benchmark --release --bin instruction_counts | tee base-opcodes
+          ci_run cargo bench --manifest-path ./core/Cargo.toml \
+            --package vm-benchmark --bench instructions -- --verbose || echo "Instructions benchmark is missing"
+          ci_run cargo run --manifest-path ./core/Cargo.toml \
+            --package vm-benchmark --release --bin instruction_counts | tee base-opcodes
 
       - name: checkout PR
         run: |
@@ -69,15 +71,17 @@ jobs:
           ci_run zkstack dev contracts
           ci_run cargo bench --package vm-benchmark --bench instructions -- --verbose
 
-          ci_run cargo bench --package vm-benchmark --bench instructions -- --print > instructions.log 2>/dev/null
+          ci_run cargo bench --manifest-path ./core/Cargo.toml \
+            --package vm-benchmark --bench instructions -- --print > instructions.log 2>/dev/null
           # Output all lines from the benchmark result starting from the "## ..." comparison header.
           # Since the output spans multiple lines, we use a heredoc declaration.
           EOF=$(dd if=/dev/urandom bs=15 count=1 status=none | base64)
           echo "speedup<<$EOF" >> $GITHUB_OUTPUT
           sed -n '/^## /,$p' instructions.log >> $GITHUB_OUTPUT
           echo "$EOF" >> $GITHUB_OUTPUT
           
-          ci_run cargo run --package vm-benchmark --release --bin instruction_counts -- --diff base-opcodes > opcodes.log
+          ci_run cargo run --manifest-path ./core/Cargo.toml \
+            --package vm-benchmark --release --bin instruction_counts -- --diff base-opcodes > opcodes.log
           echo "opcodes<<$EOF" >> $GITHUB_OUTPUT
           sed -n '/^## /,$p' opcodes.log >> $GITHUB_OUTPUT
           echo "$EOF" >> $GITHUB_OUTPUT

.gitignore

@@ -26,12 +26,6 @@ zksync_pk.key
 dist
 todo
 
-Cargo.lock
-!/Cargo.lock
-!/infrastructure/zksync-crypto/Cargo.lock
-!/prover/Cargo.lock
-!/zkstack_cli/Cargo.lock
-
 /etc/env/target/*
 /etc/env/.current
 /etc/env/configs/*