ci: fix jobs after core workspace refactoring (#3492)

## What ❔

Fix CI jobs after core workspace refactoring:

* [x] [Run VM
benchmarks](https://github.com/matter-labs/zksync-era/actions/runs/12826132552/job/35765453916?pr=3492)
* [x] [Protobuf
compatibility](https://github.com/matter-labs/zksync-era/actions/runs/12826132555/job/35765453747?pr=3492)

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## Checklist

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

Author: antonbaliasnikov

.github/workflows/protobuf.yaml

@@ -46,24 +46,28 @@ jobs:
         run:
           git checkout $(git merge-base $BASE $HEAD) --recurse-submodules
         working-directory: ./before
+
       - name: compile 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/core/target/debug/build/*/output`
-          | xargs cat > ./before/.binpb
+          | xargs cat > ./before.binpb
 
       # after
       - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4
         with:
           ref: ${{ env.HEAD }}
           path: after
           submodules: recursive
+
       - name: compile after
         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="(.*)"/'

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

@@ -69,7 +69,7 @@ jobs:
         run: |
           ci_run zkstackup -g --local
           ci_run zkstack dev contracts
-          ci_run cargo bench --package vm-benchmark --bench instructions -- --verbose
+          ci_run cargo bench --manifest-path ./core/Cargo.toml --package vm-benchmark --bench instructions -- --verbose
 
           ci_run cargo bench --manifest-path ./core/Cargo.toml \
             --package vm-benchmark --bench instructions -- --print > instructions.log 2>/dev/null

.github/workflows/vm-perf-to-prometheus.yml

@@ -45,8 +45,8 @@ jobs:
 
       - name: run benchmarks
         run: |
-          ci_run cargo bench --package vm-benchmark --bench oneshot
+          ci_run cargo bench --manifest-path ./core/Cargo.toml --package vm-benchmark --bench oneshot
           # Run only benches with 1,000 transactions per batch to not spend too much time
-          ci_run cargo bench --package vm-benchmark --bench batch '/1000$'
-          ci_run cargo bench --package vm-benchmark --bench instructions -- --verbose
-          ci_run cargo bench --package vm-benchmark --bench instructions -- --print
+          ci_run cargo bench --manifest-path ./core/Cargo.toml --package vm-benchmark --bench batch '/1000$'
+          ci_run cargo bench --manifest-path ./core/Cargo.toml --package vm-benchmark --bench instructions -- --verbose
+          ci_run cargo bench --manifest-path ./core/Cargo.toml --package vm-benchmark --bench instructions -- --print