try to fix more issues

.github/workflows/protobuf.yaml

@@ -45,10 +45,10 @@ jobs:
       - name: checkout LCA
         run:
           git checkout $(git merge-base $BASE $HEAD) --recurse-submodules
-        working-directory: ./before/core
+        working-directory: ./before
       - name: compile before
-        run: cargo check --all-targets
-        working-directory: ./before/core
+        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="(.*)"/'
@@ -62,8 +62,8 @@ jobs:
           path: after
           submodules: recursive
       - name: compile after
-        run: cargo check --all-targets
-        working-directory: ./after/core
+        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="(.*)"/'
@@ -75,6 +75,9 @@ jobs:
         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'
+          

docker/contract-verifier/Dockerfile

@@ -96,7 +96,7 @@ RUN mkdir -p /etc/vyper-bin/0.4.0 \
     && mv vyper0.4.0 /etc/vyper-bin/0.4.0/vyper \
     && chmod +x /etc/vyper-bin/0.4.0/vyper
 
-COPY --from=builder /usr/src/zksync/target/release/zksync_contract_verifier /usr/bin/
+COPY --from=builder /usr/src/zksync/core/target/release/zksync_contract_verifier /usr/bin/
 COPY contracts/system-contracts/zkout/ /contracts/system-contracts/zkout/
 
 # CMD tail -f /dev/null

docker/external-node/Dockerfile

@@ -20,8 +20,8 @@ RUN cargo build --release --bin zksync_external_node --bin block_reverter
 
 FROM ghcr.io/matter-labs/zksync-runtime-base:latest
 
-COPY --from=builder /usr/src/zksync/target/release/zksync_external_node /usr/bin
-COPY --from=builder /usr/src/zksync/target/release/block_reverter /usr/bin
+COPY --from=builder /usr/src/zksync/core/target/release/zksync_external_node /usr/bin
+COPY --from=builder /usr/src/zksync/core/target/release/block_reverter /usr/bin
 COPY --from=builder /usr/local/cargo/bin/sqlx /usr/bin
 COPY --from=builder /usr/src/zksync/docker/external-node/entrypoint.sh /usr/bin
 COPY contracts/system-contracts/zkout/ /contracts/system-contracts/zkout/

docker/server-v2/Dockerfile

@@ -28,9 +28,9 @@ EXPOSE 3000
 EXPOSE 3031
 EXPOSE 3030
 
-COPY --from=builder /usr/src/zksync/target/release/zksync_server /usr/bin
-COPY --from=builder /usr/src/zksync/target/release/block_reverter /usr/bin
-COPY --from=builder /usr/src/zksync/target/release/merkle_tree_consistency_checker /usr/bin
+COPY --from=builder /usr/src/zksync/core/target/release/zksync_server /usr/bin
+COPY --from=builder /usr/src/zksync/core/target/release/block_reverter /usr/bin
+COPY --from=builder /usr/src/zksync/core/target/release/merkle_tree_consistency_checker /usr/bin
 COPY contracts/system-contracts/zkout/ /contracts/system-contracts/zkout/
 COPY contracts/l1-contracts/out/ /contracts/l1-contracts/out/
 COPY contracts/l2-contracts/zkout/ /contracts/l2-contracts/zkout/

docker/snapshots-creator/Dockerfile

@@ -22,6 +22,6 @@ FROM ghcr.io/matter-labs/zksync-runtime-base:latest
 RUN apt-get update && apt-get install -y liburing-dev && \
     rm -rf /var/lib/apt/lists/*
 
-COPY --from=builder /usr/src/zksync/target/release/snapshots_creator /usr/bin
+COPY --from=builder /usr/src/zksync/core/target/release/snapshots_creator /usr/bin
 
 ENTRYPOINT ["snapshots_creator"]

zkstack_cli/crates/zkstack/src/commands/contract_verifier/run.rs

@@ -16,7 +16,7 @@ pub(crate) async fn run(shell: &Shell) -> anyhow::Result<()> {
     let config_path = chain.path_to_general_config();
     let secrets_path = chain.path_to_secrets_config();
 
-    let _dir_guard = shell.push_dir(&chain.link_to_code);
+    let _dir_guard = shell.push_dir(&chain.link_to_code.join("core"));
 
     logger::info(MSG_RUNNING_CONTRACT_VERIFIER);
 

zkstack_cli/crates/zkstack/src/commands/dev/commands/snapshot.rs

@@ -32,7 +32,7 @@ async fn create(shell: &Shell) -> anyhow::Result<()> {
 
     logger::info(MSG_RUNNING_SNAPSHOT_CREATOR);
 
-    let mut cmd = Cmd::new(cmd!(shell, "cargo run --bin snapshots_creator --release -- --config-path={config_path} --secrets-path={secrets_path}"))
+    let mut cmd = Cmd::new(cmd!(shell, "cargo run --manifest-path ./core/Cargo.toml --bin snapshots_creator --release -- --config-path={config_path} --secrets-path={secrets_path}"))
         .env("RUST_LOG", "snapshots_creator=debug");
 
     cmd = cmd.with_force_run();

zkstack_cli/crates/zkstack/src/commands/dev/commands/test/loadtest.rs

@@ -17,7 +17,7 @@ pub fn run(shell: &Shell) -> anyhow::Result<()> {
         .api_config
         .context("API config is not found")?;
 
-    let mut command = cmd!(shell, "cargo run --release --bin loadnext")
+    let mut command = cmd!(shell, "cargo run --manifest-path ./core/Cargo.toml --release --bin loadnext")
         .env(
             "L2_CHAIN_ID",
             chain_config

zkstack_cli/crates/zkstack/src/commands/dev/commands/test/rust.rs

@@ -24,7 +24,7 @@ pub async fn run(shell: &Shell, args: RustArgs) -> anyhow::Result<()> {
         .load_chain(Some(ecosystem.default_chain))
         .context(MSG_CHAIN_NOT_FOUND_ERR)?;
     let general_config = chain.get_general_config();
-    let link_to_code = ecosystem.link_to_code.join("core");
+    let link_to_code = ecosystem.link_to_code;
 
     let (test_server_url, test_prover_url) = if let Ok(general_config) = general_config {
         let postgres = general_config
@@ -59,7 +59,7 @@ pub async fn run(shell: &Shell, args: RustArgs) -> anyhow::Result<()> {
 
     reset_test_databases(shell, &link_to_code, dals).await?;
 
-    let _dir_guard = shell.push_dir(&link_to_code);
+    let _dir_guard = shell.push_dir(&link_to_code.join("core"));
 
     logger::info(MSG_USING_CARGO_NEXTEST);
     let cmd = cmd!(shell, "cargo nextest run --release");

zkstack_cli/crates/zkstack/src/commands/prover/run.rs

@@ -145,7 +145,7 @@ fn run_binary_component(
 
     let mut cmd = Cmd::new(cmd!(
         shell,
-        "cargo run {application_args...} --release --bin {binary_name} -- {args...}"
+        "cargo run --manifest-path ./core/Cargo.toml {application_args...} --release --bin {binary_name} -- {args...}"
     ));
     cmd = cmd.with_force_run();
     cmd.run().context(error)