diff --git a/substrate/.gitlab-ci.yml b/substrate/.gitlab-ci.yml
index ede9f2fd7d..dee459cea7 100644
--- a/substrate/.gitlab-ci.yml
+++ b/substrate/.gitlab-ci.yml
@@ -357,20 +357,15 @@ check_polkadot:
   <<:                              *docker-env
   allow_failure:                   true
   script:
-    - COMMIT_HASH=$(git rev-parse HEAD)
     - SUBSTRATE_PATH=$(pwd)
     # Clone the current Polkadot master branch into ./polkadot.
     - git clone --depth 1 https://gitlab.parity.io/parity/polkadot.git
     - cd polkadot
-    # Within Polkadot 'master' alter each Cargo.toml that references the
-    # Substrate 'polkadot-master' branch:
-    # 1. Replace the 'branch = "polkadot-master"' statements with the rev of our
-    #    commit.
-    # 2. Replace 'git = "https://.*"' with 'git = "file://.*"' (the local
-    #    checked out Substrate repository one folder above).
-    # 3. Remove any trailing commas.
-    - git grep -l "polkadot-master" | grep toml | xargs sed -i "s/branch.*=.*\"polkadot-master\"/rev = \"$COMMIT_HASH\"/; s~https://github.com/paritytech/substrate~file://$SUBSTRATE_PATH~; s/,\s*}/ }/"
-    # Make sure 'Cargo.lock' matches 'Cargo.toml'. It's enough to update one
+    # Make sure we override the crates in native and wasm build
+    - mkdir .cargo
+    - echo "paths = [ \"$SUBSTRATE_PATH\" ]" > .cargo/config
+    - mkdir -p target/debug/wbuild/.cargo
+    - echo "paths = [ \"$SUBSTRATE_PATH\" ]" > target/debug/wbuild/.cargo/config
     # package, others are updated along the way.
     - cargo update -p sp-io
     # Check whether Polkadot 'master' branch builds with this Substrate commit.
diff --git a/substrate/utils/wasm-builder/src/wasm_project.rs b/substrate/utils/wasm-builder/src/wasm_project.rs
index 701a50fe1c..bb32d62218 100644
--- a/substrate/utils/wasm-builder/src/wasm_project.rs
+++ b/substrate/utils/wasm-builder/src/wasm_project.rs
@@ -181,6 +181,7 @@ fn create_wasm_workspace_project(wasm_workspace: &Path, cargo_manifest: &Path) {
 		.map(|d| d.into_path())
 		.filter(|p| p.is_dir() && !p.ends_with("target"))
 		.filter_map(|p| p.file_name().map(|f| f.to_owned()).and_then(|s| s.into_string().ok()))
+		.filter(|f| !f.starts_with("."))
 		.collect::<Vec<_>>();
 
 	let crate_metadata = MetadataCommand::new()