diff --git a/.github/workflows/ql-for-ql-tests.yml b/.github/workflows/ql-for-ql-tests.yml
index bc247165198a..4502dded53f4 100644
--- a/.github/workflows/ql-for-ql-tests.yml
+++ b/.github/workflows/ql-for-ql-tests.yml
@@ -40,7 +40,7 @@ jobs:
             ql/target
           key: ${{ runner.os }}-${{ steps.os_version.outputs.version }}-qltest-cargo-${{ hashFiles('ql/rust-toolchain.toml', 'ql/**/Cargo.lock') }}
       - name: Check formatting
-        run: cd ql; cargo fmt --all -- --check
+        run: cd ql; cargo fmt -- --check
       - name: Build extractor
         run: |
           cd ql;
diff --git a/.github/workflows/ruby-build.yml b/.github/workflows/ruby-build.yml
index b1ae2e2b7db1..343e896151c2 100644
--- a/.github/workflows/ruby-build.yml
+++ b/.github/workflows/ruby-build.yml
@@ -79,7 +79,7 @@ jobs:
           key: ${{ runner.os }}-${{ steps.os_version.outputs.version }}-ruby-rust-cargo-${{ hashFiles('ruby/extractor/rust-toolchain.toml', 'ruby/extractor/**/Cargo.lock') }}
       - name: Check formatting
         if: steps.cache-extractor.outputs.cache-hit != 'true'
-        run: cd extractor && cargo fmt --all -- --check
+        run: cd extractor && cargo fmt -- --check
       - name: Build
         if: steps.cache-extractor.outputs.cache-hit != 'true'
         run: cd extractor && cargo build --verbose
diff --git a/.github/workflows/rust.yml b/.github/workflows/rust.yml
index e5f4bb2140f5..cc880072555e 100644
--- a/.github/workflows/rust.yml
+++ b/.github/workflows/rust.yml
@@ -23,26 +23,48 @@ permissions:
   contents: read
 
 jobs:
-  rust-code:
+  rust-ast-generator:
     runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: rust/ast-generator
     steps:
       - name: Checkout
         uses: actions/checkout@v4
+      - name: Inject sources
+        shell: bash
+        run: |
+          bazel run //rust/ast-generator:inject-sources
       - name: Format
-        working-directory: rust/extractor
         shell: bash
         run: |
           cargo fmt --check
       - name: Compilation
-        working-directory: rust/extractor
         shell: bash
         run: cargo check
       - name: Clippy
+        shell: bash
+        run: |
+          cargo clippy --no-deps -- -D warnings
+  rust-code:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
         working-directory: rust/extractor
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Format
+        shell: bash
+        run: |
+          cargo fmt --check
+      - name: Compilation
+        shell: bash
+        run: cargo check
+      - name: Clippy
         shell: bash
         run: |
-          cargo clippy --fix
-          git diff --exit-code
+          cargo clippy --no-deps -- -D warnings
   rust-codegen:
     runs-on: ubuntu-latest
     steps:
diff --git a/.github/workflows/tree-sitter-extractor-test.yml b/.github/workflows/tree-sitter-extractor-test.yml
index acc68e7ec2c7..9a71e1fc7c54 100644
--- a/.github/workflows/tree-sitter-extractor-test.yml
+++ b/.github/workflows/tree-sitter-extractor-test.yml
@@ -32,17 +32,17 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Check formatting
-        run: cargo fmt --all -- --check
+        run: cargo fmt -- --check
       - name: Run tests
         run: cargo test --verbose
   fmt:
-    runs-on: ubuntu-latest  
+    runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
       - name: Check formatting
         run: cargo fmt --check
   clippy:
-    runs-on: ubuntu-latest  
+    runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
       - name: Run clippy
diff --git a/ql/ql/test/dataflow/getAStringValue/getAStringValue.expected b/ql/ql/test/dataflow/getAStringValue/getAStringValue.expected
index 48de9172b362..e69de29bb2d1 100644
--- a/ql/ql/test/dataflow/getAStringValue/getAStringValue.expected
+++ b/ql/ql/test/dataflow/getAStringValue/getAStringValue.expected
@@ -1,2 +0,0 @@
-failures
-testFailures
diff --git a/rust/ast-generator/BUILD.bazel b/rust/ast-generator/BUILD.bazel
index b9a4baf018d6..b5956d096067 100644
--- a/rust/ast-generator/BUILD.bazel
+++ b/rust/ast-generator/BUILD.bazel
@@ -75,7 +75,7 @@ write_file(
         'DST_DIR="$(dirname "$(rlocation "$1")")"',
         'mkdir -p "$DST_DIR/src/codegen/grammar"',
     ] + [
-        'cp "$(rlocation "$%s")" "$DST_DIR/%s"' % item
+        'cp -f --no-preserve=mode "$(rlocation "$%s")" "$DST_DIR/%s"' % item
         for item in enumerate(_codegen_outs, 2)
     ],
     is_executable = True,
diff --git a/rust/ast-generator/patches/rust-analyzer.patch b/rust/ast-generator/patches/rust-analyzer.patch
index dceb60fbf4c2..e799e90f48a4 100644
--- a/rust/ast-generator/patches/rust-analyzer.patch
+++ b/rust/ast-generator/patches/rust-analyzer.patch
@@ -1,16 +1,19 @@
 diff --git a/xtask/src/codegen/grammar.rs b/xtask/src/codegen/grammar.rs
-index e7534582f2..8bc9237737 100644
+index e7534582f2..49c96f1be3 100644
 --- a/xtask/src/codegen/grammar.rs
 +++ b/xtask/src/codegen/grammar.rs
-@@ -3,6 +3,7 @@
+@@ -3,7 +3,9 @@
  //! Specifically, it generates the `SyntaxKind` enum and a number of newtype
  //! wrappers around `SyntaxNode` which implement `syntax::AstNode`.
  
+-#![allow(clippy::disallowed_types)]
 +#![allow(warnings)]
- #![allow(clippy::disallowed_types)]
++#![allow(clippy)]
++#![cfg_attr(any(), rustfmt::skip)]
  
  use std::{
-@@ -23,7 +24,7 @@ use crate::{
+     collections::{BTreeSet, HashSet},
+@@ -23,7 +25,7 @@ use crate::{
      project_root,
  };
  
@@ -19,7 +22,7 @@ index e7534582f2..8bc9237737 100644
  use self::ast_src::{AstEnumSrc, AstNodeSrc, AstSrc, Cardinality, Field, KindsSrc};
  
  pub(crate) fn generate(check: bool) {
-@@ -624,7 +625,7 @@ fn pluralize(s: &str) -> String {
+@@ -624,7 +626,7 @@ fn pluralize(s: &str) -> String {
  }
  
  impl Field {
@@ -28,7 +31,7 @@ index e7534582f2..8bc9237737 100644
          matches!(self, Field::Node { cardinality: Cardinality::Many, .. })
      }
      fn token_kind(&self) -> Option<proc_macro2::TokenStream> {
-@@ -636,7 +637,7 @@ impl Field {
+@@ -636,7 +638,7 @@ impl Field {
              _ => None,
          }
      }
@@ -37,7 +40,7 @@ index e7534582f2..8bc9237737 100644
          match self {
              Field::Token(name) => {
                  let name = match name.as_str() {
-@@ -682,7 +683,7 @@ impl Field {
+@@ -682,7 +684,7 @@ impl Field {
              }
          }
      }
@@ -46,7 +49,7 @@ index e7534582f2..8bc9237737 100644
          match self {
              Field::Token(_) => format_ident!("SyntaxToken"),
              Field::Node { ty, .. } => format_ident!("{}", ty),
-@@ -699,7 +700,7 @@ fn clean_token_name(name: &str) -> String {
+@@ -699,7 +701,7 @@ fn clean_token_name(name: &str) -> String {
      }
  }
  
@@ -55,3 +58,16 @@ index e7534582f2..8bc9237737 100644
      let mut res = AstSrc {
          tokens:
              "Whitespace Comment String ByteString CString IntNumber FloatNumber Char Byte Ident"
+diff --git a/xtask/src/codegen/grammar/ast_src.rs b/xtask/src/codegen/grammar/ast_src.rs
+index 9269d15423..babe7ca1bf 100644
+--- a/xtask/src/codegen/grammar/ast_src.rs
++++ b/xtask/src/codegen/grammar/ast_src.rs
+@@ -1,5 +1,8 @@
+ //! Defines input for code generation process.
+ 
++#![allow(clippy)]
++#![cfg_attr(any(), rustfmt::skip)]
++
+ use quote::ToTokens;
+ 
+ use crate::codegen::grammar::to_upper_snake_case;
diff --git a/rust/ast-generator/src/main.rs b/rust/ast-generator/src/main.rs
index a0e524689c12..2cc77fe5fff1 100644
--- a/rust/ast-generator/src/main.rs
+++ b/rust/ast-generator/src/main.rs
@@ -9,8 +9,7 @@ use std::env;
 use ungrammar::Grammar;
 
 fn project_root() -> PathBuf {
-    let dir =
-        env::var("CARGO_MANIFEST_DIR").unwrap().to_owned();
+    let dir = env::var("CARGO_MANIFEST_DIR").unwrap().to_owned();
     PathBuf::from(dir).parent().unwrap().to_owned()
 }
 
@@ -593,7 +592,7 @@ impl Translator<'_> {{
 fn main() -> std::io::Result<()> {
     let grammar = PathBuf::from("..").join(env::args().nth(1).expect("grammar file path required"));
     let grammar: Grammar = fs::read_to_string(&grammar)
-        .expect(&format!("Failed to parse grammar file: {}", grammar.display()))
+        .unwrap_or_else(|_| panic!("Failed to parse grammar file: {}", grammar.display()))
         .parse()
         .expect("Failed to parse grammar");
     let mut grammar = codegen::grammar::lower(&grammar);
diff --git a/rust/lint.py b/rust/lint.py
index 3a231c157df3..bb3109a0f501 100755
--- a/rust/lint.py
+++ b/rust/lint.py
@@ -10,9 +10,11 @@
 cargo = shutil.which("cargo")
 assert cargo, "no cargo binary found on `PATH`"
 
-fmt = subprocess.run([cargo, "fmt", "--all", "--quiet"], cwd=this_dir)
+runs = []
+runs.append(subprocess.run([cargo, "fmt", "--all", "--quiet"], cwd=this_dir))
+
 for manifest in this_dir.rglob("Cargo.toml"):
     if not manifest.is_relative_to(this_dir / "ql") and not manifest.is_relative_to(this_dir / "integration-tests"):
-        clippy = subprocess.run([cargo, "clippy", "--fix", "--allow-dirty", "--allow-staged", "--quiet"],
-                                cwd=manifest.parent)
-sys.exit(fmt.returncode or clippy.returncode)
+        runs.append(subprocess.run([cargo, "clippy", "--fix", "--allow-dirty", "--allow-staged", "--quiet", "--", "-D", "warnings"],
+                                   cwd=manifest.parent))
+sys.exit(max(r.returncode for r in runs))