set CompileForOverlayEval in java pack

Java: disable failing maven fetches expectations for now

.bazelrc

@@ -37,5 +37,6 @@ build --java_language_version=17
 build --tool_java_language_version=17
 build --tool_java_runtime_version=remotejdk_17
 build --java_runtime_version=remotejdk_17
+build --@rules_python//python/config_settings:python_version=3.12
 
 try-import %workspace%/local.bazelrc

.bazelrc.internal

@@ -8,3 +8,5 @@ common --registry=https://bcr.bazel.build
 # its implementation packages without providing any code itself.
 # We either can depend on internal implementation details, or turn of strict deps.
 common --@rules_dotnet//dotnet/settings:strict_deps=false
+
+build --@rules_python//python/config_settings:python_version=3.12

.bazelversion

@@ -1 +1 @@
-8.0.0
+8.1.1

.devcontainer/Dockerfile.codespaces

@@ -0,0 +1,7 @@
+FROM mcr.microsoft.com/devcontainers/base:ubuntu-24.04
+
+USER root
+# Install needed packages according to https://codeql.github.com/docs/codeql-overview/system-requirements/
+# most come from the base image, but we need to install some additional ones
+RUN DEBIAN_FRONTEND=noninteractive apt update && apt install -y sudo man-db python3.12 npm unminimize
+RUN yes | unminimize

.devcontainer/devcontainer.json

@@ -1,5 +1,4 @@
 {
-  "image": "mcr.microsoft.com/devcontainers/base:ubuntu-24.04",
   "extensions": [
     "rust-lang.rust-analyzer",
     "bungcip.better-toml",
@@ -8,6 +7,10 @@
     "ms-vscode.test-adapter-converter",
     "slevesque.vscode-zipexplorer"
   ],
+  "build": {
+    // Path is relative to the devcontainer.json file.
+    "dockerfile": "Dockerfile.codespaces"
+  },
   "settings": {
     "files.watcherExclude": {
       "**/target/**": true

.github/codeql/codeql-config.yml

@@ -4,9 +4,13 @@ queries:
   - uses: security-and-quality
 
 paths-ignore:
+  - '/actions/ql/test'
   - '/cpp/'
   - '/java/'
   - '/python/'
   - '/javascript/ql/test'
+  - '/javascript/ql/integration-tests'
   - '/javascript/extractor/tests'
+  - '/javascript/extractor/parser-tests'
+  - '/javascript/ql/src/'
   - '/rust/ql'

.github/copilot-instructions.md

@@ -0,0 +1,4 @@
+When reviewing code:
+* do not review changes in files with `.expected` extension (they are automatically ensured to be correct).
+* in `.ql` and `.qll` files, do not try to review the code itself as you don't understand the programming language
+  well enough to make comments in these languages. You can still check for typos or comment improvements.

.github/workflows/build-ripunzip.yml

@@ -6,18 +6,18 @@ on:
       ripunzip-version:
         description: "what reference to checktout from google/runzip"
         required: false
-        default: v1.2.1
+        default: v2.0.2
       openssl-version:
         description: "what reference to checkout from openssl/openssl for Linux"
         required: false
-        default: openssl-3.3.0
+        default: openssl-3.5.0
 
 jobs:
   build:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-20.04, macos-13, windows-2019]
+        os: [ubuntu-22.04, macos-13, windows-2022]
     runs-on: ${{ matrix.os }}
     steps:
       - uses: actions/checkout@v4

.github/workflows/check-change-note.yml

@@ -16,7 +16,6 @@ on:
       - "shared/**/*.qll"
       - "!**/experimental/**"
       - "!ql/**"
-      - "!rust/**"
       - ".github/workflows/check-change-note.yml"
 
 jobs:

.github/workflows/check-overlay-annotations.yml

@@ -0,0 +1,23 @@
+name: Check overlay annotations
+
+on:
+  push:
+    branches:
+      - main
+      - 'rc/*'
+  pull_request:
+    branches:
+      - main
+      - 'rc/*'
+
+permissions:
+  contents: read
+
+jobs:
+  sync:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Check overlay annotations
+        run: python config/add-overlay-annotations.py --check java
+

.github/workflows/codeql-analysis.yml

@@ -18,6 +18,10 @@ on:
 
 jobs:
   CodeQL-Build:
+    strategy:
+      fail-fast: false
+      matrix:
+        language: ['actions', 'csharp']
 
     runs-on: ubuntu-latest
 
@@ -38,9 +42,8 @@ jobs:
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL
       uses: github/codeql-action/init@main
-      # Override language selection by uncommenting this and choosing your languages
       with:
-        languages: csharp
+        languages: ${{ matrix.language }}
         config-file: ./.github/codeql/codeql-config.yml
 
     # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).

.github/workflows/csharp-qltest.yml

@@ -36,7 +36,7 @@ jobs:
   unit-tests:
     strategy:
       matrix:
-        os: [ubuntu-latest, windows-2019]
+        os: [ubuntu-latest, windows-latest]
     runs-on: ${{ matrix.os }}
     steps:
       - uses: actions/checkout@v4
@@ -66,6 +66,6 @@ jobs:
           # Update existing stubs in the repo with the freshly generated ones
           mv "$STUBS_PATH/output/stubs/_frameworks" ql/test/resources/stubs/
           git status
-          codeql test run --threads=0 --search-path "${{ github.workspace }}" --check-databases --check-undefined-labels --check-repeated-labels --check-redefined-labels --consistency-queries ql/consistency-queries -- ql/test/library-tests/dataflow/flowsources/aspremote
+          codeql test run --threads=0 --search-path "${{ github.workspace }}" --check-databases --check-diff-informed --check-undefined-labels --check-repeated-labels --check-redefined-labels --consistency-queries ql/consistency-queries -- ql/test/library-tests/dataflow/flowsources/aspremote
         env:
           GITHUB_TOKEN: ${{ github.token }}

.github/workflows/go-tests-other-os.yml

@@ -26,9 +26,8 @@ jobs:
         uses: ./go/actions/test
 
   test-win:
-    if: github.repository_owner == 'github'
     name: Test Windows
-    runs-on: windows-latest-xl
+    runs-on: windows-latest
     steps:
       - name: Check out code
         uses: actions/checkout@v4

.github/workflows/go-tests-rtjo.yml

@@ -0,0 +1,22 @@
+name: "Go: Run RTJO Tests"
+on:
+  pull_request:
+    types:
+      - labeled
+
+permissions:
+  contents: read
+
+jobs:
+  test-linux:
+    if: "github.repository_owner == 'github' && github.event.label.name == 'Run: RTJO Language Tests'"
+    name: RTJO Test Linux (Ubuntu)
+    runs-on: ubuntu-latest-xl
+    steps:
+      - name: Check out code
+        uses: actions/checkout@v4
+      - name: Run tests
+        uses: ./go/actions/test
+        with:
+          run-code-checks: true
+          dynamic-join-order-mode: all

.github/workflows/mad_modelDiff.yml

@@ -68,7 +68,7 @@ jobs:
             DATABASE=$2
             cd codeql-$QL_VARIANT
             SHORTNAME=`basename $DATABASE`
-            python java/ql/src/utils/modelgenerator/GenerateFlowModel.py --with-summaries --with-sinks $DATABASE $SHORTNAME/$QL_VARIANT
+            python misc/scripts/models-as-data/generate_mad.py --language java --with-summaries --with-sinks $DATABASE $SHORTNAME/$QL_VARIANT
             mkdir -p $MODELS/$SHORTNAME
             mv java/ql/lib/ext/generated/$SHORTNAME/$QL_VARIANT $MODELS/$SHORTNAME
             cd ..

.github/workflows/python-tooling.yml

@@ -0,0 +1,35 @@
+name: Python tooling
+
+on:
+  pull_request:
+    paths:
+      - "misc/bazel/**"
+      - "misc/codegen/**"
+      - "misc/scripts/models-as-data/bulk_generate_mad.py"
+      - "*.bazel*"
+      - .github/workflows/codegen.yml
+      - .pre-commit-config.yaml
+    branches:
+      - main
+      - rc/*
+      - codeql-cli-*
+
+permissions:
+  contents: read
+
+jobs:
+  check-python-tooling:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+      - uses: pre-commit/action@646c83fcd040023954eafda54b4db0192ce70507
+        name: Check that python code is properly formatted
+        with:
+          extra_args: black --all-files
+      - name: Run codegen tests
+        shell: bash
+        run: |
+          bazel test //misc/codegen/...

.github/workflows/ql-for-ql-dataset_measure.yml

@@ -53,7 +53,7 @@ jobs:
       - name: Create database
         run: |
           "${CODEQL}" database create \
-          --search-path "${{ github.workspace }}"
+          --search-path "${{ github.workspace }}" \
           --threads 4 \
             --language ql --source-root "${{ github.workspace }}/repo" \
             "${{ runner.temp }}/database"

.github/workflows/ruby-qltest-rtjo.yml

@@ -0,0 +1,40 @@
+name: "Ruby: Run RTJO Language Tests"
+
+on:
+  pull_request:
+    types:
+      - opened
+      - synchronize
+      - reopened
+      - labeled
+
+env:
+  CARGO_TERM_COLOR: always
+
+defaults:
+  run:
+    working-directory: ruby
+
+permissions:
+  contents: read
+
+jobs:
+  qltest-rtjo:
+    if: "github.repository_owner == 'github' && github.event.label.name == 'Run: RTJO Language Tests'"
+    runs-on: ubuntu-latest-xl
+    strategy:
+      fail-fast: false
+    steps:
+      - uses: actions/checkout@v4
+      - uses: ./.github/actions/fetch-codeql
+      - uses: ./ruby/actions/create-extractor-pack
+      - name: Cache compilation cache
+        id: query-cache
+        uses: ./.github/actions/cache-query-compilation
+        with:
+          key: ruby-qltest
+      - name: Run QL tests
+        run: |
+          codeql test run --dynamic-join-order-mode=all --threads=0 --ram 50000 --search-path "${{ github.workspace }}" --check-databases --check-diff-informed --check-undefined-labels --check-unused-labels --check-repeated-labels --check-redefined-labels --check-use-before-definition --consistency-queries ql/consistency-queries ql/test --compilation-cache "${{ steps.query-cache.outputs.cache-dir }}"
+        env:
+          GITHUB_TOKEN: ${{ github.token }}

.github/workflows/ruby-qltest.yml

@@ -68,6 +68,6 @@ jobs:
           key: ruby-qltest
       - name: Run QL tests
         run: |
-          codeql test run --threads=0 --ram 50000 --search-path "${{ github.workspace }}" --check-databases --check-undefined-labels --check-unused-labels --check-repeated-labels --check-redefined-labels --check-use-before-definition --consistency-queries ql/consistency-queries ql/test --compilation-cache "${{ steps.query-cache.outputs.cache-dir }}"
+          codeql test run --threads=0 --ram 50000 --search-path "${{ github.workspace }}" --check-databases --check-diff-informed --check-undefined-labels --check-unused-labels --check-repeated-labels --check-redefined-labels --check-use-before-definition --consistency-queries ql/consistency-queries ql/test --compilation-cache "${{ steps.query-cache.outputs.cache-dir }}"
         env:
           GITHUB_TOKEN: ${{ github.token }}

.github/workflows/swift.yml

@@ -18,45 +18,39 @@ on:
       - main
       - rc/*
       - codeql-cli-*
-  push:
-    paths:
-      - "swift/**"
-      - "misc/bazel/**"
-      - "misc/codegen/**"
-      - "shared/**"
-      - "*.bazel*"
-      - .github/workflows/swift.yml
-      - .github/actions/**
-      - codeql-workspace.yml
-      - .pre-commit-config.yaml
-      - "!**/*.md"
-      - "!**/*.qhelp"
-    branches:
-      - main
-      - rc/*
-      - codeql-cli-*
 
 permissions:
   contents: read
 
+defaults:
+  run:
+    shell: bash
+    working-directory: swift
+
 jobs:
-  # not using a matrix as you cannot depend on a specific job in a matrix, and we want to start linux checks
-  # without waiting for the macOS build
-  build-and-test-macos:
+  build-and-test:
     if: github.repository_owner == 'github'
-    runs-on: macos-13-xlarge
+    strategy:
+      matrix:
+        runner: [ubuntu-latest, macos-15-xlarge]
+      fail-fast: false
+    runs-on: ${{ matrix.runner }}
     steps:
       - uses: actions/checkout@v4
-      - uses: ./swift/actions/build-and-test
-  qltests-macos:
-    if: ${{ github.repository_owner == 'github' && github.event_name == 'pull_request' }}
-    needs: build-and-test-macos
-    runs-on: macos-13-xlarge
-    steps:
-      - uses: actions/checkout@v4
-      - uses: ./swift/actions/run-ql-tests
+      - name: Setup (Linux)
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y uuid-dev zlib1g-dev
+      - name: Build Swift extractor
+        shell: bash
+        run: |
+          bazel run :install
+      - name: Run Swift tests
+        shell: bash
+        run: |
+          bazel test ... --test_tag_filters=-override --test_output=errors
   clang-format:
-    if : ${{ github.event_name == 'pull_request' }}
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
@@ -65,18 +59,9 @@ jobs:
         with:
           extra_args: clang-format --all-files
   codegen:
-    if : ${{ github.event_name == 'pull_request' }}
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - uses: bazelbuild/setup-bazelisk@v2
-      - uses: actions/setup-python@v4
-        with:
-          python-version-file: 'swift/.python-version'
-      - uses: pre-commit/action@646c83fcd040023954eafda54b4db0192ce70507
-        name: Check that python code is properly formatted
-        with:
-          extra_args: autopep8 --all-files
       - uses: ./.github/actions/fetch-codeql
       - uses: pre-commit/action@646c83fcd040023954eafda54b4db0192ce70507
         name: Check that QL generated code was checked in
@@ -84,22 +69,14 @@ jobs:
           extra_args: swift-codegen --all-files
       - name: Generate C++ files
         run: |
-          bazel run //swift/codegen:codegen -- --generate=trap,cpp --cpp-output=$PWD/generated-cpp-files
+          bazel run codegen -- --generate=trap,cpp --cpp-output=$PWD/generated-cpp-files
       - uses: actions/upload-artifact@v4
         with:
           name: swift-generated-cpp-files
           path: generated-cpp-files/**
-  database-upgrade-scripts:
-    if : ${{ github.event_name == 'pull_request' }}
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - uses: ./.github/actions/fetch-codeql
-      - uses: ./swift/actions/database-upgrade-scripts
   check-no-override:
-    if : github.event_name == 'pull_request'
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - shell: bash
-        run: bazel test //swift/... --test_tag_filters=override --test_output=errors
+      - name: Check that no override is present in load.bzl
+        run: bazel test ... --test_tag_filters=override --test_output=errors

.github/workflows/validate-change-notes.yml

@@ -31,4 +31,4 @@ jobs:
       - name: Fail if there are any errors with existing change notes
 
         run: |
-          codeql pack release --groups cpp,csharp,java,javascript,python,ruby,-examples,-test,-experimental
+          codeql pack release --groups actions,cpp,csharp,go,java,javascript,python,ruby,shared,swift -examples,-test,-experimental

.gitignore

@@ -62,6 +62,7 @@ node_modules/
 
 # Temporary folders for working with generated models
 .model-temp
+/mad-generation-build
 
 # bazel-built in-tree extractor packs
 /*/extractor-pack
@@ -71,3 +72,7 @@ node_modules/
 
 # cargo build directory
 /target
+
+# some upgrade/downgrade checks create these files
+**/upgrades/*/*.dbscheme.stats
+**/downgrades/*/*.dbscheme.stats

.pre-commit-config.yaml

@@ -1,5 +1,7 @@
 # See https://pre-commit.com for more information
 # See https://pre-commit.com/hooks.html for more hooks
+default_language_version:
+  python: python3.12
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v3.2.0
@@ -7,18 +9,18 @@ repos:
       - id: trailing-whitespace
         exclude: /test/.*$(?<!\.qlref)|.*\.patch$|.*\.qll?$
       - id: end-of-file-fixer
-        exclude: /test/.*$(?<!\.qlref)|.*\.patch$|.*\.qll?$
+        exclude: Cargo.lock$|/test/.*$(?<!\.qlref)|.*\.patch$|.*\.qll?$
 
   - repo: https://github.com/pre-commit/mirrors-clang-format
     rev: v17.0.6
     hooks:
       - id: clang-format
 
-  - repo: https://github.com/pre-commit/mirrors-autopep8
-    rev: v2.0.4
+  - repo: https://github.com/psf/black
+    rev: 25.1.0
     hooks:
-      - id: autopep8
-        files: ^misc/codegen/.*\.py
+      - id: black
+        files: ^(misc/codegen/.*|misc/scripts/models-as-data/.*)\.py$
 
   - repo: local
     hooks:
@@ -72,7 +74,7 @@ repos:
 
       - id: rust-codegen
         name: Run Rust checked in code generation
-        files: ^misc/codegen/|^rust/(prefix\.dbscheme|schema/|codegen/|.*/generated/|ql/lib/(rust\.dbscheme$|codeql/rust/elements)|\.generated.list)
+        files: ^misc/codegen/|^rust/(prefix\.dbscheme|schema/|codegen/|.*/generated/|ql/lib/(rust\.dbscheme$|codeql/rust/elements)|\.generated.list|ast-generator/)
         language: system
         entry: bazel run //rust/codegen -- --quiet
         pass_filenames: false

.vscode/tasks.json

@@ -50,6 +50,11 @@
                 "${input:name}",
                 "${input:categoryQuery}"
             ],
+            "options": {
+                "env": {
+                    "EDITOR": "code -r",
+                }
+            },
             "presentation": {
                 "reveal": "never",
                 "close": true
@@ -67,6 +72,11 @@
                 "${input:name}",
                 "${input:categoryLibrary}"
             ],
+            "options": {
+                "env": {
+                    "EDITOR": "code -r"
+                }
+            },
             "presentation": {
                 "reveal": "never",
                 "close": true

CODEOWNERS

@@ -8,12 +8,17 @@
 /javascript/ @github/codeql-javascript
 /python/ @github/codeql-python
 /ruby/ @github/codeql-ruby
+/rust/ @github/codeql-rust
 /swift/ @github/codeql-swift
 /misc/codegen/ @github/codeql-swift
 /java/kotlin-extractor/ @github/codeql-kotlin
 /java/ql/test-kotlin1/ @github/codeql-kotlin
 /java/ql/test-kotlin2/ @github/codeql-kotlin
 
+# Experimental CodeQL cryptography
+**/experimental/**/quantum/ @github/ps-codeql
+/shared/quantum/ @github/ps-codeql
+
 # CodeQL tools and associated docs
 /docs/codeql/codeql-cli/ @github/codeql-cli-reviewers
 /docs/codeql/codeql-for-visual-studio-code/ @github/codeql-vscode-reviewers
@@ -38,6 +43,7 @@ MODULE.bazel @github/codeql-ci-reviewers
 /.github/workflows/go-* @github/codeql-go
 /.github/workflows/ql-for-ql-* @github/codeql-ql-for-ql-reviewers
 /.github/workflows/ruby-* @github/codeql-ruby
+/.github/workflows/rust.yml @github/codeql-rust
 /.github/workflows/swift.yml @github/codeql-swift
 
 # Misc

Cargo.toml

@@ -10,8 +10,4 @@ members = [
     "rust/ast-generator",
     "rust/autobuild",
 ]
-
-[patch.crates-io]
-# patch for build script bug preventing bazel build
-# see https://github.com/rust-lang/rustc_apfloat/pull/17
-rustc_apfloat = { git = "https://github.com/redsun82/rustc_apfloat.git", rev = "096d585100636bc2e9f09d7eefec38c5b334d47b" }
+exclude = ["mad-generation-build"]

MODULE.bazel

@@ -24,20 +24,20 @@ bazel_dep(name = "bazel_skylib", version = "1.7.1")
 bazel_dep(name = "abseil-cpp", version = "20240116.1", repo_name = "absl")
 bazel_dep(name = "nlohmann_json", version = "3.11.3", repo_name = "json")
 bazel_dep(name = "fmt", version = "10.0.0")
-bazel_dep(name = "rules_kotlin", version = "2.0.0-codeql.1")
+bazel_dep(name = "rules_kotlin", version = "2.1.3-codeql.1")
 bazel_dep(name = "gazelle", version = "0.40.0")
 bazel_dep(name = "rules_dotnet", version = "0.17.4")
 bazel_dep(name = "googletest", version = "1.14.0.bcr.1")
-bazel_dep(name = "rules_rust", version = "0.57.1")
+bazel_dep(name = "rules_rust", version = "0.58.0")
 bazel_dep(name = "zstd", version = "1.5.5.bcr.1")
 
 bazel_dep(name = "buildifier_prebuilt", version = "6.4.0", dev_dependency = True)
 
 # Keep edition and version approximately in sync with internal repo.
 # the versions there are canonical, the versions here are used for CI in github/codeql, as well as for the vendoring of dependencies.
-RUST_EDITION = "2021"
+RUST_EDITION = "2024"
 
-RUST_VERSION = "1.82.0"
+RUST_VERSION = "1.86.0"
 
 rust = use_extension("@rules_rust//rust:extensions.bzl", "rust")
 rust.toolchain(
@@ -71,57 +71,60 @@ use_repo(
 tree_sitter_extractors_deps = use_extension("//misc/bazel/3rdparty:tree_sitter_extractors_extension.bzl", "r")
 use_repo(
     tree_sitter_extractors_deps,
-    "vendor__anyhow-1.0.95",
-    "vendor__argfile-0.2.1",
-    "vendor__chrono-0.4.39",
-    "vendor__clap-4.5.26",
-    "vendor__dunce-1.0.5",
-    "vendor__either-1.13.0",
-    "vendor__encoding-0.2.33",
-    "vendor__figment-0.10.19",
-    "vendor__flate2-1.0.35",
-    "vendor__glob-0.3.2",
-    "vendor__globset-0.4.15",
-    "vendor__itertools-0.14.0",
-    "vendor__lazy_static-1.5.0",
-    "vendor__mustache-0.9.0",
-    "vendor__num-traits-0.2.19",
-    "vendor__num_cpus-1.16.0",
-    "vendor__proc-macro2-1.0.93",
-    "vendor__quote-1.0.38",
-    "vendor__ra_ap_base_db-0.0.258",
-    "vendor__ra_ap_cfg-0.0.258",
-    "vendor__ra_ap_hir-0.0.258",
-    "vendor__ra_ap_hir_def-0.0.258",
-    "vendor__ra_ap_hir_expand-0.0.258",
-    "vendor__ra_ap_ide_db-0.0.258",
-    "vendor__ra_ap_intern-0.0.258",
-    "vendor__ra_ap_load-cargo-0.0.258",
-    "vendor__ra_ap_parser-0.0.258",
-    "vendor__ra_ap_paths-0.0.258",
-    "vendor__ra_ap_project_model-0.0.258",
-    "vendor__ra_ap_span-0.0.258",
-    "vendor__ra_ap_stdx-0.0.258",
-    "vendor__ra_ap_syntax-0.0.258",
-    "vendor__ra_ap_vfs-0.0.258",
-    "vendor__rand-0.8.5",
-    "vendor__rayon-1.10.0",
-    "vendor__regex-1.11.1",
-    "vendor__serde-1.0.217",
-    "vendor__serde_json-1.0.135",
-    "vendor__serde_with-3.12.0",
-    "vendor__syn-2.0.96",
-    "vendor__toml-0.8.19",
-    "vendor__tracing-0.1.41",
-    "vendor__tracing-flame-0.2.0",
-    "vendor__tracing-subscriber-0.3.19",
-    "vendor__tree-sitter-0.24.6",
-    "vendor__tree-sitter-embedded-template-0.23.2",
-    "vendor__tree-sitter-json-0.24.8",
-    "vendor__tree-sitter-ql-0.23.1",
-    "vendor__tree-sitter-ruby-0.23.1",
-    "vendor__triomphe-0.1.14",
-    "vendor__ungrammar-1.16.1",
+    "vendor_ts__anyhow-1.0.98",
+    "vendor_ts__argfile-0.2.1",
+    "vendor_ts__chalk-ir-0.103.0",
+    "vendor_ts__chrono-0.4.41",
+    "vendor_ts__clap-4.5.40",
+    "vendor_ts__dunce-1.0.5",
+    "vendor_ts__either-1.15.0",
+    "vendor_ts__encoding-0.2.33",
+    "vendor_ts__figment-0.10.19",
+    "vendor_ts__flate2-1.1.0",
+    "vendor_ts__glob-0.3.2",
+    "vendor_ts__globset-0.4.15",
+    "vendor_ts__itertools-0.14.0",
+    "vendor_ts__lazy_static-1.5.0",
+    "vendor_ts__mustache-0.9.0",
+    "vendor_ts__num-traits-0.2.19",
+    "vendor_ts__num_cpus-1.17.0",
+    "vendor_ts__proc-macro2-1.0.95",
+    "vendor_ts__quote-1.0.40",
+    "vendor_ts__ra_ap_base_db-0.0.288",
+    "vendor_ts__ra_ap_cfg-0.0.288",
+    "vendor_ts__ra_ap_hir-0.0.288",
+    "vendor_ts__ra_ap_hir_def-0.0.288",
+    "vendor_ts__ra_ap_hir_expand-0.0.288",
+    "vendor_ts__ra_ap_hir_ty-0.0.288",
+    "vendor_ts__ra_ap_ide_db-0.0.288",
+    "vendor_ts__ra_ap_intern-0.0.288",
+    "vendor_ts__ra_ap_load-cargo-0.0.288",
+    "vendor_ts__ra_ap_parser-0.0.288",
+    "vendor_ts__ra_ap_paths-0.0.288",
+    "vendor_ts__ra_ap_project_model-0.0.288",
+    "vendor_ts__ra_ap_span-0.0.288",
+    "vendor_ts__ra_ap_stdx-0.0.288",
+    "vendor_ts__ra_ap_syntax-0.0.288",
+    "vendor_ts__ra_ap_vfs-0.0.288",
+    "vendor_ts__rand-0.9.1",
+    "vendor_ts__rayon-1.10.0",
+    "vendor_ts__regex-1.11.1",
+    "vendor_ts__serde-1.0.219",
+    "vendor_ts__serde_json-1.0.140",
+    "vendor_ts__serde_with-3.13.0",
+    "vendor_ts__syn-2.0.103",
+    "vendor_ts__toml-0.8.23",
+    "vendor_ts__tracing-0.1.41",
+    "vendor_ts__tracing-flame-0.2.0",
+    "vendor_ts__tracing-subscriber-0.3.19",
+    "vendor_ts__tree-sitter-0.24.6",
+    "vendor_ts__tree-sitter-embedded-template-0.23.2",
+    "vendor_ts__tree-sitter-json-0.24.8",
+    "vendor_ts__tree-sitter-ql-0.23.1",
+    "vendor_ts__tree-sitter-ruby-0.23.1",
+    "vendor_ts__triomphe-0.1.14",
+    "vendor_ts__ungrammar-1.16.1",
+    "vendor_ts__zstd-0.13.3",
 )
 
 http_archive = use_repo_rule("@bazel_tools//tools/build_defs/repo:http.bzl", "http_archive")
@@ -153,7 +156,7 @@ use_repo(csharp_main_extension, "paket.main")
 pip = use_extension("@rules_python//python/extensions:pip.bzl", "pip")
 pip.parse(
     hub_name = "codegen_deps",
-    python_version = "3.11",
+    python_version = "3.12",
     requirements_lock = "//misc/codegen:requirements_lock.txt",
 )
 use_repo(pip, "codegen_deps")
@@ -191,10 +194,6 @@ use_repo(
     kotlin_extractor_deps,
     "codeql_kotlin_defaults",
     "codeql_kotlin_embeddable",
-    "kotlin-compiler-1.5.0",
-    "kotlin-compiler-1.5.10",
-    "kotlin-compiler-1.5.20",
-    "kotlin-compiler-1.5.30",
     "kotlin-compiler-1.6.0",
     "kotlin-compiler-1.6.20",
     "kotlin-compiler-1.7.0",
@@ -206,10 +205,7 @@ use_repo(
     "kotlin-compiler-2.0.20-Beta2",
     "kotlin-compiler-2.1.0-Beta1",
     "kotlin-compiler-2.1.20-Beta1",
-    "kotlin-compiler-embeddable-1.5.0",
-    "kotlin-compiler-embeddable-1.5.10",
-    "kotlin-compiler-embeddable-1.5.20",
-    "kotlin-compiler-embeddable-1.5.30",
+    "kotlin-compiler-2.2.0-Beta1",
     "kotlin-compiler-embeddable-1.6.0",
     "kotlin-compiler-embeddable-1.6.20",
     "kotlin-compiler-embeddable-1.7.0",
@@ -221,10 +217,7 @@ use_repo(
     "kotlin-compiler-embeddable-2.0.20-Beta2",
     "kotlin-compiler-embeddable-2.1.0-Beta1",
     "kotlin-compiler-embeddable-2.1.20-Beta1",
-    "kotlin-stdlib-1.5.0",
-    "kotlin-stdlib-1.5.10",
-    "kotlin-stdlib-1.5.20",
-    "kotlin-stdlib-1.5.30",
+    "kotlin-compiler-embeddable-2.2.0-Beta1",
     "kotlin-stdlib-1.6.0",
     "kotlin-stdlib-1.6.20",
     "kotlin-stdlib-1.7.0",
@@ -236,6 +229,7 @@ use_repo(
     "kotlin-stdlib-2.0.20-Beta2",
     "kotlin-stdlib-2.1.0-Beta1",
     "kotlin-stdlib-2.1.20-Beta1",
+    "kotlin-stdlib-2.2.0-Beta1",
 )
 
 go_sdk = use_extension("@rules_go//go:extensions.bzl", "go_sdk")
@@ -245,24 +239,24 @@ go_deps = use_extension("@gazelle//:extensions.bzl", "go_deps")
 go_deps.from_file(go_mod = "//go/extractor:go.mod")
 use_repo(go_deps, "org_golang_x_mod", "org_golang_x_tools")
 
-lfs_files = use_repo_rule("//misc/bazel:lfs.bzl", "lfs_files")
+lfs_archive = use_repo_rule("//misc/bazel:lfs.bzl", "lfs_archive")
 
-lfs_files(
+lfs_archive(
     name = "ripunzip-linux",
-    srcs = ["//misc/ripunzip:ripunzip-linux"],
-    executable = True,
+    src = "//misc/ripunzip:ripunzip-Linux.zip",
+    build_file = "//misc/ripunzip:BUILD.ripunzip.bazel",
 )
 
-lfs_files(
+lfs_archive(
     name = "ripunzip-windows",
-    srcs = ["//misc/ripunzip:ripunzip-windows.exe"],
-    executable = True,
+    src = "//misc/ripunzip:ripunzip-Windows.zip",
+    build_file = "//misc/ripunzip:BUILD.ripunzip.bazel",
 )
 
-lfs_files(
+lfs_archive(
     name = "ripunzip-macos",
-    srcs = ["//misc/ripunzip:ripunzip-macos"],
-    executable = True,
+    src = "//misc/ripunzip:ripunzip-macOS.zip",
+    build_file = "//misc/ripunzip:BUILD.ripunzip.bazel",
 )
 
 register_toolchains(

actions/extractor/tools/autobuild-impl.ps1

@@ -1,27 +1,34 @@
-if (($null -ne $env:LGTM_INDEX_INCLUDE) -or ($null -ne $env:LGTM_INDEX_EXCLUDE) -or ($null -ne $env:LGTM_INDEX_FILTERS)) {
-    Write-Output 'Path filters set. Passing them through to the JavaScript extractor.' 
-} else {
-    Write-Output 'No path filters set. Using the default filters.'
-    # Note: We're adding the `reusable_workflows` subdirectories to proactively
-    # record workflows that were called cross-repo, check them out locally,
-    # and enable an interprocedural analysis across the workflow files.
-    # These workflows follow the convention `.github/reusable_workflows/<nwo>/*.ya?ml`
-    $DefaultPathFilters = @(
-        'exclude:**/*',
-        'include:.github/workflows/*.yml',
-        'include:.github/workflows/*.yaml',
-        'include:.github/reusable_workflows/**/*.yml',
-        'include:.github/reusable_workflows/**/*.yaml',
-        'include:**/action.yml',
-        'include:**/action.yaml'
-    )
+# Note: We're adding the `reusable_workflows` subdirectories to proactively
+# record workflows that were called cross-repo, check them out locally,
+# and enable an interprocedural analysis across the workflow files.
+# These workflows follow the convention `.github/reusable_workflows/<nwo>/*.ya?ml`
+$DefaultPathFilters = @(
+    'exclude:**/*',
+    'include:.github/workflows/*.yml',
+    'include:.github/workflows/*.yaml',
+    'include:.github/reusable_workflows/**/*.yml',
+    'include:.github/reusable_workflows/**/*.yaml',
+    'include:**/action.yml',
+    'include:**/action.yaml'
+)
 
+if ($null -ne $env:LGTM_INDEX_FILTERS) {
+    Write-Output 'LGTM_INDEX_FILTERS set. Using the default filters together with the user-provided filters, and passing through to the JavaScript extractor.'
+    # Begin with the default path inclusions only,
+    # followed by the user-provided filters.
+    # If the user provided `paths`, those patterns override the default inclusions
+    # (because `LGTM_INDEX_FILTERS` will begin with `exclude:**/*`).
+    # If the user provided `paths-ignore`, those patterns are excluded.
+    $PathFilters = ($DefaultPathFilters -join "`n") + "`n" + $env:LGTM_INDEX_FILTERS
+    $env:LGTM_INDEX_FILTERS = $PathFilters
+} else {
+    Write-Output 'LGTM_INDEX_FILTERS not set. Using the default filters, and passing through to the JavaScript extractor.'
     $env:LGTM_INDEX_FILTERS = $DefaultPathFilters -join "`n"
 }
 
 # Find the JavaScript extractor directory via `codeql resolve extractor`.
 $CodeQL = Join-Path $env:CODEQL_DIST 'codeql.exe'
-$env:CODEQL_EXTRACTOR_JAVASCRIPT_ROOT = &$CodeQL resolve extractor --language javascript
+$env:CODEQL_EXTRACTOR_JAVASCRIPT_ROOT = &"$CodeQL" resolve extractor --language javascript
 if ($LASTEXITCODE -ne 0) {
     throw 'Failed to resolve JavaScript extractor.'
 }
@@ -40,7 +47,7 @@ $env:CODEQL_EXTRACTOR_JAVASCRIPT_SOURCE_ARCHIVE_DIR = $env:CODEQL_EXTRACTOR_ACTI
 $env:CODEQL_EXTRACTOR_JAVASCRIPT_TRAP_DIR = $env:CODEQL_EXTRACTOR_ACTIONS_TRAP_DIR
 $env:CODEQL_EXTRACTOR_JAVASCRIPT_WIP_DATABASE = $env:CODEQL_EXTRACTOR_ACTIONS_WIP_DATABASE
 
-&$JavaScriptAutoBuild
+&"$JavaScriptAutoBuild"
 if ($LASTEXITCODE -ne 0) {
     throw "JavaScript autobuilder failed."
 }

actions/extractor/tools/autobuild.cmd

@@ -1,3 +1,4 @@
 @echo off
 rem All of the work is done in the PowerShell script
-powershell.exe %~dp0autobuild-impl.ps1
+echo "Running PowerShell script at '%~dp0autobuild-impl.ps1'"
+powershell.exe -File "%~dp0autobuild-impl.ps1"

actions/extractor/tools/autobuild.sh

@@ -17,16 +17,28 @@ include:**/action.yaml
 END
 )
 
-if [ -n "${LGTM_INDEX_INCLUDE:-}" ] || [ -n "${LGTM_INDEX_EXCLUDE:-}" ] || [ -n "${LGTM_INDEX_FILTERS:-}" ] ; then
-    echo "Path filters set. Passing them through to the JavaScript extractor."
+if [ -n "${LGTM_INDEX_FILTERS:-}" ]; then
+    echo "LGTM_INDEX_FILTERS set. Using the default filters together with the user-provided filters, and passing through to the JavaScript extractor."
+    # Begin with the default path inclusions only,
+    # followed by the user-provided filters.
+    # If the user provided `paths`, those patterns override the default inclusions
+    # (because `LGTM_INDEX_FILTERS` will begin with `exclude:**/*`).
+    # If the user provided `paths-ignore`, those patterns are excluded.
+    PATH_FILTERS="$(cat << END
+${DEFAULT_PATH_FILTERS}
+${LGTM_INDEX_FILTERS}
+END
+)"
+    LGTM_INDEX_FILTERS="${PATH_FILTERS}"
+    export LGTM_INDEX_FILTERS
 else
-    echo "No path filters set. Using the default filters."
+    echo "LGTM_INDEX_FILTERS not set. Using the default filters, and passing through to the JavaScript extractor."
     LGTM_INDEX_FILTERS="${DEFAULT_PATH_FILTERS}"
     export LGTM_INDEX_FILTERS
 fi
 
 # Find the JavaScript extractor directory via `codeql resolve extractor`.
-CODEQL_EXTRACTOR_JAVASCRIPT_ROOT="$($CODEQL_DIST/codeql resolve extractor --language javascript)"
+CODEQL_EXTRACTOR_JAVASCRIPT_ROOT="$("${CODEQL_DIST}/codeql" resolve extractor --language javascript)"
 export CODEQL_EXTRACTOR_JAVASCRIPT_ROOT
 
 echo "Found JavaScript extractor at '${CODEQL_EXTRACTOR_JAVASCRIPT_ROOT}'."
@@ -42,4 +54,4 @@ env CODEQL_EXTRACTOR_JAVASCRIPT_DIAGNOSTIC_DIR="${CODEQL_EXTRACTOR_ACTIONS_DIAGN
     CODEQL_EXTRACTOR_JAVASCRIPT_SOURCE_ARCHIVE_DIR="${CODEQL_EXTRACTOR_ACTIONS_SOURCE_ARCHIVE_DIR}" \
     CODEQL_EXTRACTOR_JAVASCRIPT_TRAP_DIR="${CODEQL_EXTRACTOR_ACTIONS_TRAP_DIR}" \
     CODEQL_EXTRACTOR_JAVASCRIPT_WIP_DATABASE="${CODEQL_EXTRACTOR_ACTIONS_WIP_DATABASE}" \
-    ${JAVASCRIPT_AUTO_BUILD}
+    "${JAVASCRIPT_AUTO_BUILD}"

actions/ql/integration-tests/filters-default/actions.ql

@@ -0,0 +1,5 @@
+import actions
+
+from AstNode n
+where n instanceof Workflow or n instanceof CompositeAction
+select n

actions/ql/integration-tests/filters/actions.default-filters.expected

@@ -0,0 +1,6 @@
+| src/.github/action.yaml:1:1:11:32 | name: ' ... action' |
+| src/.github/actions/action-name/action.yml:1:1:11:32 | name: ' ... action' |
+| src/.github/workflows/workflow.yml:1:1:12:33 | name: A workflow |
+| src/action.yml:1:1:11:32 | name: ' ... action' |
+| src/excluded/action.yml:1:1:11:32 | name: ' ... action' |
+| src/included/action.yml:1:1:11:32 | name: ' ... action' |

actions/ql/integration-tests/filters/actions.paths-and-paths-ignore.expected

@@ -0,0 +1,2 @@
+| src/included/action.yml:1:1:11:32 | name: ' ... action' |
+| src/included/unreachable-workflow.yml:1:1:12:33 | name: A ... orkflow |

actions/ql/integration-tests/filters/actions.paths-ignore-only.expected

@@ -0,0 +1,5 @@
+| src/.github/action.yaml:1:1:11:32 | name: ' ... action' |
+| src/.github/actions/action-name/action.yml:1:1:11:32 | name: ' ... action' |
+| src/.github/workflows/workflow.yml:1:1:12:33 | name: A workflow |
+| src/action.yml:1:1:11:32 | name: ' ... action' |
+| src/included/action.yml:1:1:11:32 | name: ' ... action' |

actions/ql/integration-tests/filters/actions.paths-only.expected

@@ -0,0 +1,2 @@
+| src/included/action.yml:1:1:11:32 | name: ' ... action' |
+| src/included/unreachable-workflow.yml:1:1:12:33 | name: A ... orkflow |

actions/ql/integration-tests/filters/actions.ql

@@ -0,0 +1,5 @@
+import actions
+
+from AstNode n
+where n instanceof Workflow or n instanceof CompositeAction
+select n

actions/ql/integration-tests/filters/codeql-config.paths-and-paths-ignore.yml

@@ -0,0 +1,4 @@
+paths:
+  - 'included'
+paths-ignore:
+  - 'excluded'

actions/ql/integration-tests/filters/codeql-config.paths-ignore-only.yml

@@ -0,0 +1,2 @@
+paths-ignore:
+  - 'excluded'

actions/ql/integration-tests/filters/codeql-config.paths-only.yml

@@ -0,0 +1,2 @@
+paths:
+  - 'included'

actions/ql/integration-tests/filters/source_archive.default-filters.expected

@@ -0,0 +1,6 @@
+src/.github/action.yaml
+src/.github/actions/action-name/action.yml
+src/.github/workflows/workflow.yml
+src/action.yml
+src/excluded/action.yml
+src/included/action.yml

actions/ql/integration-tests/filters/source_archive.paths-and-paths-ignore.expected

@@ -0,0 +1,3 @@
+src/included/action.yml
+src/included/not-an-action.yml
+src/included/unreachable-workflow.yml

actions/ql/integration-tests/filters/source_archive.paths-ignore-only.expected

@@ -0,0 +1,5 @@
+src/.github/action.yaml
+src/.github/actions/action-name/action.yml
+src/.github/workflows/workflow.yml
+src/action.yml
+src/included/action.yml

actions/ql/integration-tests/filters/source_archive.paths-only.expected

@@ -0,0 +1,3 @@
+src/included/action.yml
+src/included/not-an-action.yml
+src/included/unreachable-workflow.yml

actions/ql/integration-tests/filters/src/.github/action.yaml

@@ -0,0 +1,11 @@
+name: 'A composite action'
+description: 'Do something'
+runs:
+  using: "composite"
+  steps:
+    - name: Print
+      run: echo "Hello world"
+      shell: bash
+
+    - name: Checkout
+      uses: actions/checkout@v4

actions/ql/integration-tests/filters/src/.github/actions/action-name/action.yml

@@ -0,0 +1,11 @@
+name: 'A composite action'
+description: 'Do something'
+runs:
+  using: "composite"
+  steps:
+    - name: Print
+      run: echo "Hello world"
+      shell: bash
+
+    - name: Checkout
+      uses: actions/checkout@v4

actions/ql/integration-tests/filters/src/.github/unreachable-workflow.yml

@@ -0,0 +1,12 @@
+name: An unreachable workflow
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  job:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4

actions/ql/integration-tests/filters/src/.github/workflows/workflow.yml

@@ -0,0 +1,12 @@
+name: A workflow
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  job:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4

actions/ql/integration-tests/filters/src/action.yml

@@ -0,0 +1,11 @@
+name: 'A composite action'
+description: 'Do something'
+runs:
+  using: "composite"
+  steps:
+    - name: Print
+      run: echo "Hello world"
+      shell: bash
+
+    - name: Checkout
+      uses: actions/checkout@v4

actions/ql/integration-tests/filters/src/excluded/action.yml

@@ -0,0 +1,11 @@
+name: 'A composite action'
+description: 'Do something'
+runs:
+  using: "composite"
+  steps:
+    - name: Print
+      run: echo "Hello world"
+      shell: bash
+
+    - name: Checkout
+      uses: actions/checkout@v4

actions/ql/integration-tests/filters/src/excluded/unreachable-workflow.yml

@@ -0,0 +1,12 @@
+name: An unreachable workflow
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  job:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4

actions/ql/integration-tests/filters/src/included/action.yml

@@ -0,0 +1,11 @@
+name: 'A composite action'
+description: 'Do something'
+runs:
+  using: "composite"
+  steps:
+    - name: Print
+      run: echo "Hello world"
+      shell: bash
+
+    - name: Checkout
+      uses: actions/checkout@v4

actions/ql/integration-tests/filters/src/included/not-an-action.yml

@@ -0,0 +1 @@
+name: 'Not an action, just a YAML file'

actions/ql/integration-tests/filters/src/included/unreachable-workflow.yml

@@ -0,0 +1,12 @@
+name: An unreachable workflow
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  job:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4

actions/ql/integration-tests/filters/src/unreachable-workflow.yml

@@ -0,0 +1,12 @@
+name: An unreachable workflow
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  job:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4

actions/ql/integration-tests/filters/test.py

@@ -0,0 +1,18 @@
+import pytest
+
+@pytest.mark.ql_test(expected=".default-filters.expected")
+def test_default_filters(codeql, actions, check_source_archive):
+    check_source_archive.expected_suffix = ".default-filters.expected"
+    codeql.database.create(source_root="src")
+
+@pytest.mark.ql_test(expected=".paths-only.expected")
+def test_config_paths_only(codeql, actions):
+    codeql.database.create(source_root="src", codescanning_config="codeql-config.paths-only.yml")
+
+@pytest.mark.ql_test(expected=".paths-ignore-only.expected")
+def test_config_paths_ignore_only(codeql, actions):
+    codeql.database.create(source_root="src", codescanning_config="codeql-config.paths-ignore-only.yml")
+
+@pytest.mark.ql_test(expected=".paths-and-paths-ignore.expected")
+def test_config_paths_and_paths_ignore(codeql, actions):
+    codeql.database.create(source_root="src", codescanning_config="codeql-config.paths-and-paths-ignore.yml")

actions/ql/integration-tests/query-suite/actions-code-quality-extended.qls.expected

@@ -0,0 +1 @@
+

actions/ql/integration-tests/query-suite/actions-code-quality.qls.expected

@@ -0,0 +1 @@
+

actions/ql/integration-tests/query-suite/actions-code-scanning.qls.expected

@@ -0,0 +1,17 @@
+ql/actions/ql/src/Security/CWE-077/EnvPathInjectionCritical.ql
+ql/actions/ql/src/Security/CWE-077/EnvVarInjectionCritical.ql
+ql/actions/ql/src/Security/CWE-094/CodeInjectionCritical.ql
+ql/actions/ql/src/Security/CWE-1395/UseOfKnownVulnerableAction.ql
+ql/actions/ql/src/Security/CWE-275/MissingActionsPermissions.ql
+ql/actions/ql/src/Security/CWE-285/ImproperAccessControl.ql
+ql/actions/ql/src/Security/CWE-312/ExcessiveSecretsExposure.ql
+ql/actions/ql/src/Security/CWE-312/SecretsInArtifacts.ql
+ql/actions/ql/src/Security/CWE-312/UnmaskedSecretExposure.ql
+ql/actions/ql/src/Security/CWE-349/CachePoisoningViaCodeInjection.ql
+ql/actions/ql/src/Security/CWE-349/CachePoisoningViaDirectCache.ql
+ql/actions/ql/src/Security/CWE-349/CachePoisoningViaPoisonableStep.ql
+ql/actions/ql/src/Security/CWE-367/UntrustedCheckoutTOCTOUCritical.ql
+ql/actions/ql/src/Security/CWE-367/UntrustedCheckoutTOCTOUHigh.ql
+ql/actions/ql/src/Security/CWE-829/ArtifactPoisoningCritical.ql
+ql/actions/ql/src/Security/CWE-829/UntrustedCheckoutCritical.ql
+ql/actions/ql/src/Security/CWE-829/UntrustedCheckoutHigh.ql

actions/ql/integration-tests/query-suite/actions-security-and-quality.qls.expected

@@ -0,0 +1,27 @@
+ql/actions/ql/src/Debug/SyntaxError.ql
+ql/actions/ql/src/Security/CWE-077/EnvPathInjectionCritical.ql
+ql/actions/ql/src/Security/CWE-077/EnvPathInjectionMedium.ql
+ql/actions/ql/src/Security/CWE-077/EnvVarInjectionCritical.ql
+ql/actions/ql/src/Security/CWE-077/EnvVarInjectionMedium.ql
+ql/actions/ql/src/Security/CWE-094/CodeInjectionCritical.ql
+ql/actions/ql/src/Security/CWE-094/CodeInjectionMedium.ql
+ql/actions/ql/src/Security/CWE-1395/UseOfKnownVulnerableAction.ql
+ql/actions/ql/src/Security/CWE-275/MissingActionsPermissions.ql
+ql/actions/ql/src/Security/CWE-285/ImproperAccessControl.ql
+ql/actions/ql/src/Security/CWE-312/ExcessiveSecretsExposure.ql
+ql/actions/ql/src/Security/CWE-312/SecretsInArtifacts.ql
+ql/actions/ql/src/Security/CWE-312/UnmaskedSecretExposure.ql
+ql/actions/ql/src/Security/CWE-349/CachePoisoningViaCodeInjection.ql
+ql/actions/ql/src/Security/CWE-349/CachePoisoningViaDirectCache.ql
+ql/actions/ql/src/Security/CWE-349/CachePoisoningViaPoisonableStep.ql
+ql/actions/ql/src/Security/CWE-367/UntrustedCheckoutTOCTOUCritical.ql
+ql/actions/ql/src/Security/CWE-367/UntrustedCheckoutTOCTOUHigh.ql
+ql/actions/ql/src/Security/CWE-571/ExpressionIsAlwaysTrueCritical.ql
+ql/actions/ql/src/Security/CWE-571/ExpressionIsAlwaysTrueHigh.ql
+ql/actions/ql/src/Security/CWE-829/ArtifactPoisoningCritical.ql
+ql/actions/ql/src/Security/CWE-829/ArtifactPoisoningMedium.ql
+ql/actions/ql/src/Security/CWE-829/UnpinnedActionsTag.ql
+ql/actions/ql/src/Security/CWE-829/UntrustedCheckoutCritical.ql
+ql/actions/ql/src/Security/CWE-829/UntrustedCheckoutHigh.ql
+ql/actions/ql/src/Security/CWE-829/UntrustedCheckoutMedium.ql
+ql/actions/ql/src/Violations Of Best Practice/CodeQL/UnnecessaryUseOfAdvancedConfig.ql

actions/ql/integration-tests/query-suite/actions-security-extended.qls.expected

@@ -0,0 +1,23 @@
+ql/actions/ql/src/Security/CWE-077/EnvPathInjectionCritical.ql
+ql/actions/ql/src/Security/CWE-077/EnvPathInjectionMedium.ql
+ql/actions/ql/src/Security/CWE-077/EnvVarInjectionCritical.ql
+ql/actions/ql/src/Security/CWE-077/EnvVarInjectionMedium.ql
+ql/actions/ql/src/Security/CWE-094/CodeInjectionCritical.ql
+ql/actions/ql/src/Security/CWE-094/CodeInjectionMedium.ql
+ql/actions/ql/src/Security/CWE-1395/UseOfKnownVulnerableAction.ql
+ql/actions/ql/src/Security/CWE-275/MissingActionsPermissions.ql
+ql/actions/ql/src/Security/CWE-285/ImproperAccessControl.ql
+ql/actions/ql/src/Security/CWE-312/ExcessiveSecretsExposure.ql
+ql/actions/ql/src/Security/CWE-312/SecretsInArtifacts.ql
+ql/actions/ql/src/Security/CWE-312/UnmaskedSecretExposure.ql
+ql/actions/ql/src/Security/CWE-349/CachePoisoningViaCodeInjection.ql
+ql/actions/ql/src/Security/CWE-349/CachePoisoningViaDirectCache.ql
+ql/actions/ql/src/Security/CWE-349/CachePoisoningViaPoisonableStep.ql
+ql/actions/ql/src/Security/CWE-367/UntrustedCheckoutTOCTOUCritical.ql
+ql/actions/ql/src/Security/CWE-367/UntrustedCheckoutTOCTOUHigh.ql
+ql/actions/ql/src/Security/CWE-829/ArtifactPoisoningCritical.ql
+ql/actions/ql/src/Security/CWE-829/ArtifactPoisoningMedium.ql
+ql/actions/ql/src/Security/CWE-829/UnpinnedActionsTag.ql
+ql/actions/ql/src/Security/CWE-829/UntrustedCheckoutCritical.ql
+ql/actions/ql/src/Security/CWE-829/UntrustedCheckoutHigh.ql
+ql/actions/ql/src/Security/CWE-829/UntrustedCheckoutMedium.ql

actions/ql/integration-tests/query-suite/not_included_in_qls.expected

@@ -0,0 +1,17 @@
+ql/actions/ql/src/Debug/partial.ql
+ql/actions/ql/src/Models/CompositeActionsSinks.ql
+ql/actions/ql/src/Models/CompositeActionsSources.ql
+ql/actions/ql/src/Models/CompositeActionsSummaries.ql
+ql/actions/ql/src/Models/ReusableWorkflowsSinks.ql
+ql/actions/ql/src/Models/ReusableWorkflowsSources.ql
+ql/actions/ql/src/Models/ReusableWorkflowsSummaries.ql
+ql/actions/ql/src/experimental/Security/CWE-074/OutputClobberingHigh.ql
+ql/actions/ql/src/experimental/Security/CWE-078/CommandInjectionCritical.ql
+ql/actions/ql/src/experimental/Security/CWE-078/CommandInjectionMedium.ql
+ql/actions/ql/src/experimental/Security/CWE-088/ArgumentInjectionCritical.ql
+ql/actions/ql/src/experimental/Security/CWE-088/ArgumentInjectionMedium.ql
+ql/actions/ql/src/experimental/Security/CWE-200/SecretExfiltration.ql
+ql/actions/ql/src/experimental/Security/CWE-284/CodeExecutionOnSelfHostedRunner.ql
+ql/actions/ql/src/experimental/Security/CWE-829/ArtifactPoisoningPathTraversal.ql
+ql/actions/ql/src/experimental/Security/CWE-829/UnversionedImmutableAction.ql
+ql/actions/ql/src/experimental/Security/CWE-918/RequestForgery.ql

actions/ql/integration-tests/query-suite/test.py

@@ -0,0 +1,14 @@
+import runs_on
+import pytest
+from query_suites import *
+
+well_known_query_suites = ['actions-code-quality.qls', 'actions-code-quality-extended.qls', 'actions-security-and-quality.qls', 'actions-security-extended.qls', 'actions-code-scanning.qls']
+
+@runs_on.posix
+@pytest.mark.parametrize("query_suite", well_known_query_suites)
+def test(codeql, actions, check_query_suite, query_suite):
+    check_query_suite(query_suite)
+
+@runs_on.posix
+def test_not_included_queries(codeql, actions, check_queries_not_included):
+    check_queries_not_included('actions', well_known_query_suites)

actions/ql/lib/CHANGELOG.md

@@ -1,3 +1,40 @@
+## 0.4.12
+
+### Minor Analysis Improvements
+
+* Fixed performance issues in the parsing of Bash scripts in workflow files,
+  which led to out-of-disk errors when analysing certain workflow files with
+  complex interpolations of shell commands or quoted strings.
+
+## 0.4.11
+
+No user-facing changes.
+
+## 0.4.10
+
+No user-facing changes.
+
+## 0.4.9
+
+No user-facing changes.
+
+## 0.4.8
+
+No user-facing changes.
+
+## 0.4.7
+
+### New Features
+
+* CodeQL and Copilot Autofix support for GitHub Actions is now Generally Available.
+
+## 0.4.6
+
+### Bug Fixes
+
+* The query `actions/code-injection/medium` now produces alerts for injection
+  vulnerabilities on `pull_request` events.
+
 ## 0.4.5
 
 No user-facing changes.

actions/ql/lib/change-notes/released/0.4.10.md

@@ -0,0 +1,3 @@
+## 0.4.10
+
+No user-facing changes.

actions/ql/lib/change-notes/released/0.4.11.md

@@ -0,0 +1,3 @@
+## 0.4.11
+
+No user-facing changes.

actions/ql/lib/change-notes/released/0.4.12.md

@@ -0,0 +1,7 @@
+## 0.4.12
+
+### Minor Analysis Improvements
+
+* Fixed performance issues in the parsing of Bash scripts in workflow files,
+  which led to out-of-disk errors when analysing certain workflow files with
+  complex interpolations of shell commands or quoted strings.

actions/ql/lib/change-notes/released/0.4.6.md

@@ -0,0 +1,6 @@
+## 0.4.6
+
+### Bug Fixes
+
+* The query `actions/code-injection/medium` now produces alerts for injection
+  vulnerabilities on `pull_request` events.

actions/ql/lib/change-notes/released/0.4.7.md

@@ -0,0 +1,5 @@
+## 0.4.7
+
+### New Features
+
+* CodeQL and Copilot Autofix support for GitHub Actions is now Generally Available.

actions/ql/lib/change-notes/released/0.4.8.md

@@ -0,0 +1,3 @@
+## 0.4.8
+
+No user-facing changes.

actions/ql/lib/change-notes/released/0.4.9.md

@@ -0,0 +1,3 @@
+## 0.4.9
+
+No user-facing changes.

actions/ql/lib/codeql-pack.release.yml

@@ -1,2 +1,2 @@
 ---
-lastReleaseVersion: 0.4.5
+lastReleaseVersion: 0.4.12

actions/ql/lib/codeql/actions/Ast.qll

@@ -50,8 +50,8 @@ class Expression extends AstNode instanceof ExpressionImpl {
   string getNormalizedExpression() { result = normalizeExpr(expression) }
 }
 
-/** A common class for `env` in workflow, job or step. */
-abstract class Env extends AstNode instanceof EnvImpl {
+/** An `env` in workflow, job or step. */
+class Env extends AstNode instanceof EnvImpl {
   /** Gets an environment variable value given its name. */
   ScalarValueImpl getEnvVarValue(string name) { result = super.getEnvVarValue(name) }
 

actions/ql/lib/codeql/actions/Bash.qll

@@ -8,35 +8,64 @@ class BashShellScript extends ShellScript {
     )
   }
 
-  private string lineProducer(int i) {
-    result = this.getRawScript().regexpReplaceAll("\\\\\\s*\n", "").splitAt("\n", i)
+  /**
+   * Gets the line at 0-based index `lineIndex` within this shell script,
+   * assuming newlines as separators.
+   */
+  private string lineProducer(int lineIndex) {
+    result = this.getRawScript().regexpReplaceAll("\\\\\\s*\n", "").splitAt("\n", lineIndex)
   }
 
-  private predicate cmdSubstitutionReplacement(string cmdSubs, string id, int k) {
-    exists(string line | line = this.lineProducer(k) |
-      exists(int i, int j |
-        cmdSubs =
-          // $() cmd substitution
-          line.regexpFind("\\$\\((?:[^()]+|\\((?:[^()]+|\\([^()]*\\))*\\))*\\)", i, j)
-              .regexpReplaceAll("^\\$\\(", "")
-              .regexpReplaceAll("\\)$", "") and
-        id = "cmdsubs:" + k + ":" + i + ":" + j
-      )
-      or
-      exists(int i, int j |
-        // `...` cmd substitution
-        cmdSubs =
-          line.regexpFind("\\`[^\\`]+\\`", i, j)
-              .regexpReplaceAll("^\\`", "")
-              .regexpReplaceAll("\\`$", "") and
-        id = "cmd:" + k + ":" + i + ":" + j
-      )
+  private predicate cmdSubstitutionReplacement(string command, string id, int lineIndex) {
+    this.commandInSubstitution(lineIndex, command, id)
+    or
+    this.commandInBackticks(lineIndex, command, id)
+  }
+
+  /**
+   * Holds if there is a command substitution `$(command)` in
+   * the line at `lineIndex` in the shell script,
+   * and `id` is a unique identifier for this command.
+   */
+  private predicate commandInSubstitution(int lineIndex, string command, string id) {
+    exists(int occurrenceIndex, int occurrenceOffset |
+      command =
+        // Look for the command inside a $(...) command substitution
+        this.lineProducer(lineIndex)
+            .regexpFind("\\$\\((?:[^()]+|\\((?:[^()]+|\\([^()]*\\))*\\))*\\)", occurrenceIndex,
+              occurrenceOffset)
+            // trim starting $( - TODO do this in first regex
+            .regexpReplaceAll("^\\$\\(", "")
+            // trim ending ) - TODO do this in first regex
+            .regexpReplaceAll("\\)$", "") and
+      id = "cmdsubs:" + lineIndex + ":" + occurrenceIndex + ":" + occurrenceOffset
     )
   }
 
-  private predicate rankedCmdSubstitutionReplacements(int i, string old, string new) {
-    old = rank[i](string old2 | this.cmdSubstitutionReplacement(old2, _, _) | old2) and
-    this.cmdSubstitutionReplacement(old, new, _)
+  /**
+   * Holds if `command` is a command in backticks `` `...` `` in
+   * the line at `lineIndex` in the shell script,
+   * and `id` is a unique identifier for this command.
+   */
+  private predicate commandInBackticks(int lineIndex, string command, string id) {
+    exists(int occurrenceIndex, int occurrenceOffset |
+      command =
+        this.lineProducer(lineIndex)
+            .regexpFind("\\`[^\\`]+\\`", occurrenceIndex, occurrenceOffset)
+            // trim leading backtick - TODO do this in first regex
+            .regexpReplaceAll("^\\`", "")
+            // trim trailing backtick - TODO do this in first regex
+            .regexpReplaceAll("\\`$", "") and
+      id = "cmd:" + lineIndex + ":" + occurrenceIndex + ":" + occurrenceOffset
+    )
+  }
+
+  private predicate rankedCmdSubstitutionReplacements(int i, string command, string commandId) {
+    // rank commands by their unique IDs
+    commandId = rank[i](string c, string id | this.cmdSubstitutionReplacement(c, id, _) | id) and
+    // since we cannot output (command, ID) tuples from the rank operation,
+    // we need to work out the specific command associated with the resulting ID
+    this.cmdSubstitutionReplacement(command, commandId, _)
   }
 
   private predicate doReplaceCmdSubstitutions(int line, int round, string old, string new) {
@@ -64,31 +93,56 @@ class BashShellScript extends ShellScript {
     this.cmdSubstitutionReplacement(result, _, i)
   }
 
+  /**
+   * Holds if `quotedStr` is a string in double quotes in
+   * the line at `lineIndex` in the shell script,
+   * and `id` is a unique identifier for this quoted string.
+   */
+  private predicate doubleQuotedString(int lineIndex, string quotedStr, string id) {
+    exists(int occurrenceIndex, int occurrenceOffset |
+      // double quoted string
+      quotedStr =
+        this.cmdSubstitutedLineProducer(lineIndex)
+            .regexpFind("\"((?:[^\"\\\\]|\\\\.)*)\"", occurrenceIndex, occurrenceOffset) and
+      id =
+        "qstr:" + lineIndex + ":" + occurrenceIndex + ":" + occurrenceOffset + ":" +
+          quotedStr.length() + ":" + quotedStr.regexpReplaceAll("[^a-zA-Z0-9]", "")
+    )
+  }
+
+  /**
+   * Holds if `quotedStr` is a string in single quotes in
+   * the line at `lineIndex` in the shell script,
+   * and `id` is a unique identifier for this quoted string.
+   */
+  private predicate singleQuotedString(int lineIndex, string quotedStr, string id) {
+    exists(int occurrenceIndex, int occurrenceOffset |
+      // single quoted string
+      quotedStr =
+        this.cmdSubstitutedLineProducer(lineIndex)
+            .regexpFind("'((?:\\\\.|[^'\\\\])*)'", occurrenceIndex, occurrenceOffset) and
+      id =
+        "qstr:" + lineIndex + ":" + occurrenceIndex + ":" + occurrenceOffset + ":" +
+          quotedStr.length() + ":" + quotedStr.regexpReplaceAll("[^a-zA-Z0-9]", "")
+    )
+  }
+
   private predicate quotedStringReplacement(string quotedStr, string id) {
-    exists(string line, int k | line = this.cmdSubstitutedLineProducer(k) |
-      exists(int i, int j |
-        // double quoted string
-        quotedStr = line.regexpFind("\"((?:[^\"\\\\]|\\\\.)*)\"", i, j) and
-        id =
-          "qstr:" + k + ":" + i + ":" + j + ":" + quotedStr.length() + ":" +
-            quotedStr.regexpReplaceAll("[^a-zA-Z0-9]", "")
-      )
+    exists(int lineIndex |
+      this.doubleQuotedString(lineIndex, quotedStr, id)
       or
-      exists(int i, int j |
-        // single quoted string
-        quotedStr = line.regexpFind("'((?:\\\\.|[^'\\\\])*)'", i, j) and
-        id =
-          "qstr:" + k + ":" + i + ":" + j + ":" + quotedStr.length() + ":" +
-            quotedStr.regexpReplaceAll("[^a-zA-Z0-9]", "")
-      )
+      this.singleQuotedString(lineIndex, quotedStr, id)
     ) and
     // Only do this for strings that might otherwise disrupt subsequent parsing
     quotedStr.regexpMatch("[\"'].*[$\n\r'\"" + Bash::separator() + "].*[\"']")
   }
 
-  private predicate rankedQuotedStringReplacements(int i, string old, string new) {
-    old = rank[i](string old2 | this.quotedStringReplacement(old2, _) | old2) and
-    this.quotedStringReplacement(old, new)
+  private predicate rankedQuotedStringReplacements(int i, string quotedString, string quotedStringId) {
+    // rank quoted strings by their nearly-unique IDs
+    quotedStringId = rank[i](string s, string id | this.quotedStringReplacement(s, id) | id) and
+    // since we cannot output (string, ID) tuples from the rank operation,
+    // we need to work out the specific string associated with the resulting ID
+    this.quotedStringReplacement(quotedString, quotedStringId)
   }
 
   private predicate doReplaceQuotedStrings(int line, int round, string old, string new) {

actions/ql/lib/codeql/actions/config/Config.qll

@@ -154,3 +154,13 @@ predicate untrustedGitCommandDataModel(string cmd_regex, string flag) {
 predicate untrustedGhCommandDataModel(string cmd_regex, string flag) {
   Extensions::untrustedGhCommandDataModel(cmd_regex, flag)
 }
+
+/**
+ * MaD models for permissions needed by actions
+ * Fields:
+ *    - action: action name, e.g. `actions/checkout`
+ *    - permission: permission name, e.g. `contents: read`
+ */
+predicate actionsPermissionsDataModel(string action, string permission) {
+  Extensions::actionsPermissionsDataModel(action, permission)
+}

actions/ql/lib/codeql/actions/config/ConfigExtensions.qll

@@ -77,3 +77,14 @@ extensible predicate untrustedGitCommandDataModel(string cmd_regex, string flag)
  * Holds for gh commands that may introduce untrusted data
  */
 extensible predicate untrustedGhCommandDataModel(string cmd_regex, string flag);
+
+/**
+ * Holds if `action` needs `permission` to run.
+ * - 'action' is the name of the action without any version information.
+ *   E.g. for the action selector `actions/checkout@v2`, `action` is `actions/checkout`.
+ * - `permission` is of the form `scope-name: read|write`, for example `contents: read`.
+ * - see https://github.com/actions/checkout?tab=readme-ov-file#recommended-permissions
+ *   for an example of recommended permissions.
+ * - see https://docs.github.com/en/actions/writing-workflows/choosing-what-your-workflow-does/controlling-permissions-for-github_token for documentation of token permissions.
+ */
+extensible predicate actionsPermissionsDataModel(string action, string permission);

actions/ql/lib/codeql/actions/security/OutputClobberingQuery.qll

@@ -214,6 +214,10 @@ private module OutputClobberingConfig implements DataFlow::ConfigSig {
       )
     )
   }
+
+  predicate observeDiffInformedIncrementalMode() { any() }
+
+  Location getASelectedSourceLocation(DataFlow::Node sink) { none() }
 }
 
 /** Tracks flow of unsafe user input that is used to construct and evaluate an environment variable. */

actions/ql/lib/codeql/actions/security/RequestForgeryQuery.qll

@@ -16,6 +16,10 @@ private module RequestForgeryConfig implements DataFlow::ConfigSig {
   predicate isSource(DataFlow::Node source) { source instanceof RemoteFlowSource }
 
   predicate isSink(DataFlow::Node sink) { sink instanceof RequestForgerySink }
+
+  predicate observeDiffInformedIncrementalMode() { any() }
+
+  Location getASelectedSourceLocation(DataFlow::Node sink) { none() }
 }
 
 /** Tracks flow of unsafe user input that is used to construct and evaluate a system command. */

actions/ql/lib/codeql/actions/security/SecretExfiltrationQuery.qll

@@ -15,6 +15,10 @@ private module SecretExfiltrationConfig implements DataFlow::ConfigSig {
   predicate isSource(DataFlow::Node source) { source instanceof RemoteFlowSource }
 
   predicate isSink(DataFlow::Node sink) { sink instanceof SecretExfiltrationSink }
+
+  predicate observeDiffInformedIncrementalMode() { any() }
+
+  Location getASelectedSourceLocation(DataFlow::Node sink) { none() }
 }
 
 /** Tracks flow of unsafe user input that is used in a context where it may lead to a secret exfiltration. */

actions/ql/lib/ext/config/actions_permissions.yml

@@ -0,0 +1,42 @@
+extensions:
+  - addsTo:
+      pack: codeql/actions-all
+      extensible: actionsPermissionsDataModel
+    data:
+      - ["actions/checkout", "contents: read"]
+      - ["actions/setup-node", "contents: read"]
+      - ["actions/setup-python", "contents: read"]
+      - ["actions/setup-java", "contents: read"]
+      - ["actions/setup-go", "contents: read"]
+      - ["actions/setup-dotnet", "contents: read"]
+      - ["actions/labeler", "contents: read"]
+      - ["actions/labeler", "pull-requests: write"]
+      - ["actions/attest", "id-token: write"]
+      - ["actions/attest", "attestations: write"]
+      # No permissions needed for actions/add-to-project
+      - ["actions/dependency-review-action", "contents: read"]
+      - ["actions/attest-sbom", "id-token: write"]
+      - ["actions/attest-sbom", "attestations: write"]
+      - ["actions/stale", "contents: write"]
+      - ["actions/stale", "issues: write"]
+      - ["actions/stale", "pull-requests: write"]
+      - ["actions/attest-build-provenance", "id-token: write"]
+      - ["actions/attest-build-provenance", "attestations: write"]
+      - ["actions/deploy-pages", "pages: write"]
+      - ["actions/deploy-pages", "id-token: write"]
+      - ["actions/delete-package-versions", "packages: write"]
+      - ["actions/jekyll-build-pages", "contents: read"]
+      - ["actions/jekyll-build-pages", "pages: write"]
+      - ["actions/jekyll-build-pages", "id-token: write"]
+      - ["actions/publish-action", "contents: write"]
+      - ["actions/versions-package-tools", "contents: read"]
+      - ["actions/versions-package-tools", "actions: read"]
+      - ["actions/reusable-workflows", "contents: read"]
+      - ["actions/reusable-workflows", "actions: read"]
+      - ["actions/ai-inference", "contents: read"]
+      - ["actions/ai-inference", "models: read"]
+      # TODO: Add permissions for actions/download-artifact
+      # TODO: Add permissions for actions/upload-artifact
+      # No permissions needed for actions/upload-pages-artifact
+      # TODO: Add permissions for actions/cache
+      # No permissions needed for actions/configure-pages

actions/ql/lib/ext/config/context_event_map.yml

@@ -30,6 +30,9 @@ extensions:
       - ["pull_request_review_comment", "github.event.review"] 
       - ["pull_request_review_comment", "github.head_ref"] 
       - ["pull_request_review_comment", "github.event.changes"] 
+      - ["pull_request", "github.event.pull_request"] 
+      - ["pull_request", "github.head_ref"] 
+      - ["pull_request", "github.event.changes"] 
       - ["pull_request_target", "github.event.pull_request"] 
       - ["pull_request_target", "github.head_ref"] 
       - ["pull_request_target", "github.event.changes"] 

actions/ql/lib/ext/config/externally_triggereable_events.yml

@@ -12,6 +12,7 @@ extensions:
       - ["pull_request_comment"]
       - ["pull_request_review"]
       - ["pull_request_review_comment"]
+      - ["pull_request"]
       - ["pull_request_target"]
       - ["workflow_run"] # depending on branch filter
       - ["workflow_call"] # depending on caller

actions/ql/lib/qlpack.yml

@@ -1,5 +1,5 @@
 name: codeql/actions-all
-version: 0.4.5
+version: 0.4.13-dev
 library: true
 warnOnImplicitThis: true
 dependencies:

actions/ql/src/CHANGELOG.md

@@ -1,3 +1,59 @@
+## 0.6.4
+
+No user-facing changes.
+
+## 0.6.3
+
+No user-facing changes.
+
+## 0.6.2
+
+### Minor Analysis Improvements
+
+* The query `actions/missing-workflow-permissions` is now aware of the minimal permissions needed for the actions `deploy-pages`, `delete-package-versions`, `ai-inference`. This should lead to better alert messages and better fix suggestions.
+
+## 0.6.1
+
+No user-facing changes.
+
+## 0.6.0
+
+### Breaking Changes
+
+* The following queries have been removed from the `security-and-quality` suite.
+  They are not intended to produce user-facing
+  alerts describing vulnerabilities.
+  Any existing alerts for these queries will be closed automatically.
+  * `actions/composite-action-sinks`
+  * `actions/composite-action-sources`
+  * `actions/composite-action-summaries`
+  * `actions/reusable-workflow-sinks`
+    (renamed from `actions/reusable-wokflow-sinks`)
+  * `actions/reusable-workflow-sources`
+  * `actions/reusable-workflow-summaries`
+
+### Bug Fixes
+
+* Assigned a `security-severity` to the query `actions/excessive-secrets-exposure`.
+
+## 0.5.4
+
+### New Features
+
+* CodeQL and Copilot Autofix support for GitHub Actions is now Generally Available.
+
+### Bug Fixes
+
+* Alerts produced by the query `actions/missing-workflow-permissions` now include a minimal set of recommended permissions in the alert message, based on well-known actions seen within the workflow file.
+
+## 0.5.3
+
+### Bug Fixes
+
+* Fixed typos in the query and alert titles for the queries
+  `actions/envpath-injection/critical`, `actions/envpath-injection/medium`,
+  `actions/envvar-injection/critical`, and `actions/envvar-injection/medium`.
+
 ## 0.5.2
 
 No user-facing changes.
@@ -7,9 +63,10 @@ No user-facing changes.
 ### Bug Fixes
 
 * The `actions/unversioned-immutable-action` query will no longer report any alerts, since the
-  Immutable Actions feature is not yet available for customer use. The query remains in the
-  default Code Scanning suites for use internal to GitHub. Once the Immutable Actions feature is
-  available, the query will be updated to report alerts again.
+  Immutable Actions feature is not yet available for customer use. The query has also been moved
+  to the experimental folder and will not be used in code scanning unless it is explicitly added
+  to a code scanning configuration. Once the Immutable Actions feature is available, the query will
+  be updated to report alerts again.
 
 ## 0.5.0
 

actions/ql/src/Models/CompositeActionsSinks.ql

@@ -24,6 +24,10 @@ private module MyConfig implements DataFlow::ConfigSig {
   predicate isSink(DataFlow::Node sink) {
     sink instanceof CodeInjectionSink and not madSink(sink, "code-injection")
   }
+
+  predicate observeDiffInformedIncrementalMode() { any() }
+
+  Location getASelectedSourceLocation(DataFlow::Node sink) { none() }
 }
 
 module MyFlow = TaintTracking::Global<MyConfig>;

actions/ql/src/Models/CompositeActionsSources.ql

@@ -34,6 +34,10 @@ private module MyConfig implements DataFlow::ConfigSig {
     isSink(node) and
     set instanceof DataFlow::FieldContent
   }
+
+  predicate observeDiffInformedIncrementalMode() { any() }
+
+  Location getASelectedSourceLocation(DataFlow::Node sink) { none() }
 }
 
 module MyFlow = TaintTracking::Global<MyConfig>;

actions/ql/src/Models/CompositeActionsSummaries.ql

@@ -25,6 +25,10 @@ private module MyConfig implements DataFlow::ConfigSig {
   predicate isSink(DataFlow::Node sink) {
     exists(CompositeAction c | c.getAnOutputExpr() = sink.asExpr())
   }
+
+  predicate observeDiffInformedIncrementalMode() { any() }
+
+  Location getASelectedSourceLocation(DataFlow::Node sink) { none() }
 }
 
 module MyFlow = TaintTracking::Global<MyConfig>;

actions/ql/src/Models/ReusableWorkflowsSinks.ql

@@ -5,7 +5,7 @@
  * @problem.severity warning
  * @security-severity 9.3
  * @precision high
- * @id actions/reusable-wokflow-sinks
+ * @id actions/reusable-workflow-sinks
  * @tags actions
  *       model-generator
  *       external/cwe/cwe-020
@@ -24,6 +24,10 @@ private module MyConfig implements DataFlow::ConfigSig {
   predicate isSink(DataFlow::Node sink) {
     sink instanceof CodeInjectionSink and not madSink(sink, "code-injection")
   }
+
+  predicate observeDiffInformedIncrementalMode() { any() }
+
+  Location getASelectedSourceLocation(DataFlow::Node sink) { none() }
 }
 
 module MyFlow = TaintTracking::Global<MyConfig>;

actions/ql/src/Models/ReusableWorkflowsSources.ql

@@ -34,6 +34,10 @@ private module MyConfig implements DataFlow::ConfigSig {
     isSink(node) and
     set instanceof DataFlow::FieldContent
   }
+
+  predicate observeDiffInformedIncrementalMode() { any() }
+
+  Location getASelectedSourceLocation(DataFlow::Node sink) { none() }
 }
 
 module MyFlow = TaintTracking::Global<MyConfig>;

actions/ql/src/Models/ReusableWorkflowsSummaries.ql

@@ -25,6 +25,10 @@ private module MyConfig implements DataFlow::ConfigSig {
   predicate isSink(DataFlow::Node sink) {
     exists(ReusableWorkflow w | w.getAnOutputExpr() = sink.asExpr())
   }
+
+  predicate observeDiffInformedIncrementalMode() { any() }
+
+  Location getASelectedSourceLocation(DataFlow::Node sink) { none() }
 }
 
 module MyFlow = TaintTracking::Global<MyConfig>;

actions/ql/src/Security/CWE-077/EnvPathInjectionCritical.md

@@ -1,6 +1,4 @@
-# Environment Path Injection
-
-## Description
+## Overview
 
 GitHub Actions allow to define the system PATH variable by writing to a file pointed to by the `GITHUB_PATH` environment variable. Writing to this file appends a directory to the system PATH variable and automatically makes it available to all subsequent actions in the current job.
 
@@ -12,11 +10,11 @@ echo "$HOME/.local/bin" >> $GITHUB_PATH
 
 If an attacker can control the contents of the system PATH, they are able to influence what commands are run in subsequent steps of the same job.
 
-## Recommendations
+## Recommendation
 
 Do not allow untrusted data to influence the system PATH: Avoid using untrusted data sources (e.g., artifact content) to define the system PATH.
 
-## Examples
+## Example
 
 ### Incorrect Usage
 
@@ -36,4 +34,4 @@ If an attacker can manipulate the value being set, such as through artifact down
 
 ## References
 
-- [Workflow commands for GitHub Actions](https://docs.github.com/en/actions/writing-workflows/choosing-what-your-workflow-does/workflow-commands-for-github-actions)
+- GitHub Docs: [Workflow commands for GitHub Actions](https://docs.github.com/en/actions/writing-workflows/choosing-what-your-workflow-does/workflow-commands-for-github-actions).

actions/ql/src/Security/CWE-077/EnvPathInjectionCritical.ql

@@ -1,5 +1,5 @@
 /**
- * @name PATH Enviroment Variable built from user-controlled sources
+ * @name PATH environment variable built from user-controlled sources
  * @description Building the PATH environment variable from user-controlled sources may alter the execution of following system commands
  * @kind path-problem
  * @problem.severity error

actions/ql/src/Security/CWE-077/EnvPathInjectionMedium.md

@@ -1,6 +1,4 @@
-# Environment Path Injection
-
-## Description
+## Overview
 
 GitHub Actions allow to define the system PATH variable by writing to a file pointed to by the `GITHUB_PATH` environment variable. Writing to this file appends a directory to the system PATH variable and automatically makes it available to all subsequent actions in the current job.
 
@@ -12,11 +10,11 @@ echo "$HOME/.local/bin" >> $GITHUB_PATH
 
 If an attacker can control the contents of the system PATH, they are able to influence what commands are run in subsequent steps of the same job.
 
-## Recommendations
+## Recommendation
 
 Do not allow untrusted data to influence the system PATH: Avoid using untrusted data sources (e.g., artifact content) to define the system PATH.
 
-## Examples
+## Example
 
 ### Incorrect Usage
 
@@ -36,4 +34,4 @@ If an attacker can manipulate the value being set, such as through artifact down
 
 ## References
 
-- [Workflow commands for GitHub Actions](https://docs.github.com/en/actions/writing-workflows/choosing-what-your-workflow-does/workflow-commands-for-github-actions)
+- GitHub Docs: [Workflow commands for GitHub Actions](https://docs.github.com/en/actions/writing-workflows/choosing-what-your-workflow-does/workflow-commands-for-github-actions).

actions/ql/src/Security/CWE-077/EnvPathInjectionMedium.ql

@@ -1,5 +1,5 @@
 /**
- * @name PATH Enviroment Variable built from user-controlled sources
+ * @name PATH environment variable built from user-controlled sources
  * @description Building the PATH environment variable from user-controlled sources may alter the execution of following system commands
  * @kind path-problem
  * @problem.severity error

actions/ql/src/Security/CWE-077/EnvVarInjectionCritical.md

@@ -1,6 +1,4 @@
-# Environment Variable Injection
-
-## Description
+## Overview
 
 GitHub Actions allow to define environment variables by writing to a file pointed to by the `GITHUB_ENV` environment variable:
 
@@ -37,7 +35,7 @@ steps:
 
 If an attacker can control the values assigned to environment variables and there is no sanitization in place, the attacker will be able to inject additional variables by injecting new lines or `{delimiters}`.
 
-## Recommendations
+## Recommendation
 
 1. **Do not allow untrusted data to influence environment variables**:
 
@@ -64,7 +62,7 @@ If an attacker can control the values assigned to environment variables and ther
           } >> "$GITHUB_ENV"
     ```
 
-## Examples
+## Example
 
 ### Example of Vulnerability
 
@@ -113,5 +111,5 @@ An attacker is be able to run arbitrary code by injecting environment variables
 
 ## References
 
-- [Workflow commands for GitHub Actions](https://docs.github.com/en/actions/writing-workflows/choosing-what-your-workflow-does/workflow-commands-for-github-actions)
-- [GitHub Actions Exploitation: Repo Jacking and Environment Manipulation](https://www.synacktiv.com/publications/github-actions-exploitation-repo-jacking-and-environment-manipulation)
+- GitHub Docs: [Workflow commands for GitHub Actions](https://docs.github.com/en/actions/writing-workflows/choosing-what-your-workflow-does/workflow-commands-for-github-actions).
+- Synacktiv: [GitHub Actions Exploitation: Repo Jacking and Environment Manipulation](https://www.synacktiv.com/publications/github-actions-exploitation-repo-jacking-and-environment-manipulation).

actions/ql/src/Security/CWE-077/EnvVarInjectionCritical.ql

@@ -1,5 +1,5 @@
 /**
- * @name Enviroment Variable built from user-controlled sources
+ * @name Environment variable built from user-controlled sources
  * @description Building an environment variable from user-controlled sources may alter the execution of following system commands
  * @kind path-problem
  * @problem.severity error

actions/ql/src/Security/CWE-077/EnvVarInjectionMedium.md

@@ -1,6 +1,4 @@
-# Environment Variable Injection
-
-## Description
+## Overview
 
 GitHub Actions allow to define environment variables by writing to a file pointed to by the `GITHUB_ENV` environment variable:
 
@@ -37,7 +35,7 @@ steps:
 
 If an attacker can control the values assigned to environment variables and there is no sanitization in place, the attacker will be able to inject additional variables by injecting new lines or `{delimiters}`.
 
-## Recommendations
+## Recommendation
 
 1. **Do not allow untrusted data to influence environment variables**:
 
@@ -64,7 +62,7 @@ If an attacker can control the values assigned to environment variables and ther
           } >> "$GITHUB_ENV"
     ```
 
-## Examples
+## Example
 
 ### Example of Vulnerability
 
@@ -109,9 +107,9 @@ An attacker could craft a malicious artifact that writes dangerous environment v
 
 ### Exploitation
 
-An attacker is be able to run arbitrary code by injecting environment variables such as `LD_PRELOAD`, `BASH_ENV`, etc.
+An attacker would be able to run arbitrary code by injecting environment variables such as `LD_PRELOAD`, `BASH_ENV`, etc.
 
 ## References
 
-- [Workflow commands for GitHub Actions](https://docs.github.com/en/actions/writing-workflows/choosing-what-your-workflow-does/workflow-commands-for-github-actions)
-- [GitHub Actions Exploitation: Repo Jacking and Environment Manipulation](https://www.synacktiv.com/publications/github-actions-exploitation-repo-jacking-and-environment-manipulation)
+- GitHub Docs: [Workflow commands for GitHub Actions](https://docs.github.com/en/actions/writing-workflows/choosing-what-your-workflow-does/workflow-commands-for-github-actions).
+- Synacktiv: [GitHub Actions Exploitation: Repo Jacking and Environment Manipulation](https://www.synacktiv.com/publications/github-actions-exploitation-repo-jacking-and-environment-manipulation).

actions/ql/src/Security/CWE-077/EnvVarInjectionMedium.ql

@@ -1,5 +1,5 @@
 /**
- * @name Enviroment Variable built from user-controlled sources
+ * @name Environment variable built from user-controlled sources
  * @description Building an environment variable from user-controlled sources may alter the execution of following system commands
  * @kind path-problem
  * @problem.severity error

actions/ql/src/Security/CWE-094/CodeInjectionCritical.md

@@ -1,18 +1,16 @@
-# Code Injection in GitHub Actions
-
-## Description
+## Overview
 
 Using user-controlled input in GitHub Actions may lead to code injection in contexts like _run:_ or _script:_.
 
 Code injection in GitHub Actions may allow an attacker to exfiltrate any secrets used in the workflow and the temporary GitHub repository authorization token. The token may have write access to the repository, allowing an attacker to make changes to the repository.
 
-## Recommendations
+## Recommendation
 
 The best practice to avoid code injection vulnerabilities in GitHub workflows is to set the untrusted input value of the expression to an intermediate environment variable and then use the environment variable using the native syntax of the shell/script interpreter (that is, not _${{ env.VAR }}_).
 
 It is also recommended to limit the permissions of any tokens used by a workflow such as the GITHUB_TOKEN.
 
-## Examples
+## Example
 
 ### Incorrect Usage
 

actions/ql/src/Security/CWE-094/CodeInjectionMedium.md

@@ -1,18 +1,16 @@
-# Code Injection in GitHub Actions
-
-## Description
+## Overview
 
 Using user-controlled input in GitHub Actions may lead to code injection in contexts like _run:_ or _script:_.
 
 Code injection in GitHub Actions may allow an attacker to exfiltrate any secrets used in the workflow and the temporary GitHub repository authorization token. The token may have write access to the repository, allowing an attacker to make changes to the repository.
 
-## Recommendations
+## Recommendation
 
 The best practice to avoid code injection vulnerabilities in GitHub workflows is to set the untrusted input value of the expression to an intermediate environment variable and then use the environment variable using the native syntax of the shell/script interpreter (that is, not _${{ env.VAR }}_).
 
 It is also recommended to limit the permissions of any tokens used by a workflow such as the GITHUB_TOKEN.
 
-## Examples
+## Example
 
 ### Incorrect Usage