set compileForOverlayEval true for java

Release preparation for version 2.21.3

.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/workflows/build-ripunzip.yml

@@ -17,7 +17,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-20.04, macos-13, windows-2019]
+        os: [ubuntu-22.04, macos-13, windows-2019]
     runs-on: ${{ matrix.os }}
     steps:
       - uses: actions/checkout@v4

.github/workflows/codegen.yml

@@ -0,0 +1,34 @@
+name: Codegen
+
+on:
+  pull_request:
+    paths:
+      - "misc/bazel/**"
+      - "misc/codegen/**"
+      - "*.bazel*"
+      - .github/workflows/codegen.yml
+      - .pre-commit-config.yaml
+    branches:
+      - main
+      - rc/*
+      - codeql-cli-*
+
+permissions:
+  contents: read
+
+jobs:
+  codegen:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v4
+        with:
+          python-version-file: 'misc/codegen/.python-version'
+      - uses: pre-commit/action@646c83fcd040023954eafda54b4db0192ce70507
+        name: Check that python code is properly formatted
+        with:
+          extra_args: autopep8 --all-files
+      - name: Run codegen tests
+        shell: bash
+        run: |
+          bazel test //misc/codegen/...

.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/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/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 "${{ github.workspace }}" --check-databases --check-undefined-labels --check-unused-labels --check-repeated-labels --check-redefined-labels --check-use-before-definition --consistency-queries ql/consistency-queries ql/test --compilation-cache "${{ 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-13-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

.pre-commit-config.yaml

@@ -72,7 +72,7 @@ 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

@@ -14,4 +14,4 @@ members = [
 [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" }
+rustc_apfloat = { git = "https://github.com/redsun82/rustc_apfloat.git", rev = "32968f16ef1b082243f9bf43a3fbd65c381b3e27" }

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 = "1.85.0"
 
 rust = use_extension("@rules_rust//rust:extensions.bzl", "rust")
 rust.toolchain(
@@ -71,57 +71,59 @@ 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-1.0.97",
+    "vendor_ts__argfile-0.2.1",
+    "vendor_ts__chalk-ir-0.100.0",
+    "vendor_ts__chrono-0.4.40",
+    "vendor_ts__clap-4.5.35",
+    "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-1.16.0",
+    "vendor_ts__proc-macro2-1.0.94",
+    "vendor_ts__quote-1.0.40",
+    "vendor_ts__ra_ap_base_db-0.0.273",
+    "vendor_ts__ra_ap_cfg-0.0.273",
+    "vendor_ts__ra_ap_hir-0.0.273",
+    "vendor_ts__ra_ap_hir_def-0.0.273",
+    "vendor_ts__ra_ap_hir_expand-0.0.273",
+    "vendor_ts__ra_ap_hir_ty-0.0.273",
+    "vendor_ts__ra_ap_ide_db-0.0.273",
+    "vendor_ts__ra_ap_intern-0.0.273",
+    "vendor_ts__ra_ap_load-cargo-0.0.273",
+    "vendor_ts__ra_ap_parser-0.0.273",
+    "vendor_ts__ra_ap_paths-0.0.273",
+    "vendor_ts__ra_ap_project_model-0.0.273",
+    "vendor_ts__ra_ap_span-0.0.273",
+    "vendor_ts__ra_ap_stdx-0.0.273",
+    "vendor_ts__ra_ap_syntax-0.0.273",
+    "vendor_ts__ra_ap_vfs-0.0.273",
+    "vendor_ts__rand-0.9.0",
+    "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-3.12.0",
+    "vendor_ts__syn-2.0.100",
+    "vendor_ts__toml-0.8.20",
+    "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",
 )
 
 http_archive = use_repo_rule("@bazel_tools//tools/build_defs/repo:http.bzl", "http_archive")
@@ -153,7 +155,7 @@ 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 +193,6 @@ 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 +204,7 @@ 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 +216,7 @@ 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 +228,7 @@ 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")

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.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-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 +1,24 @@
+## 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/0.4.6.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: 0.4.9

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/ext/config/actions_permissions.yml

@@ -0,0 +1,37 @@
+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/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"]
+      # TODO: Add permissions for actions/download-artifact
+      # TODO: Add permissions for actions/upload-artifact
+      # TODO: Add permissions for actions/cache
+
+      

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: 0.4.9
 library: true
 warnOnImplicitThis: true
 dependencies:

actions/ql/src/CHANGELOG.md

@@ -1,3 +1,45 @@
+## 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 +49,10 @@ 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/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

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.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.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

@@ -109,7 +109,7 @@ 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
 

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-1395/UseOfKnownVulnerableAction.ql

@@ -1,5 +1,5 @@
 /**
- * @name Use of a known vulnerable action.
+ * @name Use of a known vulnerable action
  * @description The workflow is using an action with known vulnerabilities.
  * @kind problem
  * @problem.severity error

actions/ql/src/Security/CWE-275/MissingActionsPermissions.ql

@@ -1,6 +1,6 @@
 /**
  * @name Workflow does not contain permissions
- * @description Workflows should contain permissions to provide a clear understanding has permissions to run the workflow.
+ * @description Workflows should contain explicit permissions to restrict the scope of the default GITHUB_TOKEN.
  * @kind problem
  * @security-severity 5.0
  * @problem.severity warning
@@ -14,7 +14,19 @@
 
 import actions
 
-from Job job
+Step stepInJob(Job job) { result = job.(LocalJob).getAStep() }
+
+string jobNeedsPermission(Job job) {
+  actionsPermissionsDataModel(stepInJob(job).(UsesStep).getCallee(), result)
+}
+
+/** Gets a suggestion for the minimal token permissions for `job`, as a JSON string. */
+string permissionsForJob(Job job) {
+  result =
+    "{" + concat(string permission | permission = jobNeedsPermission(job) | permission, ", ") + "}"
+}
+
+from Job job, string permissions
 where
   not exists(job.getPermissions()) and
   not exists(job.getEnclosingWorkflow().getPermissions()) and
@@ -22,5 +34,8 @@ where
   exists(Event e |
     e = job.getATriggerEvent() and
     not e.getName() = "workflow_call"
-  )
-select job, "Actions Job or Workflow does not set permissions"
+  ) and
+  permissions = permissionsForJob(job)
+select job,
+  "Actions job or workflow does not limit the permissions of the GITHUB_TOKEN. Consider setting an explicit permissions block, using the following as a minimal starting point: "
+    + permissions

actions/ql/src/Security/CWE-312/ExcessiveSecretsExposure.ql

@@ -3,6 +3,7 @@
  * @description All organization and repository secrets are passed to the workflow runner.
  * @kind problem
  * @precision high
+ * @security-severity 5.0
  * @problem.severity warning
  * @id actions/excessive-secrets-exposure
  * @tags actions

actions/ql/src/Security/CWE-312/UnmaskedSecretExposure.md

@@ -2,11 +2,11 @@
 
 ## Description
 
-Secrets derived from other secrets are not know to the workflow runner and therefore not masked unless explicitly registered.
+Secrets derived from other secrets are not known to the workflow runner, and therefore are not masked unless explicitly registered.
 
 ## Recommendations
 
-Avoid defining non-plain secrets. For example, do not define a new secret containing a JSON object and then read properties out of it from the workflow since these read values will not be masked by the workflow runner.
+Avoid defining non-plain secrets. For example, do not define a new secret containing a JSON object and then read properties out of it from the workflow, since these read values will not be masked by the workflow runner.
 
 ## Examples
 

actions/ql/src/Security/CWE-829/ArtifactPoisoningCritical.md

@@ -43,7 +43,7 @@ jobs:
 The following example, correctly creates a temporary directory and extracts the contents of the artifact there before calling `cmd.sh`.
 
 ```yaml
-name: Insecure Workflow
+name: Secure Workflow
 
 on:
   workflow_run:

actions/ql/src/Security/CWE-829/ArtifactPoisoningMedium.md

@@ -43,7 +43,7 @@ jobs:
 The following example, correctly creates a temporary directory and extracts the contents of the artifact there before calling `cmd.sh`.
 
 ```yaml
-name: Insecure Workflow
+name: Secure Workflow
 
 on:
   workflow_run:

actions/ql/src/Security/CWE-829/UntrustedCheckoutCritical.ql

@@ -1,5 +1,5 @@
 /**
- * @name Checkout of untrusted code in trusted context
+ * @name Checkout of untrusted code in a privileged context
  * @description Privileged workflows have read/write access to the base repository and access to secrets.
  *              By explicitly checking out and running the build script from a fork the untrusted code is running in an environment
  *              that is able to push to the base repository and to access secrets.

actions/ql/src/change-notes/released/0.5.1.md

@@ -3,6 +3,7 @@
 ### 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.

actions/ql/src/change-notes/released/0.5.3.md

@@ -0,0 +1,7 @@
+## 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`.

actions/ql/src/change-notes/released/0.5.4.md

@@ -0,0 +1,9 @@
+## 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.

actions/ql/src/change-notes/released/0.6.0.md

@@ -0,0 +1,19 @@
+## 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`.

actions/ql/src/change-notes/released/0.6.1.md

@@ -0,0 +1,3 @@
+## 0.6.1
+
+No user-facing changes.

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

@@ -1,2 +1,2 @@
 ---
-lastReleaseVersion: 0.5.2
+lastReleaseVersion: 0.6.1

actions/ql/src/codeql-suites/actions-ccr.qls

@@ -1 +0,0 @@
-[]

actions/ql/src/codeql-suites/actions-code-quality.qls

@@ -0,0 +1,3 @@
+- queries: .
+- apply: code-quality-selectors.yml
+  from: codeql/suite-helpers

actions/ql/src/codeql-suites/actions-security-and-quality.qls

@@ -1,2 +1,4 @@
 - description: Security-and-quality queries for GitHub Actions
-- import: codeql-suites/actions-security-extended.qls
+- queries: .
+- apply: security-and-quality-selectors.yml
+  from: codeql/suite-helpers

actions/ql/src/codeql-suites/actions-security-experimental.qls

@@ -1,2 +1,4 @@
 - description: Extended and experimental security queries for GitHub Actions
-- import: codeql-suites/actions-code-scanning.qls
+- queries: .
+- apply: security-experimental-selectors.yml
+  from: codeql/suite-helpers

actions/ql/src/experimental/Security/CWE-829/UnversionedImmutableAction.ql

@@ -8,6 +8,7 @@
  * @tags security
  *       actions
  *       internal
+ *       experimental
  *       external/cwe/cwe-829
  */
 

actions/ql/src/qlpack.yml

@@ -1,5 +1,5 @@
 name: codeql/actions-queries
-version: 0.5.2
+version: 0.6.1
 library: false
 warnOnImplicitThis: true
 groups: [actions, queries]
@@ -8,3 +8,4 @@ extractor: actions
 defaultSuiteFile: codeql-suites/actions-code-scanning.qls
 dependencies:
   codeql/actions-all: ${workspace}
+  codeql/suite-helpers: ${workspace}

actions/ql/test/query-tests/Security/CWE-094/CodeInjectionCritical.expected

@@ -400,6 +400,7 @@ nodes
 | .github/workflows/level0.yml:44:20:44:49 | github.event.issue.body | semmle.label | github.event.issue.body |
 | .github/workflows/level0.yml:69:35:69:66 | github.event.comment.body | semmle.label | github.event.comment.body |
 | .github/workflows/level1.yml:37:38:37:81 | github.event.workflow_run.head_branch | semmle.label | github.event.workflow_run.head_branch |
+| .github/workflows/priv_pull_request.yml:14:21:14:57 | github.event.pull_request.body | semmle.label | github.event.pull_request.body |
 | .github/workflows/pull_request_review.yml:7:19:7:56 | github.event.pull_request.title | semmle.label | github.event.pull_request.title |
 | .github/workflows/pull_request_review.yml:8:19:8:55 | github.event.pull_request.body | semmle.label | github.event.pull_request.body |
 | .github/workflows/pull_request_review.yml:9:19:9:61 | github.event.pull_request.head.label | semmle.label | github.event.pull_request.head.label |
@@ -629,6 +630,7 @@ nodes
 | .github/workflows/test19.yml:124:9:129:6 | Run Step: title3 [title] | semmle.label | Run Step: title3 [title] |
 | .github/workflows/test19.yml:125:14:128:50 | TITLE=$(gh issue view "$ISSUE_NUMBER" --json title,author)\nTITLE=$(echo $TITLE \| jq -r '.title')\necho "title=$TITLE" >> "$GITHUB_OUTPUT"\n | semmle.label | TITLE=$(gh issue view "$ISSUE_NUMBER" --json title,author)\nTITLE=$(echo $TITLE \| jq -r '.title')\necho "title=$TITLE" >> "$GITHUB_OUTPUT"\n |
 | .github/workflows/test19.yml:129:21:129:52 | steps.title3.outputs.title | semmle.label | steps.title3.outputs.title |
+| .github/workflows/test20.yml:15:54:15:94 | github.event.pull_request.head.ref | semmle.label | github.event.pull_request.head.ref |
 | .github/workflows/test21.yml:22:35:22:73 | github.event.head_commit.message | semmle.label | github.event.head_commit.message |
 | .github/workflows/test21.yml:23:36:23:74 | github.event.head_commit.message | semmle.label | github.event.head_commit.message |
 | .github/workflows/test21.yml:24:50:24:88 | github.event.head_commit.message | semmle.label | github.event.head_commit.message |

actions/ql/test/query-tests/Security/CWE-094/CodeInjectionMedium.expected

@@ -400,6 +400,7 @@ nodes
 | .github/workflows/level0.yml:44:20:44:49 | github.event.issue.body | semmle.label | github.event.issue.body |
 | .github/workflows/level0.yml:69:35:69:66 | github.event.comment.body | semmle.label | github.event.comment.body |
 | .github/workflows/level1.yml:37:38:37:81 | github.event.workflow_run.head_branch | semmle.label | github.event.workflow_run.head_branch |
+| .github/workflows/priv_pull_request.yml:14:21:14:57 | github.event.pull_request.body | semmle.label | github.event.pull_request.body |
 | .github/workflows/pull_request_review.yml:7:19:7:56 | github.event.pull_request.title | semmle.label | github.event.pull_request.title |
 | .github/workflows/pull_request_review.yml:8:19:8:55 | github.event.pull_request.body | semmle.label | github.event.pull_request.body |
 | .github/workflows/pull_request_review.yml:9:19:9:61 | github.event.pull_request.head.label | semmle.label | github.event.pull_request.head.label |
@@ -629,6 +630,7 @@ nodes
 | .github/workflows/test19.yml:124:9:129:6 | Run Step: title3 [title] | semmle.label | Run Step: title3 [title] |
 | .github/workflows/test19.yml:125:14:128:50 | TITLE=$(gh issue view "$ISSUE_NUMBER" --json title,author)\nTITLE=$(echo $TITLE \| jq -r '.title')\necho "title=$TITLE" >> "$GITHUB_OUTPUT"\n | semmle.label | TITLE=$(gh issue view "$ISSUE_NUMBER" --json title,author)\nTITLE=$(echo $TITLE \| jq -r '.title')\necho "title=$TITLE" >> "$GITHUB_OUTPUT"\n |
 | .github/workflows/test19.yml:129:21:129:52 | steps.title3.outputs.title | semmle.label | steps.title3.outputs.title |
+| .github/workflows/test20.yml:15:54:15:94 | github.event.pull_request.head.ref | semmle.label | github.event.pull_request.head.ref |
 | .github/workflows/test21.yml:22:35:22:73 | github.event.head_commit.message | semmle.label | github.event.head_commit.message |
 | .github/workflows/test21.yml:23:36:23:74 | github.event.head_commit.message | semmle.label | github.event.head_commit.message |
 | .github/workflows/test21.yml:24:50:24:88 | github.event.head_commit.message | semmle.label | github.event.head_commit.message |
@@ -706,6 +708,7 @@ subpaths
 | .github/workflows/inter-job2.yml:45:20:45:53 | needs.job1.outputs.job_output | .github/workflows/inter-job2.yml:22:9:26:6 | Uses Step: source | .github/workflows/inter-job2.yml:45:20:45:53 | needs.job1.outputs.job_output | Potential code injection in $@, which may be controlled by an external user. | .github/workflows/inter-job2.yml:45:20:45:53 | needs.job1.outputs.job_output | ${{needs.job1.outputs.job_output}} |
 | .github/workflows/inter-job4.yml:44:20:44:53 | needs.job1.outputs.job_output | .github/workflows/inter-job4.yml:22:9:26:6 | Uses Step: source | .github/workflows/inter-job4.yml:44:20:44:53 | needs.job1.outputs.job_output | Potential code injection in $@, which may be controlled by an external user. | .github/workflows/inter-job4.yml:44:20:44:53 | needs.job1.outputs.job_output | ${{needs.job1.outputs.job_output}} |
 | .github/workflows/inter-job5.yml:45:20:45:53 | needs.job1.outputs.job_output | .github/workflows/inter-job5.yml:45:20:45:53 | needs.job1.outputs.job_output | .github/workflows/inter-job5.yml:45:20:45:53 | needs.job1.outputs.job_output | Potential code injection in $@, which may be controlled by an external user. | .github/workflows/inter-job5.yml:45:20:45:53 | needs.job1.outputs.job_output | ${{needs.job1.outputs.job_output}} |
+| .github/workflows/priv_pull_request.yml:14:21:14:57 | github.event.pull_request.body | .github/workflows/priv_pull_request.yml:14:21:14:57 | github.event.pull_request.body | .github/workflows/priv_pull_request.yml:14:21:14:57 | github.event.pull_request.body | Potential code injection in $@, which may be controlled by an external user. | .github/workflows/priv_pull_request.yml:14:21:14:57 | github.event.pull_request.body | ${{ github.event.pull_request.body }} |
 | .github/workflows/push.yml:7:19:7:57 | github.event.commits[11].message | .github/workflows/push.yml:7:19:7:57 | github.event.commits[11].message | .github/workflows/push.yml:7:19:7:57 | github.event.commits[11].message | Potential code injection in $@, which may be controlled by an external user. | .github/workflows/push.yml:7:19:7:57 | github.event.commits[11].message | ${{ github.event.commits[11].message }} |
 | .github/workflows/push.yml:8:19:8:62 | github.event.commits[11].author.email | .github/workflows/push.yml:8:19:8:62 | github.event.commits[11].author.email | .github/workflows/push.yml:8:19:8:62 | github.event.commits[11].author.email | Potential code injection in $@, which may be controlled by an external user. | .github/workflows/push.yml:8:19:8:62 | github.event.commits[11].author.email | ${{ github.event.commits[11].author.email }} |
 | .github/workflows/push.yml:9:19:9:61 | github.event.commits[11].author.name | .github/workflows/push.yml:9:19:9:61 | github.event.commits[11].author.name | .github/workflows/push.yml:9:19:9:61 | github.event.commits[11].author.name | Potential code injection in $@, which may be controlled by an external user. | .github/workflows/push.yml:9:19:9:61 | github.event.commits[11].author.name | ${{ github.event.commits[11].author.name }} |

actions/ql/test/query-tests/Security/CWE-275/.github/workflows/perms6.yml

@@ -0,0 +1,13 @@
+on:
+  workflow_call:
+  workflow_dispatch:
+
+jobs:
+  build:
+    name: Build and test
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - uses: actions/jekyll-build-pages
+
+

actions/ql/test/query-tests/Security/CWE-275/.github/workflows/perms7.yml

@@ -0,0 +1,10 @@
+on:
+  workflow_call:
+  workflow_dispatch:
+
+jobs:
+  build:
+    name: Build and test
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/add-to-project@v2

actions/ql/test/query-tests/Security/CWE-275/MissingActionsPermissions.expected

@@ -1,3 +1,5 @@
-| .github/workflows/perms1.yml:6:5:9:32 | Job: build | Actions Job or Workflow does not set permissions |
-| .github/workflows/perms2.yml:6:5:10:2 | Job: build | Actions Job or Workflow does not set permissions |
-| .github/workflows/perms5.yml:7:5:10:32 | Job: build | Actions Job or Workflow does not set permissions |
+| .github/workflows/perms1.yml:6:5:9:32 | Job: build | Actions job or workflow does not limit the permissions of the GITHUB_TOKEN. Consider setting an explicit permissions block, using the following as a minimal starting point: {contents: read} |
+| .github/workflows/perms2.yml:6:5:10:2 | Job: build | Actions job or workflow does not limit the permissions of the GITHUB_TOKEN. Consider setting an explicit permissions block, using the following as a minimal starting point: {contents: read} |
+| .github/workflows/perms5.yml:7:5:10:32 | Job: build | Actions job or workflow does not limit the permissions of the GITHUB_TOKEN. Consider setting an explicit permissions block, using the following as a minimal starting point: {contents: read} |
+| .github/workflows/perms6.yml:7:5:11:39 | Job: build | Actions job or workflow does not limit the permissions of the GITHUB_TOKEN. Consider setting an explicit permissions block, using the following as a minimal starting point: {contents: read, id-token: write, pages: write} |
+| .github/workflows/perms7.yml:7:5:10:38 | Job: build | Actions job or workflow does not limit the permissions of the GITHUB_TOKEN. Consider setting an explicit permissions block, using the following as a minimal starting point: {} |

actions/ql/test/query-tests/Security/CWE-829/UnversionedImmutableAction.qlref

@@ -1 +1 @@
-Security/CWE-829/UnversionedImmutableAction.ql
+experimental/Security/CWE-829/UnversionedImmutableAction.ql

config/annotate-overlay-local.py

@@ -0,0 +1,175 @@
+# This script is used to annotate .qll files with overlay[local?] annotations.
+# It will walk the directory tree and annotate most .qll files, skipping only
+# some specific cases (e.g., empty files, files that configure dataflow for queries).
+# It will also add overlay[caller] annotations to predicates that are pragma[inline]
+# and either not private or in a hardcoded list of predicates.
+
+# The script takes a list of languages and processes the corresponding directories.
+
+# Usage: python3 annotate-overlay-local.py <language1> <language2> ...
+
+# The script will modify the files in place and print the changes made.
+# The script is designed to be run from the root of the repository.
+
+#!/usr/bin/python3
+import sys
+import os
+from difflib import *
+
+# These are the only two predicates that are pragma[inline], private, and must be
+# overlay[caller] in order to successfully compile our internal java queries.
+hardcoded_overlay_caller_preds = [
+    "fwdFlowInCand", "fwdFlowInCandTypeFlowDisabled"]
+
+
+def filter_out_annotations(filename):
+    '''
+    Read the file and strip all existing overlay[...] annotations from the contents.
+    Return the file modified file content as a list of lines.
+    '''
+    overlays = ["local", "local?", "global", "caller"]
+    annotations = [f"overlay[{t}]" for t in overlays]
+    with open(filename, 'r') as file_in:
+        lines = [l for l in file_in if not l.strip() in annotations]
+    for ann in annotations:
+        if any(line for line in lines if ann in line):
+            raise Exception(f"Failed to filter out {ann} from {filename}.")
+    return lines
+
+
+def insert_toplevel_maybe_local_anntotation(filename, lines):
+    '''
+    Find a suitable place to insert an overlay[local?] annotation at the top of the file.
+    Return a pair: (string describing action taken, modified content as list of lines).
+    '''
+    out_lines = []
+    status = 0
+
+    for line in lines:
+        if status == 0 and line.rstrip().endswith("module;"):
+            out_lines.append("overlay[local?]\n")
+            status = 1
+        out_lines.append(line)
+
+    if status == 1:
+        return (f"Annotating \"{filename}\" via existing file-level module statement", out_lines)
+
+    out_lines = []
+    empty_line_buffer = []
+    status = 0
+    for line in lines:
+        trimmed = line.strip()
+        if not trimmed:
+            empty_line_buffer.append(line)
+            continue
+        if status <= 1 and trimmed.endswith("*/"):
+            status = 2
+        elif status == 0 and trimmed.startswith("/**"):
+            status = 1
+        elif status == 0 and not trimmed.startswith("/*"):
+            out_lines.append("overlay[local?]\n")
+            out_lines.append("module;\n")
+            out_lines.append("\n")
+            status = 3
+        elif status == 2 and (trimmed.startswith("import ") or trimmed.startswith("private import ")):
+            out_lines.append("overlay[local?]\n")
+            out_lines.append("module;\n")
+            status = 3
+        elif status == 2 and (trimmed.startswith("class ") or trimmed.startswith("predicate ")
+                              or trimmed.startswith("module ") or trimmed.startswith("signature ")):
+            out_lines = ["overlay[local?]\n", "module;\n", "\n"] + out_lines
+            status = 3
+        elif status == 2 and trimmed.startswith("/*"):
+            out_lines.append("overlay[local?]\n")
+            out_lines.append("module;\n")
+            status = 3
+        elif status == 2:
+            status = 4
+        if empty_line_buffer:
+            out_lines += empty_line_buffer
+            empty_line_buffer = []
+        out_lines.append(line)
+    if status == 3:
+        out_lines += empty_line_buffer
+
+    if status == 3:
+        return (f"Annotating \"{filename}\" after file-level module qldoc", out_lines)
+
+    raise Exception(f"Failed to annotate \"{filename}\" as overlay[local?].")
+
+
+def insert_overlay_caller_annotations(lines):
+    '''
+    Mark pragma[inline] predicates as overlay[caller] if they are not declared private
+    or if they are private but are in the list of hardcoded_overlay_caller_preds.
+    '''
+    out_lines = []
+    for i, line in enumerate(lines):
+        trimmed = line.strip()
+        if trimmed == "pragma[inline]":
+            if (not "private" in lines[i+1] or
+                    any(pred in lines[i+1] for pred in hardcoded_overlay_caller_preds)):
+                whitespace = line[0: line.find(trimmed)]
+                out_lines.append(f"{whitespace}overlay[caller]\n")
+        out_lines.append(line)
+    return out_lines
+
+
+def annotate_as_appropriate(filename):
+    '''
+    Read file and strip all existing overlay[...] annotations from the contents;
+    then insert new overlay[...] annotations according to heuristics.
+    Return a pair: (string describing action taken, modified content as list of lines).
+    '''
+    lines = filter_out_annotations(filename)
+    lines = insert_overlay_caller_annotations(lines)
+
+    # These simple heuristics filter out those .qll files that we no _not_ want to annotate
+    # as overlay[local?].  It is not clear that these heuristics are exactly what we want,
+    # but they seem to work well enough for now (as determined by speed and accuracy numbers).
+    if (filename.endswith("Test.qll") or
+        ((filename.endswith("Query.qll") or filename.endswith("Config.qll")) and
+         any("implements DataFlow::ConfigSig" in line for line in lines))):
+        return (f"Keeping \"{filename}\" global because it configures dataflow for a query", lines)
+    elif not any(line for line in lines if line.strip()):
+        return (f"Keeping \"{filename}\" global because it is empty", lines)
+
+    return insert_toplevel_maybe_local_anntotation(filename, lines)
+
+
+def process_single_file(filename):
+    '''
+    Process a single file, annotating it as appropriate and writing the changes back to the file.
+    '''
+    annotate_result = annotate_as_appropriate(filename)
+
+    old = [line for line in open(filename)]
+    new = annotate_result[1]
+
+    if old != new:
+        diff = context_diff(old, new, fromfile=filename, tofile=filename)
+        diff = [line for line in diff]
+        if diff:
+            print(annotate_result[0])
+            for line in diff:
+                print(line.rstrip())
+            with open(filename, "w") as out_file:
+                for line in new:
+                    out_file.write(line)
+
+
+dirs = []
+for lang in sys.argv[1:]:
+    if lang in ["cpp", "go", "csharp", "java", "javascript", "python", "ruby", "rust", "swift"]:
+        dirs.append(f"{lang}/ql/lib")
+    else:
+        raise Exception(f"Unknown language \"{lang}\".")
+
+if dirs:
+    dirs.append("shared")
+
+for roots in dirs:
+    for dirpath, dirnames, filenames in os.walk(roots):
+        for filename in filenames:
+            if filename.endswith(".qll") and not dirpath.endswith("tutorial"):
+                process_single_file(os.path.join(dirpath, filename))

config/sync-files.py

@@ -58,7 +58,19 @@ def file_checksum(filename):
     with open(filename, 'rb') as file_handle:
         return hashlib.sha1(file_handle.read()).hexdigest()
 
-def check_group(group_name, files, master_file_picker, emit_error):
+def accept_prefix(line1, line2):
+    suffix = line2.removeprefix(line1)
+    return not suffix or suffix.lstrip().startswith("//")
+
+def equivalent_lines(lines1, lines2):
+    if len(lines1) != len(lines2):
+        return False
+    for line1, line2 in zip(lines1, lines2):
+        if not accept_prefix(line1, line2) and not accept_prefix(line2, line1):
+            return False
+    return True
+
+def check_group(group_name, files, master_file_picker, emit_error, accept_prefix):
     extant_files = [f for f in files if path.isfile(f)]
     if len(extant_files) == 0:
         emit_error(__file__, 0, "No files found from group '" + group_name + "'.")
@@ -70,11 +82,23 @@ def check_group(group_name, files, master_file_picker, emit_error):
         return
 
     checksums = {file_checksum(f) for f in extant_files}
-
-    if len(checksums) == 1 and len(extant_files) == len(files):
+    same_lengths = len(extant_files) == len(files)
+    if len(checksums) == 1 and same_lengths:
         # All files are present and identical.
         return
 
+    # In this case we also consider files indentical, if
+    # (1) The group only containts two files.
+    # (2) The lines of one file are the same as the lines of another file
+    # modulo comments.
+    if accept_prefix and same_lengths and len(extant_files) == 2:
+        with open(extant_files[0], 'r') as f1:
+            file1_lines = [l.strip('\n\r') for l in f1.readlines()]
+        with open(extant_files[1], 'r') as f2:
+            file2_lines = [l.strip('\n\r') for l in f2.readlines()]
+        if equivalent_lines(file1_lines, file2_lines):
+            return
+
     master_file = master_file_picker(extant_files)
     if master_file is None:
         emit_error(__file__, 0,
@@ -139,9 +163,10 @@ def sync_identical_files(emit_error):
         raise Exception("Bad command line or file not found")
     chdir_repo_root()
     load_if_exists('.', 'config/identical-files.json')
-    file_groups.update(csharp_test_files())
+    for group_name, files in csharp_test_files().items():
+        check_group(group_name, files, master_file_picker, emit_error, True)
     for group_name, files in file_groups.items():
-        check_group(group_name, files, master_file_picker, emit_error)
+        check_group(group_name, files, master_file_picker, emit_error, False)
 
 def main():
     sync_identical_files(emit_local_error)