Merge main into Python prompt-injection branch

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

Author: BazookaMusic

.bazelrc

@@ -11,6 +11,9 @@ build --compilation_mode opt
 common --override_module=semmle_code=%workspace%/misc/bazel/semmle_code_stub
 
 build --repo_env=CC=clang --repo_env=CXX=clang++
+# The standalone Linux toolchain uses gold, which does not support the
+# LLD-specific -z nostart-stop-gc workaround enabled by rules_swift.
+build:linux --features=-swift.lld_gc_workaround
 # Disable Android SDK auto-detection (we don't use it, and rules_android has Bazel 9 compatibility issues)
 build --repo_env=ANDROID_HOME=
 

.bazelversion

@@ -1 +1 @@
-9.0.0
+9.3.1

.gitattributes

@@ -75,6 +75,9 @@
 /ruby/extractor/cargo-bazel-lock.json linguist-generated=true
 /ruby/extractor/cargo-bazel-lock.json -merge
 
+# GitHub Agentic Workflows compiled output
+.github/workflows/*.lock.yml linguist-generated=true
+
 # auto-generated files for the C# build
 /csharp/paket.lock linguist-generated=true
 # needs eol=crlf, as `paket` touches this file and saves it as crlf

.github/dependabot.yml

@@ -4,16 +4,22 @@ updates:
     directory: "ruby"
     schedule:
       interval: "daily"
+    cooldown:
+      default-days: 7
 
   - package-ecosystem: "cargo"
     directory: "ql"
     schedule:
       interval: "daily"
+    cooldown:
+      default-days: 7
 
   - package-ecosystem: "github-actions"
     directory: "/"
     schedule:
       interval: "daily"
+    cooldown:
+      default-days: 7
     ignore:
       - dependency-name: '*'
         update-types: ['version-update:semver-patch', 'version-update:semver-minor']
@@ -22,6 +28,8 @@ updates:
     directory: "go/extractor"
     schedule:
       interval: "daily"
+    cooldown:
+      default-days: 7
     allow:
       - dependency-name: "golang.org/x/mod"
       - dependency-name: "golang.org/x/tools"
@@ -36,6 +44,8 @@ updates:
     directory: "go/ql/test"
     schedule:
       interval: "monthly"
+    cooldown:
+      default-days: 7
     ignore:
       - dependency-name: "*"
     reviewers:
@@ -45,5 +55,7 @@ updates:
     directory: "/"
     schedule:
       interval: weekly
+    cooldown:
+      default-days: 7
     exclude-paths:
       - "misc/bazel/registry/**"

.github/instructions/expected-files.instructions.md

@@ -1,4 +1,4 @@
 ---
 applyTo: "**/*.expected"
 ---
-Ignore these files. These are generated to be correct by running the tests, and should not be edited manually.
+Do not edit these files directly. They are generated by running the tests. If a `.expected` file has a non-empty `testFailures `section it should not be committed - you may want to update the inline expectation comments in the corresponding test source file (e.g. marking expected results as `MISSING` / `SPURIOUS`) then re-run the test.

.github/instructions/ql-files.instructions.md

@@ -38,6 +38,10 @@ Swift:
   - swift/**/*
   - change-notes/**/*swift*
 
+Unified:
+  - unified/**/*
+  - change-notes/**/*unified*
+
 Actions:
   - actions/**/*
   - change-notes/**/*actions*

.github/labeler.yml

@@ -0,0 +1,174 @@
+---
+name: bazel
+description: Conventions for editing Bazel files in the github/codeql repository: the shared `misc/bazel` helpers, `codeql_platform_select` and the `{CODEQL_PLATFORM}` packaging placeholder, adding `MODULE.bazel` dependencies, and the `semmle_code` stub that keeps the standalone build working. Use when editing any `BUILD.bazel`, `*.bzl`, `MODULE.bazel` or `.bazelrc` here, and before validating such an edit.
+---
+
+# Bazel in the codeql repository
+
+A bzlmod module named `ql`, repo name `@codeql` ([`MODULE.bazel`](../../../MODULE.bazel)). It builds standalone, and is
+also consumed by an internal module; standalone builds replace that module with a stub.
+
+## Traps
+
+Things that will waste your time or produce a wrong edit here. Read this section even if you skip the rest.
+
+* **`//...` does not work.** `bazel build //...`, and even `bazel query //...`, fail at the repo root: the patched
+  modules under [`misc/bazel/registry`](../../../misc/bazel/registry) are real packages referencing repos that are not
+  visible from the main repo, and [`.bazelrc`](../../../.bazelrc) notes separately that transitions break `...` builds.
+  The error names a registry directory unrelated to your edit, so it is easy to misdiagnose. **Validate the specific
+  target or package you changed**, not a recursive pattern.
+* **There is no `MODULE.bazel.lock`, deliberately.** [`.bazelrc`](../../../.bazelrc) sets `--lockfile_mode=off` because
+  the workspace-relative module override makes a lockfile unstable. Do not add one, and do not "fix" its absence.
+* **`linux_arm64` vs `linux-arm64`.** The keyword argument and config setting use an underscore; the platform *string*
+  substituted into paths and zip names uses a hyphen. They are not interchangeable.
+* **Do not stub your way out of a missing internal dependency.** See [Building standalone](#building-standalone) for the
+  one narrow case where extending the stub is correct.
+
+## Conventions
+
+* **Copy a neighboring target rather than inventing a shape.** Packaging is not uniform: some packages use the
+  `codeql_*` wrappers, others still use `pkg_files` directly. Copy the closest *working* neighbor, and prefer the
+  wrapper for new code.
+* **Pin anything fetched over the network** with `sha256` or `integrity`. Bazel only *warns* on an unpinned download, so
+  nothing fails loudly, but the build stops being reproducible and a retagged upstream release silently changes what you
+  build. `lfs_archive` is the exception: content is pinned by git object.
+* **Format with `bazel run //misc/bazel/buildifier`.** It rewrites in place, so do not hand-tune formatting. Also wired
+  as a `pre-commit` hook ([`.pre-commit-config.yaml`](../../../.pre-commit-config.yaml)).
+
+## Where new code goes
+
+Bazel's own macro / rule / repository-rule distinction applies as usual. What is repo-specific:
+
+| Adding | Goes in |
+| --- | --- |
+| a new packaging shape | extend [`misc/bazel/pkg.bzl`](../../../misc/bazel/pkg.bzl), do not fork `pkg_files` |
+| a new OS or arch split | [`misc/bazel/os.bzl`](../../../misc/bazel/os.bzl), do not hand-roll a `select()` over `@platforms//` |
+| a fetch of something external | a repository rule ([`lfs.bzl`](../../../misc/bazel/lfs.bzl), [`ripunzip.bzl`](../../../misc/ripunzip/ripunzip.bzl)), not a `genrule` |
+| a wrapper used by one language | next to that language ([`swift/rules.bzl`](../../../swift/rules.bzl)) |
+| a wrapper used across languages | `misc/bazel/` |
+
+Prefer inline rules in `BUILD.bazel`. A `.bzl` file earns its `load()` only when the shape repeats across packages or a
+value must be computed: [`rust.bzl`](../../../misc/bazel/rust.bzl) is worth it because every Rust binary that ships in a
+pack must get the same universal-binary wrapper and symbols test, and forgetting either is a release bug. A local
+debugging aid opts out and declares a plain `rust_binary`; see `swift-syntax-parse` in
+[`unified/swift-syntax-rs/BUILD.bazel`](../../../unified/swift-syntax-rs/BUILD.bazel). The `_gen_binaries` list in
+[`go/BUILD.bazel`](../../../go/BUILD.bazel) does not earn a `.bzl`, because it is shared within a single file, where a
+local variable does the job.
+
+Macros here are typically a thin public wrapper around a private rule (`codeql_csharp_binary`, `swift_cc_binary`). Keep
+the rule narrow and the ergonomics in the macro. Each macro decorates the caller's `name` to mint its helper targets,
+for example `internal/<name>` or `single_arch/<name>`. Their visibility is that macro's choice (private, package
+default, or the caller's own), so read the macro instead of assuming. When an error names a target you cannot find in
+any source file, a macro minted it: grep the suffix under `misc/bazel/`.
+
+## Shared helpers
+
+Frequently-used pieces, so you load the existing one instead of rewriting it. Read the file for its actual exports.
+
+| `load()` path | Covers |
+| --- | --- |
+| `//misc/bazel:pkg.bzl` | CodeQL packs and packaging |
+| `//misc/bazel:os.bzl` | platform and architecture selection |
+| `//misc/bazel:lfs.bzl` | on-demand git-LFS repositories |
+| `//misc/bazel:rust.bzl` | Rust binary wrapper |
+| `//misc/bazel:csharp.bzl` | C# binary/library/test wrappers |
+| `//misc/bazel:utils.bzl` | `select_os`; prefer `os.bzl`'s `os_select` in new code |
+
+[`defs.bzl`](../../../defs.bzl) at the root exports `codeql_platform` for *dependent* modules. It is not the way to get
+the platform string here; use `os.bzl`.
+
+## Platform selection
+
+[`codeql_platform_select`](../../../misc/bazel/os.bzl) takes one keyword argument per CodeQL platform: `linux64`,
+`linux_arm64`, `osx64` and `win64`. `otherwise` supplies the value for whichever of those you leave unset; it is **not**
+a `//conditions:default`. If you only care about the OS, use `os_select`, which gives Linux the same value on both
+architectures and has a `posix` shorthand for the shared Linux/macOS value.
+
+In a macro (no `ctx`) it returns a `select()`:
+
+```python
+load("//misc/bazel:os.bzl", "codeql_platform_select")
+load("//misc/bazel:pkg.bzl", "codeql_pkg_files")
+
+codeql_pkg_files(
+    name = "extractor-arch",
+    exes = codeql_platform_select(
+        otherwise = ["//unified/extractor"],
+        win64 = ["//unified/extractor-unsupported-os:extractor"],
+    ),
+    prefix = "tools/{CODEQL_PLATFORM}",
+)
+```
+
+If implementation code needs to *branch* on the value rather than pass it through, pass `ctx` and add
+`OS_DETECTION_ATTRS` to the rule's attributes. The value is then resolved eagerly instead of being an opaque `select()`:
+
+```python
+load("//misc/bazel:os.bzl", "OS_DETECTION_ATTRS", "os_select")
+
+def _impl(ctx):
+    ext = os_select(ctx, windows = ".exe", posix = "")
+    ...
+
+my_rule = rule(
+    implementation = _impl,
+    attrs = {"src": attr.label()} | OS_DETECTION_ATTRS,
+)
+```
+
+## Packs
+
+`codeql_pack` assembles the files that become an extractor pack. See [`unified/BUILD.bazel`](../../../unified/BUILD.bazel)
+for a minimal complete example and [`pkg.bzl`](../../../misc/bazel/pkg.bzl) for the arguments. The non-obvious parts:
+
+* **`{CODEQL_PLATFORM}` in a destination path is the routing mechanism**, not just a substitution. A path containing it
+  is *arch-specific* and lands in the per-architecture zip; every other path is *common*. So `prefix =
+  "tools/{CODEQL_PLATFORM}"` both places the file and marks it arch-specific. `arch_overrides` forces named
+  destinations into the arch-specific part without a placeholder.
+* **`codeql_pkg_files` splits `srcs` (plain) from `exes` (mode 755)** and **rejects `attributes =`** with an explicit
+  error. Use `exes` rather than hand-rolling `pkg_attributes(mode = "755")`.
+* **`pkg_dirs` and `pkg_symlinks` are unsupported** and fail at analysis time.
+* `codeql_pack` also generates an installer and an `install` alias, hence `bazel run //unified:install`. Pass
+  `installer_alias = None` if one package defines several packs.
+* `codeql_pack_group` exists for bundling packs into distribution zips, but nothing in this repo instantiates it.
+
+## Adding a dependency
+
+In order of preference:
+
+1. **A [Bazel Central Registry](https://registry.bazel.build/) module.** Add a `bazel_dep` in
+   [`MODULE.bazel`](../../../MODULE.bazel).
+2. **A patched upstream module.** Add it under [`misc/bazel/registry`](../../../misc/bazel/registry), which `.bazelrc`
+   puts ahead of the BCR. Put patches in `modules/<repo>/<version>/patches`, rename the version with a `-codeql.N`
+   suffix, and run [`fix.py`](../../../misc/bazel/registry/fix.py) to realign the metadata.
+3. **A raw archive.** Use `http_archive` via `use_repo_rule`, or a repository rule. Copy an adjacent declaration and
+   keep its checksum field populated.
+
+Vendored Rust crates under [`misc/bazel/3rdparty`](../../../misc/bazel/3rdparty) are generated. Regenerate with
+[`update_cargo_deps.sh`](../../../misc/bazel/3rdparty/update_cargo_deps.sh) rather than editing, and keep the
+`use_repo` lists in sync, which `bazel mod tidy` does for module extensions.
+
+## Building standalone
+
+[`MODULE.bazel`](../../../MODULE.bazel) declares `semmle_code` with a `local_path_override` pointing at `..`, which
+resolves when this repo is checked out inside the internal module. [`.bazelrc`](../../../.bazelrc), which Bazel reads
+when invoked in *this* workspace, overrides that with a stub. This line is the whole reason a standalone build resolves:
+
+```
+common --override_module=semmle_code=%workspace%/misc/bazel/semmle_code_stub
+```
+
+Do not change either the override path or the `local_path_override`; they work as a pair.
+
+[`misc/bazel/semmle_code_stub`](../../../misc/bazel/semmle_code_stub) is an otherwise empty module supplying no-op
+versions of the internal helpers that shared `.bzl` files load *unconditionally*. That is its only job, and it is small
+enough to read.
+
+**Extend the stub only when a `.bzl` file every standalone target loads gains a new internal `load()`**, which breaks
+package loading outright, for everyone. Prefer not needing one. **Never add a stub so that an internal-only target
+appears to build**: some targets depend on internal libraries (`grep -rl @semmle_code --include=*.bazel` finds them) and
+are correctly unbuildable here. Unlike a `load()`, such a dependency only fails when that target is actually requested.
+
+[`.bazelrc.internal`](../../../.bazelrc.internal) is **not** read here; it carries settings for the internal build. A
+setting needed by both has to be written in both files, with paths differing because this repo sits at a different depth
+there.

.github/skills/bazel/SKILL.md

@@ -1,10 +1,11 @@
 name: Check change note
 
 permissions:
+  contents: read
   pull-requests: read
 
 on:
-  pull_request_target:
+  pull_request:
     types: [labeled, unlabeled, opened, synchronize, reopened, ready_for_review]
     paths:
       - "*/ql/src/**/*.ql"
@@ -23,7 +24,7 @@ jobs:
     env:
       REPO: ${{ github.repository }}
       PULL_REQUEST_NUMBER: ${{ github.event.number }}
-      GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      GH_TOKEN: ${{ github.token }}
     runs-on: ubuntu-latest
     steps:
 

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

@@ -34,7 +34,7 @@ jobs:
     - name: Setup dotnet
       uses: actions/setup-dotnet@v4
       with:
-        dotnet-version: 10.0.100
+        dotnet-version: 10.0.201
 
     - name: Checkout repository
       uses: actions/checkout@v5