Fix is not an extension target of warning for extension packs

.github/scripts/pr-suites-packs.sh

@@ -22,7 +22,16 @@ if [[ -z "$PR_NUMBER" ]]; then
     for pack_dir in "$LANGUAGE/src" "$LANGUAGE/lib" "$LANGUAGE/ext" "$LANGUAGE/ext-library-sources"; do
         if [[ -f "$pack_dir/qlpack.yml" ]]; then
             echo "[+] Compiling Pack: $pack_dir"
-            codeql pack install "$pack_dir"
+            # `ext`/`ext-library-sources` are CodeQL model/extension packs (`extensionTargets`,
+            # no `dependencies`) - deliberately skip `codeql pack install` for them. Installing
+            # writes a `codeql-pack.lock.yml` with an empty `dependencies: {}` map, and a
+            # checked-in lock file in that state makes `codeql pack create` emit a bogus
+            # `addsTo.pack '...' is not an extension target of '...'` warning for every data
+            # extension in the pack (a known CodeQL CLI bug, see
+            # https://github.com/github/codeql/issues/20211). See CONTRIBUTING.md.
+            if [[ "$pack_dir" != "$LANGUAGE/ext" && "$pack_dir" != "$LANGUAGE/ext-library-sources" ]]; then
+                codeql pack install "$pack_dir"
+            fi
             codeql pack create "$pack_dir"
         fi
     done

.github/workflows/ci.yml

@@ -189,7 +189,13 @@ jobs:
           GITHUB_TOKEN: ${{ github.token }}
         run: |
           gh extension install github/gh-codeql
-          gh codeql pack install "${{ matrix.language }}/ext/"
+          # NOTE: deliberately no `gh codeql pack install` here. `ext` is a CodeQL model/extension
+          # pack (`library: true`, `extensionTargets`, no `dependencies`) - installing it just
+          # (re)writes a `codeql-pack.lock.yml` with an empty `dependencies: {}` map, and a
+          # checked-in lock file in that state makes a subsequent `codeql pack create` emit a
+          # bogus `addsTo.pack '...' is not an extension target of '...'` warning for every data
+          # extension in the pack (a known CodeQL CLI bug, see
+          # https://github.com/github/codeql/issues/20211). See CONTRIBUTING.md.
           gh codeql pack create "${{ matrix.language }}/ext/"
 
   library-sources:
@@ -221,7 +227,8 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ github.token }}
         run: |
-          codeql pack install "${{ matrix.language }}/ext-library-sources/"
+          # NOTE: deliberately no `codeql pack install` here - see the matching comment in the
+          # `extensions` job above.
           codeql pack create "${{ matrix.language }}/ext-library-sources/"
 
   configs:

.github/workflows/publish.yml

@@ -226,7 +226,13 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: |
           echo "Publishing codeql-${{ matrix.language }}-extensions."
-          codeql pack install "${{ matrix.language }}/ext"
+          # NOTE: deliberately no `codeql pack install` here. `ext` is a CodeQL model/extension
+          # pack (`library: true`, `extensionTargets`, no `dependencies`) - installing it just
+          # (re)writes a `codeql-pack.lock.yml` with an empty `dependencies: {}` map, and a
+          # checked-in lock file in that state makes a subsequent `codeql pack publish`/`create`
+          # emit a bogus `addsTo.pack '...' is not an extension target of '...'` warning for every
+          # data extension in the pack (a known CodeQL CLI bug, see
+          # https://github.com/github/codeql/issues/20211). See CONTRIBUTING.md.
           codeql pack publish "${{ matrix.language }}/ext"
 
       - name: Record publish result
@@ -307,7 +313,8 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: |
           echo "Publishing codeql-${{ matrix.language }}-library-sources."
-          codeql pack install "${{ matrix.language }}/ext-library-sources"
+          # NOTE: deliberately no `codeql pack install` here - see the matching comment in the
+          # `extensions` job above.
           codeql pack publish "${{ matrix.language }}/ext-library-sources"
 
       - name: Record publish result

.github/workflows/update-codeql-version.yml

@@ -91,8 +91,10 @@ jobs:
           GITHUB_TOKEN: ${{ github.token }}
         run: |
           set -euo pipefail
-          # Exclusions (kept in sync with the same exclusions in
-          # .github/scripts/pin-codeql-library-versions.sh):
+          # Exclusions (the first three below are also excluded in
+          # .github/scripts/pin-codeql-library-versions.sh; the last one is
+          # NOT - ext/ext-library-sources still need their extensionTargets
+          # versions pinned, but must be skipped here to avoid lock-file churn):
           #  - ./ql/hotspots is a standalone local dev tool (see
           #    ql/hotspots/README.md and .github/workflows/hotspots.yml), not
           #    one of the per-language src/lib/ext/ext-library-sources packs
@@ -106,7 +108,16 @@ jobs:
           #  - ./codeql and */.codeql are a locally-cloned github/codeql
           #    checkout (used by ql/hotspots) and CodeQL's own per-pack build
           #    caches, respectively - neither is a repo pack either.
-          for dir in $(find . -name qlpack.yml -not -path "./ql/hotspots/*" -not -path "./codeql_home/*" -not -path "./codeql/*" -not -path "*/.codeql/*" -exec dirname {} \;); do
+          #  - <lang>/ext and <lang>/ext-library-sources are CodeQL model/extension packs
+          #    (`extensionTargets`, no `dependencies`) - NOT excluded from
+          #    pin-codeql-library-versions.sh (their extensionTargets versions still need
+          #    pinning), but excluded here: `codeql pack upgrade` (re)writes their
+          #    codeql-pack.lock.yml with an empty `dependencies: {}` map, and a checked-in
+          #    lock file in that state makes a later `codeql pack create`/`publish` emit a
+          #    bogus `addsTo.pack '...' is not an extension target of '...'` warning for
+          #    every data extension in the pack (a known CodeQL CLI bug, see
+          #    https://github.com/github/codeql/issues/20211). See CONTRIBUTING.md.
+          for dir in $(find . -name qlpack.yml -not -path "./ql/hotspots/*" -not -path "./codeql_home/*" -not -path "./codeql/*" -not -path "*/.codeql/*" -not -path "*/ext/*" -not -path "*/ext-library-sources/*" -exec dirname {} \;); do
             echo "::group::codeql pack upgrade $dir"
             codeql pack upgrade "$dir"
             echo "::endgroup::"

CONTRIBUTING.md

@@ -293,6 +293,27 @@ coding agent) in the loop for the hard part — fixing whatever the new CLI brea
 > `codeql pack upgrade`/the pinning script can never resolve it. This is a pre-existing, unrelated
 > quirk of that tool, not something the version-bump automation needs to (or can) fix.
 
+> [!NOTE]
+> <a id="ext-packs-no-install"></a>**Why `<language>/ext` and `<language>/ext-library-sources` are
+> never `codeql pack install`ed or `codeql pack upgrade`d:** these are CodeQL
+> [model/extension packs](https://docs.github.com/en/code-security/tutorials/customize-code-scanning/create-and-work-with-codeql-packs#creating-a-codeql-model-pack)
+> — `library: true`, an `extensionTargets` map, and (by design) **no `dependencies`**. `codeql pack
+> install`/`codeql pack upgrade` still (re)write a `codeql-pack.lock.yml` for them, but since there's
+> nothing to resolve it's always an empty `dependencies: {}` map. A *checked-in* lock file in that
+> state triggers a known CodeQL CLI bug
+> ([github/codeql#20211](https://github.com/github/codeql/issues/20211)): a later `codeql pack
+> create`/`codeql pack publish` on the same pack emits a bogus `WARNING: In extension for
+> codeql/<language>-all:<extensible>, addsTo.pack 'codeql/<language>-all' is not an extension target
+> of '...'` for every data extension file in the pack, even though `extensionTargets` correctly lists
+> that pack. CI (`ci.yml`'s `extensions`/`library-sources` jobs, `publish.yml`'s `extensions`/
+> `library_sources_extensions` jobs, `pr-suites-packs.sh`) and
+> [`update-codeql-version.yml`](#updating-the-pinned-codeql-clilibrary-version)'s `codeql pack
+> upgrade` loop deliberately skip `install`/`upgrade` for these two pack types and go straight to
+> `codeql pack create`/`publish` — and no `codeql-pack.lock.yml` should ever be committed for them.
+> If you run `codeql pack install`/`upgrade` against one of these directories locally while
+> developing (e.g. to sanity-check a new data extension), delete the resulting
+> `codeql-pack.lock.yml` before committing.
+
 > [!WARNING]
 > The `.codeqlversion` bump and the pack version bumps don't have to land in the same PR, but
 > splitting them is risky: [#124][pr-124] refreshed `.codeqlversion` and every language's