Add version update script & fix packs for release

Add server/scripts/update-release-version.sh that deterministically
updates all 22 version-bearing files (.codeql-version, package.json
files, codeql-pack.yml files). Validates the base version (X.Y.Z)
matches the installed CodeQL CLI before updating.

Update release.yml workflow:
- Add publish_codeql_packs input to skip pack publishing
- Run update-release-version.sh to set tag version
- Move CodeQL setup before version update for CLI validation
- Use npm install (not npm ci) to sync lock file
- Improve summary output with tabular format

Update upgrade SKILL.md to reference the new script.

Author: data-douser

.github/skills/upgrade-codeql-cli-and-packs/SKILL.md

@@ -69,17 +69,25 @@ gh codeql set-version vX.XX.Y
 codeql version  # Verify installation
 ```
 
-#### 1.3 Update package.json Versions
+#### 1.3 Update All Version-Bearing Files
 
-All `package.json` files must have their `version` field set to match the CLI version (without the "v" prefix):
+Use the `update-release-version.sh` script to deterministically update `.codeql-version`, all `package.json` files, and all `codeql-pack.yml` files in a single command:
 
-| File                  | Field to Update |
-| --------------------- | --------------- |
-| `package.json`        | `version`       |
-| `client/package.json` | `version`       |
-| `server/package.json` | `version`       |
+```bash
+./server/scripts/update-release-version.sh X.XX.Y
+```
+
+This updates all 22 version-bearing files. Preview changes first with `--dry-run`:
+
+```bash
+./server/scripts/update-release-version.sh --dry-run X.XX.Y
+```
 
-Example: If `.codeql-version` is `v2.24.1`, set all `package.json` versions to `"version": "2.24.1"`.
+Verify consistency with `--check`:
+
+```bash
+./server/scripts/update-release-version.sh --check X.XX.Y
+```
 
 After updating, regenerate the lock file:
 
@@ -125,6 +133,8 @@ Then re-verify the `cliVersion` is compatible.
 
 ### Phase 3: Update codeql-pack.yml Files
 
+> **Note**: The `version` field in all `codeql-pack.yml` files is already updated by the `update-release-version.sh` script in Phase 1.3. This phase focuses on updating `codeql/*-all` **dependency versions** for compatibility.
+
 #### 3.1 Files to Update
 
 All `codeql-pack.yml` files under `server/ql/*/tools/`:

.github/workflows/release.yml

@@ -6,6 +6,11 @@ on:
       - 'v*'
   workflow_dispatch:
     inputs:
+      publish_codeql_packs:
+        default: true
+        description: 'Publish CodeQL tool query packs to GHCR. Disable for pre-release or re-run scenarios where packs already exist.'
+        required: false
+        type: boolean
       version:
         description: 'Release version (e.g., vX.Y.Z). Must start with "v".'
         required: true
@@ -90,23 +95,31 @@ jobs:
             echo "::warning::Tag ${TAG} not found, building from current checkout at ${CURRENT_SHA:0:8}"
           fi
 
-      - name: Release - Install dependencies
-        run: npm ci --include=optional
-
-      - name: Release - Build server
-        run: npm run build -w server
-
       - name: Release - Setup CodeQL environment
         uses: ./.github/actions/setup-codeql-environment
         with:
           add-to-path: true
           install-language-runtimes: false
 
+      - name: Release - Update release version
+        run: |
+          TAG_VERSION="${{ steps.version.outputs.release_name }}"
+          echo "Updating all version-bearing files to '${TAG_VERSION}'..."
+          ./server/scripts/update-release-version.sh "${TAG_VERSION}"
+
+      - name: Release - Install dependencies
+        run: npm install --include=optional
+
+      - name: Release - Build server
+        run: npm run build -w server
+
       - name: Release - Install CodeQL pack dependencies
         run: server/scripts/install-packs.sh
 
       - name: Release - Publish CodeQL tool query packs
-        if: startsWith(github.ref, 'refs/tags/') || github.event_name == 'workflow_dispatch'
+        if: |
+          (startsWith(github.ref, 'refs/tags/') || github.event_name == 'workflow_dispatch')
+          && (github.event_name != 'workflow_dispatch' || inputs.publish_codeql_packs)
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: |
@@ -123,6 +136,10 @@ jobs:
             fi
           done
 
+      - name: Release - Skip CodeQL tool query pack publishing
+        if: github.event_name == 'workflow_dispatch' && !inputs.publish_codeql_packs
+        run: echo "⏭️ CodeQL tool query pack publishing disabled via workflow input"
+
       - name: Release - Bundle CodeQL tool query packs
         run: |
           mkdir -p dist-packs
@@ -206,13 +223,19 @@ jobs:
       - name: Release - Summary
         run: |
           echo "## Release Summary" >> $GITHUB_STEP_SUMMARY
-          echo "✅ Server built successfully" >> $GITHUB_STEP_SUMMARY
-          echo "✅ npm package published to GitHub Packages" >> $GITHUB_STEP_SUMMARY
-          echo "✅ CodeQL tool query packs published to GHCR" >> $GITHUB_STEP_SUMMARY
-          echo "✅ Distribution package created" >> $GITHUB_STEP_SUMMARY
-          echo "✅ Production dependencies installed" >> $GITHUB_STEP_SUMMARY
-          echo "✅ Archive created: codeql-development-mcp-server-${{ steps.version.outputs.version }}.tar.gz" >> $GITHUB_STEP_SUMMARY
-          echo "✅ CodeQL tool query pack archives bundled" >> $GITHUB_STEP_SUMMARY
+          echo "" >> $GITHUB_STEP_SUMMARY
+          echo "| Step | Status |" >> $GITHUB_STEP_SUMMARY
+          echo "| ---- | ------ |" >> $GITHUB_STEP_SUMMARY
+          echo "| Server build | ✅ Success |" >> $GITHUB_STEP_SUMMARY
+          echo "| Version validation | ✅ All files match ${{ steps.version.outputs.release_name }} |" >> $GITHUB_STEP_SUMMARY
+          if [[ "${{ github.event_name }}" == "workflow_dispatch" && "${{ inputs.publish_codeql_packs }}" != "true" ]]; then
+            echo "| CodeQL pack publish | ⏭️ Skipped (disabled via input) |" >> $GITHUB_STEP_SUMMARY
+          else
+            echo "| CodeQL pack publish | ✅ Published to GHCR |" >> $GITHUB_STEP_SUMMARY
+          fi
+          echo "| npm package | ✅ Published to GitHub Packages |" >> $GITHUB_STEP_SUMMARY
+          echo "| Distribution archive | ✅ Created |" >> $GITHUB_STEP_SUMMARY
+          echo "| CodeQL pack bundles | ✅ Bundled |" >> $GITHUB_STEP_SUMMARY
           echo "" >> $GITHUB_STEP_SUMMARY
           echo "### Package Contents" >> $GITHUB_STEP_SUMMARY
           echo "- \`server/dist/\` - Bundled JavaScript output" >> $GITHUB_STEP_SUMMARY