Merge pull request #2788 from github/v1.8.11

v1.8.11

.github/codeql/queries/assert-no-vscode-dependency.ql

@@ -0,0 +1,37 @@
+/**
+ * @name Unwanted dependency on vscode API
+ * @kind path-problem
+ * @problem.severity error
+ * @id vscode-codeql/assert-no-vscode-dependency
+ * @description The modules stored under `common` should not have dependencies on the VS Code API
+ */
+
+import javascript
+
+class VSCodeImport extends ImportDeclaration {
+  VSCodeImport() { this.getImportedPath().getValue() = "vscode" }
+}
+
+class CommonFile extends File {
+  CommonFile() {
+    this.getRelativePath().regexpMatch(".*/src/common/.*") and
+    not this.getRelativePath().regexpMatch(".*/vscode/.*")
+  }
+}
+
+Import getANonTypeOnlyImport(Module m) {
+  result = m.getAnImport() and not result.(ImportDeclaration).isTypeOnly()
+}
+
+query predicate edges(AstNode a, AstNode b) {
+  getANonTypeOnlyImport(a) = b or
+  a.(Import).getImportedModule() = b
+}
+
+from Module m, VSCodeImport v
+where
+  m.getFile() instanceof CommonFile and
+  edges+(m, v)
+select m, m, v,
+  "This module is in the 'common' directory but has a transitive dependency on the vscode API imported $@",
+  v, "here"

.github/codeql/queries/assert-pure.ql

@@ -1,21 +0,0 @@
-/**
- * @name Unwanted dependency on vscode API
- * @kind problem
- * @problem.severity error
- * @id vscode-codeql/assert-pure
- * @description The modules stored under `pure` and tested in the `pure-tests`
- * are intended to be "pure".
- */
-import javascript
-
-class VSCodeImport extends ASTNode {
-  VSCodeImport() {
-    this.(Import).getImportedPath().getValue() = "vscode"
-  }
-}
-
-from Module m, VSCodeImport v
-where
-  m.getFile().getRelativePath().regexpMatch(".*src/pure/.*")  and
-  m.getAnImportedModule*().getAnImport() = v
-select m, "This module is not pure: it has a transitive dependency on the vscode API imported $@", v, "here"

.github/codeql/queries/qlpack.yml

@@ -1,3 +1,4 @@
 name: vscode-codeql-custom-queries-javascript
 version: 0.0.0
-libraryPathDependencies: codeql-javascript
+dependencies:
+  codeql/javascript-queries: "*"

.github/codeql/queries/unique-command-use.ql

@@ -15,134 +15,145 @@
  * that should be changed to fix the alert.
  */
 
- import javascript
+import javascript
 
- /**
-  * The name of a VS Code command.
-  */
- class CommandName extends string {
-   CommandName() { exists(CommandUsage e | e.getCommandName() = this) }
- 
-   /**
-    * In how many ways is this command used. Will always be at least 1.
-    */
-   int getNumberOfUsages() { result = count(this.getAUse()) }
+/**
+ * The name of a VS Code command.
+ */
+class CommandName extends string {
+  CommandName() { exists(CommandUsage e | e.getCommandName() = this) }
 
-   /**
-    * Get a usage of this command.
-    */
-   CommandUsage getAUse() { result.getCommandName() = this }
- 
-   /**
-    * Get the canonical first usage of this command, to use for the location
-    * of the alert. The implementation of this ordering of usages is arbitrary
-    * and the usage given may not be the one that should be changed when fixing
-    * the alert.
-    */
-   CommandUsage getFirstUsage() {
-     result =
-       max(CommandUsage use |
-         use = this.getAUse()
-       |
-         use
-         order by
-           use.getFile().getRelativePath(), use.getLocation().getStartLine(),
-           use.getLocation().getStartColumn()
-       )
-   }
- }
- 
- /**
-  * Represents a single usage of a command, either from within code or
-  * from the command's definition in package.json
-  */
- abstract class CommandUsage extends Locatable {
-   abstract string getCommandName();
- }
- 
- /**
-  * A usage of a command from the typescript code, by calling `executeCommand`.
-  */
- class CommandUsageCallExpr extends CommandUsage, CallExpr {
-   CommandUsageCallExpr() {
-     this.getCalleeName() = "executeCommand" and
-     this.getArgument(0).(StringLiteral).getValue().matches("%codeQL%") and
-     not this.getFile().getRelativePath().matches("extensions/ql-vscode/test/%")
-   }
- 
-   override string getCommandName() { result = this.getArgument(0).(StringLiteral).getValue() }
- }
+  /**
+   * In how many ways is this command used. Will always be at least 1.
+   */
+  int getNumberOfUsages() { result = count(this.getAUse()) }
 
- /**
-  * A usage of a command from the typescript code, by calling `CommandManager.execute`.
-  */
- class CommandUsageCommandManagerMethodCallExpr extends CommandUsage, MethodCallExpr {
-   CommandUsageCommandManagerMethodCallExpr() {
-     this.getCalleeName() = "execute" and
-     this.getReceiver().getType().unfold().(TypeReference).getTypeName().getName() = "CommandManager" and
-     this.getArgument(0).(StringLiteral).getValue().matches("%codeQL%") and
-     not this.getFile().getRelativePath().matches("extensions/ql-vscode/test/%")
-   }
+  /**
+   * Get a usage of this command.
+   */
+  CommandUsage getAUse() { result.getCommandName() = this }
 
-   override string getCommandName() { result = this.getArgument(0).(StringLiteral).getValue() }
- }
- 
- /**
-  * A usage of a command from any menu that isn't the command palette.
-  * This means a user could invoke the command by clicking on a button in
-  * something like a menu or a dropdown.
-  */
- class CommandUsagePackageJsonMenuItem extends CommandUsage, JsonObject {
-   CommandUsagePackageJsonMenuItem() {
-     exists(this.getPropValue("command")) and
-     exists(PackageJson packageJson, string menuName |
-       packageJson
-           .getPropValue("contributes")
-           .getPropValue("menus")
-           .getPropValue(menuName)
-           .getElementValue(_) = this and
-       menuName != "commandPalette"
-     )
-   }
- 
-   override string getCommandName() { result = this.getPropValue("command").getStringValue() }
- }
- 
- /**
-  * Is the given command disabled for use in the command palette by
-  * a block with a `"when": "false"` field.
-  */
- predicate isDisabledInCommandPalette(string commandName) {
-   exists(PackageJson packageJson, JsonObject commandPaletteObject |
-     packageJson
-         .getPropValue("contributes")
-         .getPropValue("menus")
-         .getPropValue("commandPalette")
-         .getElementValue(_) = commandPaletteObject and
-     commandPaletteObject.getPropValue("command").getStringValue() = commandName and
-     commandPaletteObject.getPropValue("when").getStringValue() = "false"
-   )
- }
- 
- /**
-  * Represents a command being usable from the command palette.
-  * This means that a user could choose to manually invoke the command.
-  */
- class CommandUsagePackageJsonCommandPalette extends CommandUsage, JsonObject {
-   CommandUsagePackageJsonCommandPalette() {
-     this.getFile().getBaseName() = "package.json" and
-     exists(this.getPropValue("command")) and
-     exists(PackageJson packageJson |
-       packageJson.getPropValue("contributes").getPropValue("commands").getElementValue(_) = this
-     ) and
-     not isDisabledInCommandPalette(this.getPropValue("command").getStringValue())
-   }
- 
-   override string getCommandName() { result = this.getPropValue("command").getStringValue() }
- }
- 
- from CommandName c
- where c.getNumberOfUsages() > 1
- select c.getFirstUsage(),
-   "The " + c + " command is used from " + c.getNumberOfUsages() + " locations"
- 
+  /**
+   * Get the canonical first usage of this command, to use for the location
+   * of the alert. The implementation of this ordering of usages is arbitrary
+   * and the usage given may not be the one that should be changed when fixing
+   * the alert.
+   */
+  CommandUsage getFirstUsage() {
+    result =
+      max(CommandUsage use |
+        use = this.getAUse()
+      |
+        use
+        order by
+          use.getFile().getRelativePath(), use.getLocation().getStartLine(),
+          use.getLocation().getStartColumn()
+      )
+  }
+}
+
+/**
+ * Matches one of the members of `BuiltInVsCodeCommands` from `extensions/ql-vscode/src/common/commands.ts`.
+ */
+class BuiltInVSCodeCommand extends string {
+  BuiltInVSCodeCommand() {
+    exists(TypeAliasDeclaration tad |
+      tad.getIdentifier().getName() = "BuiltInVsCodeCommands" and
+      tad.getDefinition().(InterfaceTypeExpr).getAMember().getName() = this
+    )
+  }
+}
+
+/**
+ * Represents a single usage of a command, either from within code or
+ * from the command's definition in package.json
+ */
+abstract class CommandUsage extends Locatable {
+  abstract string getCommandName();
+}
+
+/**
+ * A usage of a command from the typescript code, by calling `executeCommand`.
+ */
+class CommandUsageCallExpr extends CommandUsage, CallExpr {
+  CommandUsageCallExpr() {
+    this.getCalleeName() = "executeCommand" and
+    this.getArgument(0).(StringLiteral).getValue().matches("%codeQL%") and
+    not this.getFile().getRelativePath().matches("extensions/ql-vscode/test/%")
+  }
+
+  override string getCommandName() { result = this.getArgument(0).(StringLiteral).getValue() }
+}
+
+/**
+ * A usage of a command from the typescript code, by calling `CommandManager.execute`.
+ */
+class CommandUsageCommandManagerMethodCallExpr extends CommandUsage, MethodCallExpr {
+  CommandUsageCommandManagerMethodCallExpr() {
+    this.getCalleeName() = "execute" and
+    this.getReceiver().getType().unfold().(TypeReference).getTypeName().getName() = "CommandManager" and
+    this.getArgument(0).(StringLiteral).getValue().matches("%codeQL%") and
+    not this.getFile().getRelativePath().matches("extensions/ql-vscode/test/%")
+  }
+
+  override string getCommandName() { result = this.getArgument(0).(StringLiteral).getValue() }
+}
+
+/**
+ * A usage of a command from any menu that isn't the command palette.
+ * This means a user could invoke the command by clicking on a button in
+ * something like a menu or a dropdown.
+ */
+class CommandUsagePackageJsonMenuItem extends CommandUsage, JsonObject {
+  CommandUsagePackageJsonMenuItem() {
+    exists(this.getPropValue("command")) and
+    exists(PackageJson packageJson, string menuName |
+      packageJson
+          .getPropValue("contributes")
+          .getPropValue("menus")
+          .getPropValue(menuName)
+          .getElementValue(_) = this and
+      menuName != "commandPalette"
+    )
+  }
+
+  override string getCommandName() { result = this.getPropValue("command").getStringValue() }
+}
+
+/**
+ * Is the given command disabled for use in the command palette by
+ * a block with a `"when": "false"` field.
+ */
+predicate isDisabledInCommandPalette(string commandName) {
+  exists(PackageJson packageJson, JsonObject commandPaletteObject |
+    packageJson
+        .getPropValue("contributes")
+        .getPropValue("menus")
+        .getPropValue("commandPalette")
+        .getElementValue(_) = commandPaletteObject and
+    commandPaletteObject.getPropValue("command").getStringValue() = commandName and
+    commandPaletteObject.getPropValue("when").getStringValue() = "false"
+  )
+}
+
+/**
+ * Represents a command being usable from the command palette.
+ * This means that a user could choose to manually invoke the command.
+ */
+class CommandUsagePackageJsonCommandPalette extends CommandUsage, JsonObject {
+  CommandUsagePackageJsonCommandPalette() {
+    this.getFile().getBaseName() = "package.json" and
+    exists(this.getPropValue("command")) and
+    exists(PackageJson packageJson |
+      packageJson.getPropValue("contributes").getPropValue("commands").getElementValue(_) = this
+    ) and
+    not isDisabledInCommandPalette(this.getPropValue("command").getStringValue())
+  }
+
+  override string getCommandName() { result = this.getPropValue("command").getStringValue() }
+}
+
+from CommandName c
+where c.getNumberOfUsages() > 1 and not c instanceof BuiltInVSCodeCommand
+select c.getFirstUsage(),
+  "The " + c + " command is used from " + c.getNumberOfUsages() + " locations"

.github/workflows/cli-test.yml

@@ -0,0 +1,111 @@
+name: Run CLI tests
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: '0 0 * * *'
+  pull_request:
+    types: [opened, synchronize, reopened, ready_for_review]
+    paths:
+      - .github/workflows/cli-test.yml
+      - extensions/ql-vscode/src/codeql-cli/**
+      - extensions/ql-vscode/src/language-support/**
+      - extensions/ql-vscode/src/query-server/**
+      - extensions/ql-vscode/supported_cli_versions.json
+
+jobs:
+  find-nightly:
+    name: Find Nightly Release
+    runs-on: ubuntu-latest
+    outputs:
+      url: ${{ steps.get-url.outputs.nightly-url }}
+    steps:
+      - name: Get Nightly Release URL
+        id: get-url
+        env:
+          GITHUB_TOKEN: '${{ secrets.GITHUB_TOKEN }}'
+        shell: bash
+        # This workflow step gets an unstable testing version of the CodeQL CLI. It should not be used outside of these tests.
+        run: |
+          LATEST=`gh api repos/dsp-testing/codeql-cli-nightlies/releases --jq '.[].tag_name' --method GET --raw-field 'per_page=1'`
+          echo "nightly-url=https://github.com/dsp-testing/codeql-cli-nightlies/releases/download/$LATEST" >> "$GITHUB_OUTPUT"
+
+  set-matrix:
+    name: Set Matrix for cli-test
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Set the variables
+        id: set-variables
+        run: echo "cli-versions=$(cat ./extensions/ql-vscode/supported_cli_versions.json | jq -rc)" >> $GITHUB_OUTPUT
+    outputs:
+      cli-versions: ${{ steps.set-variables.outputs.cli-versions }}
+
+  cli-test:
+    name: CLI Test
+    runs-on: ${{ matrix.os }}
+    needs: [find-nightly, set-matrix]
+    timeout-minutes: 30
+    strategy:
+      matrix:
+        os: [ubuntu-latest, windows-latest]
+        version: ${{ fromJson(needs.set-matrix.outputs.cli-versions) }}
+      fail-fast: false
+    env:
+      CLI_VERSION: ${{ matrix.version }}
+      NIGHTLY_URL: ${{ needs.find-nightly.outputs.url }}
+      TEST_CODEQL_PATH: '${{ github.workspace }}/codeql'
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+
+      - uses: actions/setup-node@v3
+        with:
+          node-version: '16.17.1'
+          cache: 'npm'
+          cache-dependency-path: extensions/ql-vscode/package-lock.json
+
+      - name: Install dependencies
+        working-directory: extensions/ql-vscode
+        run: |
+          npm ci
+        shell: bash
+
+      - name: Build
+        working-directory: extensions/ql-vscode
+        run: |
+          npm run build
+        shell: bash
+
+      - name: Decide on ref of CodeQL repo
+        id: choose-ref
+        shell: bash
+        run: |
+          if [[ "${{ matrix.version }}" == "nightly" ]]
+          then
+            REF="codeql-cli/latest"
+          else
+            REF="codeql-cli/${{ matrix.version }}"
+          fi
+          echo "ref=$REF" >> "$GITHUB_OUTPUT"
+
+      - name: Checkout QL
+        uses: actions/checkout@v3
+        with:
+          repository: github/codeql
+          ref: ${{ steps.choose-ref.outputs.ref }}
+          path: codeql
+
+      - name: Run CLI tests (Linux)
+        working-directory: extensions/ql-vscode
+        if: matrix.os == 'ubuntu-latest'
+        run: |
+          unset DBUS_SESSION_BUS_ADDRESS
+          /usr/bin/xvfb-run npm run test:cli-integration
+
+      - name: Run CLI tests (Windows)
+        working-directory: extensions/ql-vscode
+        if: matrix.os == 'windows-latest'
+        run: |
+          npm run test:cli-integration

.github/workflows/main.yml

@@ -22,7 +22,7 @@ jobs:
 
       - uses: actions/setup-node@v3
         with:
-          node-version: '16.14.2'
+          node-version: '16.17.1'
           cache: 'npm'
           cache-dependency-path: extensions/ql-vscode/package-lock.json
 
@@ -53,22 +53,6 @@ jobs:
           name: vscode-codeql-extension
           path: artifacts
 
-  find-nightly:
-    name: Find Nightly Release
-    runs-on: ubuntu-latest
-    outputs:
-      url: ${{ steps.get-url.outputs.nightly-url }}
-    steps:
-      - name: Get Nightly Release URL
-        id: get-url
-        env:
-          GITHUB_TOKEN: '${{ secrets.GITHUB_TOKEN }}'
-        shell: bash
-        # This workflow step gets an unstable testing version of the CodeQL CLI. It should not be used outside of these tests.
-        run: |
-          LATEST=`gh api repos/dsp-testing/codeql-cli-nightlies/releases --jq '.[].tag_name' --method GET --raw-field 'per_page=1'`
-          echo "nightly-url=https://github.com/dsp-testing/codeql-cli-nightlies/releases/download/$LATEST" >> "$GITHUB_OUTPUT"
-
   lint:
     name: Lint
     runs-on: ubuntu-latest
@@ -80,7 +64,7 @@ jobs:
 
       - uses: actions/setup-node@v3
         with:
-          node-version: '16.14.2'
+          node-version: '16.17.1'
           cache: 'npm'
           cache-dependency-path: extensions/ql-vscode/package-lock.json
 
@@ -110,6 +94,11 @@ jobs:
         run: |
           npm run lint:scenarios
 
+      - name: Find deadcode
+        working-directory: extensions/ql-vscode
+        run: |
+          npm run find-deadcode
+
   unit-test:
     name: Unit Test
     runs-on: ${{ matrix.os }}
@@ -124,7 +113,7 @@ jobs:
 
       - uses: actions/setup-node@v3
         with:
-          node-version: '16.14.2'
+          node-version: '16.17.1'
           cache: 'npm'
           cache-dependency-path: extensions/ql-vscode/package-lock.json
 
@@ -158,7 +147,7 @@ jobs:
 
       - uses: actions/setup-node@v3
         with:
-          node-version: '16.14.2'
+          node-version: '16.17.1'
           cache: 'npm'
           cache-dependency-path: extensions/ql-vscode/package-lock.json
 
@@ -193,30 +182,31 @@ jobs:
         run: |
           npm run test:vscode-integration
 
-  set-matrix:
-    name: Set Matrix for cli-test
+  get-latest-cli-version:
+    name: Get latest CLI version
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
         uses: actions/checkout@v3
-      - name: Set the variables
-        id: set-variables
-        run: echo "cli-versions=$(cat ./extensions/ql-vscode/supported_cli_versions.json | jq -rc)" >> $GITHUB_OUTPUT
+      - name: Set the variable
+        id: set-variable
+        run: |
+          echo "cli-version=$(cat ./extensions/ql-vscode/supported_cli_versions.json | jq -rc '.[0]')" >> $GITHUB_OUTPUT
+          echo "$cli-version"
     outputs:
-      cli-versions: ${{ steps.set-variables.outputs.cli-versions }}
+      cli-version: ${{ steps.set-variable.outputs.cli-version }}
 
   cli-test:
     name: CLI Test
     runs-on: ${{ matrix.os }}
-    needs: [find-nightly, set-matrix]
+    needs: [get-latest-cli-version]
+    timeout-minutes: 30
     strategy:
       matrix:
         os: [ubuntu-latest, windows-latest]
-        version: ${{ fromJson(needs.set-matrix.outputs.cli-versions) }}
       fail-fast: false
     env:
-      CLI_VERSION: ${{ matrix.version }}
-      NIGHTLY_URL: ${{ needs.find-nightly.outputs.url }}
+      CLI_VERSION: ${{ needs.get-latest-cli-version.outputs.cli-version }}
       TEST_CODEQL_PATH: '${{ github.workspace }}/codeql'
 
     steps:
@@ -225,7 +215,7 @@ jobs:
 
       - uses: actions/setup-node@v3
         with:
-          node-version: '16.14.2'
+          node-version: '16.17.1'
           cache: 'npm'
           cache-dependency-path: extensions/ql-vscode/package-lock.json
 
@@ -241,23 +231,11 @@ jobs:
           npm run build
         shell: bash
 
-      - name: Decide on ref of CodeQL repo
-        id: choose-ref
-        shell: bash
-        run: |
-          if [[ "${{ matrix.version }}" == "nightly" ]]
-          then
-            REF="codeql-cli/latest"
-          else
-            REF="codeql-cli/${{ matrix.version }}"
-          fi
-          echo "ref=$REF" >> "$GITHUB_OUTPUT"
-
       - name: Checkout QL
         uses: actions/checkout@v3
         with:
           repository: github/codeql
-          ref: ${{ steps.choose-ref.outputs.ref }}
+          ref: 'codeql-cli/${{ needs.get-latest-cli-version.outputs.cli-version }}'
           path: codeql
 
       - name: Run CLI tests (Linux)

.github/workflows/release.yml

@@ -22,7 +22,7 @@ jobs:
 
       - uses: actions/setup-node@v3
         with:
-          node-version: '16.14.2'
+          node-version: '16.17.1'
 
       - name: Install dependencies
         run: |

CODEOWNERS

@@ -1,4 +1,5 @@
 **/* @github/codeql-vscode-reviewers
 **/variant-analysis/ @github/code-scanning-secexp-reviewers
 **/databases/ @github/code-scanning-secexp-reviewers
-**/data-extensions-editor/ @github/code-scanning-secexp-reviewers
+**/model-editor/ @github/code-scanning-secexp-reviewers
+**/queries-panel/ @github/code-scanning-secexp-reviewers

docs/releasing.md

@@ -1,5 +1,6 @@
 # Releasing (write access required)
 
+1. Run the ["Run CLI tests" workflow](https://github.com/github/vscode-codeql/actions/workflows/cli-test.yml) and make sure the tests are green. If there were no merges between the time the workflow ran (it runs daily), and the release, you can skip this step.  
 1. Double-check the `CHANGELOG.md` contains all desired change comments and has the version to be released with date at the top.
     * Go through all recent PRs and make sure they are properly accounted for.
     * Make sure all changelog entries have links back to their PR(s) if appropriate.
@@ -10,7 +11,7 @@
       * New telemetry events are added.
       * Deprecation or removal of commands.
       * Accumulation of many changes, none of which are individually big enough to warrant a minor bump, but which together are. This does not include changes which are purely internal to the extension, such as refactoring, or which are only available behind a feature flag.
-1. Double-check that the node version we're using matches the one used for VS Code. If it doesn't, you will then need to update the node version in the following files:
+1. Double-check that the node version we're using matches the one used for VS Code. You can find this info by seleting "About Visual Studio Code" from the top menu. If it doesn't match, you will then need to update the node version in the following files:
     * `.nvmrc` - this will enable `nvm` to automatically switch to the correct node version when you're in the project folder
     * `.github/workflows/main.yml` - all the "node-version: '[VERSION]'" settings
     * `.github/workflows/release.yml` - the "node-version: '[VERSION]'" setting

docs/test-plan.md

@@ -11,16 +11,67 @@ We don't need to test features (and permutations of features) that are covered b
 
 ## Before releasing the VS Code extension
 
-- Go through the required test cases listed below
+- Run at least one local query and MRVA using the existing version of the extension (to generate "old" query history items).
+- Go through the required test cases listed below.
 - Check major PRs since the previous release for specific one-off things to test. Based on that, you might want to
 choose to go through some of the Optional Test Cases.
-- Run a query using the existing version of the extension (to generate an "old" query history item)
 
 ## Required Test Cases
 
-### Test Case 1: MRVA - Running a problem path query and viewing results
+### Local databases
 
-1. Open the [UnsafeJQueryPlugin query](https://github.com/github/codeql/blob/main/javascript/ql/src/Security/CWE-079/UnsafeJQueryPlugin.ql).
+#### Test case 1: Download a database from GitHub
+
+1. Click "Download Database from GitHub" and enter `angular-cn/ng-nice` and select the javascript language if prompted
+
+#### Test case 2: Import a database from an archive
+
+1. Obtain a javascript database for `babel/babel`
+   - You can do `gh api "/repos/babel/babel/code-scanning/codeql/databases/javascript" -H "Accept: application/zip" > babel.zip` to fetch a database from GitHub.
+2. Click "Choose Database from Archive" and select the file you just downloaded above.
+
+### Local queries
+
+#### Test case 1: Running a path problem query and viewing results
+
+1. Open the [javascript UnsafeJQueryPlugin query](https://github.com/github/codeql/blob/main/javascript/ql/src/Security/CWE-079/UnsafeJQueryPlugin.ql).
+2. Select the `angular-cn/ng-nice` database (or download it if you don't have one already)
+3. Run a local query.
+4. Once the query completes:
+   - Check that the result messages are rendered
+   - Check that the paths can be opened and paths are rendered correctly
+   - Check that alert locations can be clicked on
+
+#### Test case 2: Running a problem query and viewing results
+
+1. Open the [javascript ReDoS query](https://github.com/github/codeql/blob/main/javascript/ql/src/Performance/ReDoS.ql).
+2. Select the `babel/babel` database (or download it if you don't have one already)
+3. Run a local query.
+4. Once the query completes:
+   - Check that the result messages are rendered
+   - Check that alert locations can be clicked on
+
+#### Test case 3: Running a non-problem query and viewing results
+
+1. Open the [cpp FunLinesOfCode query](https://github.com/github/codeql/blob/main/cpp/ql/src/Metrics/Functions/FunLinesOfCode.ql).
+2. Select the `google/brotli` database (or download it if you don't have one already)
+3. Run a local query.
+4. Once the query completes:
+   - Check that the results table is rendered
+   - Check that result locations can be clicked on
+
+#### Test case 3: Can use AST viewer
+
+1. Click on any code location from a previous query to open a source file from a database
+2. Open the AST viewing panel and click "View AST"
+3. Once the AST is computed:
+   - Check that it can be navigated
+
+### MRVA
+
+#### Test Case 1: Running a path problem query and viewing results
+
+1. Open the [javascript UnsafeJQueryPlugin query](https://github.com/github/codeql/blob/main/javascript/ql/src/Security/CWE-079/UnsafeJQueryPlugin.ql).
 2. Run a MRVA against the following repo list:
 
    ```json
@@ -47,40 +98,44 @@ choose to go through some of the Optional Test Cases.
 6. Once the query completes:
    - Check that the query history item is updated to show the query status as "complete"
 
-### Test Case 2: MRVA - Running a problem query and viewing results
+#### Test Case 2: Running a problem query and viewing results
 
-1. Open the [ReDoS query](https://github.com/github/codeql/blob/main/javascript/ql/src/Performance/ReDoS.ql).
+1. Open the [javascript ReDoS query](https://github.com/github/codeql/blob/main/javascript/ql/src/Performance/ReDoS.ql).
 2. Run a MRVA against the "Top 10" repositories.
-3. Check that there is a notification message.
+3. Check that a notification message pops up and the results view is opened.
 4. Check the query history. It should:
    - Show that an item has been added to the query history
    - The item should be marked as "in progress".
-5. Once the query starts:
-   - Check that a notification is shown with a link to the results view
+5. Once the query completes:
    - Check that the results are rendered with an alert message and a highlighted code snippet:
-![highlighted-code-snippet](images/highlighted-code-snippet.png)
 
-### Test Case 3: MRVA - Running a non-problem query and viewing results
+   ![highlighted-code-snippet](images/highlighted-code-snippet.png)
 
-1. Open the [FunLinesOfCode query](https://github.com/github/codeql/blob/main/cpp/ql/src/Metrics/Functions/FunLinesOfCode.ql).
+#### Test Case 3: Running a non-problem query and viewing results
+
+1. Open the [cpp FunLinesOfCode query](https://github.com/github/codeql/blob/main/cpp/ql/src/Metrics/Functions/FunLinesOfCode.ql).
 2. Run a MRVA against a single repository (e.g. `google/brotli`).
-3. Once the query starts:
-   - Open the query results
+3. Check that a notification message pops up and the results view is opened.
+4. Check the query history. It should:
+   - Show that an item has been added to the query history
+   - The item should be marked as "in progress".
+5. Once the query completes:
    - Check that the results show up in a table:
-![results-table](images/results-table.png)
 
-### Test Case 4: MRVA - Interacting with query history
+   ![results-table](images/results-table.png)
+
+#### Test Case 4: Interacting with query history
 
 1. Click a history item (for MRVA):
    - Check that exporting results works
    - Check that sorting results works
    - Check that copying repo lists works
-2. Open the query results directory:
+2. Click "Open Results Directory":
    - Check that the correct directory is opened and there are results in it
-3. View logs
+3. Click "View Logs":
    - Check that the correct workflow is opened
 
-### Test Case 5: MRVA - Canceling a variant analysis run
+#### Test Case 5: Canceling a variant analysis run
 
 Run one of the above MRVAs, but cancel it from within VS Code:
 
@@ -88,9 +143,11 @@ Run one of the above MRVAs, but cancel it from within VS Code:
 - Check that the workflow run is also canceled.
 - Check that any available results are visible in VS Code.
 
-### Test Case 6: MRVA - Change to a different colour theme
+### General
 
-Open one of the above MRVAs, try changing to a different colour theme and check that everything looks sensible.
+#### Test case 1: Change to a different colour theme
+
+Open at least one of the above MRVAs and at least one local query, then try changing to a different colour theme and check that everything looks sensible.
 Are there any components that are not showing up?
 
 ## Optional Test Cases
@@ -261,7 +318,6 @@ This requires running a MRVA query and seeing the results view.
    1. Alphabetically
    2. By number of results
    3. By popularity
-   4. By most recent commit
 9. Can filter repos
 10. Shows correct statistics
     1. Total number of results
@@ -321,6 +377,7 @@ This requires running a MRVA query and seeing the results view.
 1. Make changes via config file (ensure JSON schema is helping out)
 1. Close and re-open VS Code (ensure lists are there)
 1. Collapse/expand tree nodes
+1. Create a new list, right click and select "Add repositories with GitHub Code Search". Enter the language 'python' and the query "UserMixin". This should show a rate limiting notification after a while but eventually populate the list with roughly 770 items.
 
 Error cases that trigger an error notification:
 

docs/testing.md

@@ -133,4 +133,4 @@ Once the scenario has been recorded, it's often useful to remove some of the req
 
 ### Scenario data location
 
-Pre-recorded scenarios are stored in `./src/variant-analysis/github-api/mocks/scenarios`. However, it's possible to configure the location, by setting the `codeQL.mockGitHubApiServer.scenariosPath` configuration property in the VS Code user settings.
+Pre-recorded scenarios are stored in `./src/common/mock-gh-api/scenarios`. However, it's possible to configure the location, by setting the `codeQL.mockGitHubApiServer.scenariosPath` configuration property in the VS Code user settings.

extensions/ql-vscode/.eslintrc.js

@@ -65,10 +65,6 @@ const baseConfig = {
     "import/no-namespace": "off",
     "import/no-unresolved": "off",
     "import/no-webpack-loader-syntax": "off",
-    "jsx-a11y/anchor-is-valid": "off",
-    "jsx-a11y/no-noninteractive-element-interactions": "off",
-    "jsx-a11y/no-static-element-interactions": "off",
-    "jsx-a11y/click-events-have-key-events": "off",
     "no-invalid-this": "off",
     "no-fallthrough": "off",
     "no-console": "off",

extensions/ql-vscode/.nvmrc

@@ -1 +1 @@
-v16.14.2
+v16.17.1

extensions/ql-vscode/.storybook/main.ts

@@ -1,4 +1,4 @@
-import type { StorybookConfig } from "@storybook/core-common";
+import type { StorybookConfig } from "@storybook/react-webpack5";
 
 const config: StorybookConfig = {
   stories: ["../src/**/*.stories.mdx", "../src/**/*.stories.@(js|jsx|ts|tsx)"],
@@ -8,13 +8,13 @@ const config: StorybookConfig = {
     "@storybook/addon-interactions",
     "./vscode-theme-addon/preset.ts",
   ],
-  framework: "@storybook/react",
-  core: {
-    builder: "@storybook/builder-webpack5",
+  framework: {
+    name: "@storybook/react-webpack5",
+    options: {},
   },
-  features: {
-    babelModeV7: true,
+  docs: {
+    autodocs: "tag",
   },
 };
 
-module.exports = config;
+export default config;

extensions/ql-vscode/.storybook/manager.ts

@@ -1,4 +1,4 @@
-import { addons } from "@storybook/addons";
+import { addons } from "@storybook/manager-api";
 import { themes } from "@storybook/theming";
 
 addons.setConfig({

extensions/ql-vscode/.storybook/preview.ts

@@ -1,31 +1,36 @@
+import { Preview } from "@storybook/react";
 import { themes } from "@storybook/theming";
 import { action } from "@storybook/addon-actions";
 
 // Allow all stories/components to use Codicons
 import "@vscode/codicons/dist/codicon.css";
 
-// https://storybook.js.org/docs/react/configure/overview#configure-story-rendering
-export const parameters = {
-  // All props starting with `on` will automatically receive an action as a prop
-  actions: { argTypesRegex: "^on[A-Z].*" },
-  // All props matching these names will automatically get the correct control
-  controls: {
-    matchers: {
-      color: /(background|color)$/i,
-      date: /Date$/,
-    },
-  },
-  // Use a dark theme to be aligned with VSCode
-  docs: {
-    theme: themes.dark,
-  },
-  backgrounds: {
-    // The background is injected by our theme CSS files
-    disable: true,
-  },
-};
-
 (window as any).acquireVsCodeApi = () => ({
   postMessage: action("post-vscode-message"),
   setState: action("set-vscode-state"),
 });
+
+// https://storybook.js.org/docs/react/configure/overview#configure-story-rendering
+const preview: Preview = {
+  parameters: {
+    // All props starting with `on` will automatically receive an action as a prop
+    actions: { argTypesRegex: "^on[A-Z].*" },
+    // All props matching these names will automatically get the correct control
+    controls: {
+      matchers: {
+        color: /(background|color)$/i,
+        date: /Date$/,
+      },
+    },
+    // Use a dark theme to be aligned with VSCode
+    docs: {
+      theme: themes.dark,
+    },
+    backgrounds: {
+      // The background is injected by our theme CSS files
+      disable: true,
+    },
+  },
+};
+
+export default preview;

extensions/ql-vscode/.storybook/vscode-theme-addon/ThemeSelector.tsx

@@ -1,14 +1,12 @@
 import * as React from "react";
 import { FunctionComponent, useCallback } from "react";
 
-import { useGlobals } from "@storybook/api";
+import { useGlobals } from "@storybook/manager-api";
 import {
   IconButton,
   Icons,
-  WithTooltip,
   TooltipLinkList,
-  Link,
-  WithHideFn,
+  WithTooltip,
 } from "@storybook/components";
 
 import { themeNames, VSCodeTheme } from "./theme";
@@ -26,7 +24,7 @@ export const ThemeSelector: FunctionComponent = () => {
   );
 
   const createLinks = useCallback(
-    (onHide: () => void): Link[] =>
+    (onHide: () => void) =>
       Object.values(VSCodeTheme).map((theme) => ({
         id: theme,
         onClick() {
@@ -44,8 +42,8 @@ export const ThemeSelector: FunctionComponent = () => {
     <WithTooltip
       placement="top"
       trigger="click"
-      closeOnClick
-      tooltip={({ onHide }: WithHideFn) => (
+      closeOnOutsideClick
+      tooltip={({ onHide }: { onHide: () => void }) => (
         <TooltipLinkList links={createLinks(onHide)} />
       )}
     >

extensions/ql-vscode/.storybook/vscode-theme-addon/manager.tsx

@@ -1,5 +1,5 @@
 import * as React from "react";
-import { addons, types } from "@storybook/addons";
+import { addons, types } from "@storybook/manager-api";
 import { ThemeSelector } from "./ThemeSelector";
 
 const ADDON_ID = "vscode-theme-addon";

extensions/ql-vscode/.storybook/vscode-theme-addon/preset.ts

@@ -1,4 +1,4 @@
-export function config(entry = []) {
+export function previewAnnotations(entry = []) {
   return [...entry, require.resolve("./preview.ts")];
 }
 

extensions/ql-vscode/.storybook/vscode-theme-addon/withTheme.ts

@@ -1,6 +1,5 @@
-import { useEffect, useGlobals } from "@storybook/addons";
+import { useEffect } from "react";
 import type {
-  AnyFramework,
   PartialStoryFn as StoryFunction,
   StoryContext,
 } from "@storybook/csf";
@@ -34,11 +33,8 @@ const themeFiles: { [key in VSCodeTheme]: string } = {
       .default,
 };
 
-export const withTheme = (
-  StoryFn: StoryFunction<AnyFramework>,
-  context: StoryContext<AnyFramework>,
-) => {
-  const [{ vscodeTheme }] = useGlobals();
+export const withTheme = (StoryFn: StoryFunction, context: StoryContext) => {
+  const { vscodeTheme } = context.globals;
 
   useEffect(() => {
     const styleSelectorId =

extensions/ql-vscode/CHANGELOG.md

@@ -1,5 +1,46 @@
 # CodeQL for Visual Studio Code: Changelog
 
+## 1.8.11 - 7 September 2023
+
+- Update how variant analysis results are displayed. For queries with ["path-problem" or "problem" `@kind`](https://codeql.github.com/docs/writing-codeql-queries/metadata-for-codeql-queries/#metadata-properties), you can choose to display the results as rendered alerts or as a table of raw results. For queries with any other `@kind`, the results are displayed as a table. [#2745](https://github.com/github/vscode-codeql/pull/2745) & [#2749](https://github.com/github/vscode-codeql/pull/2749)
+- When running variant analyses, don't download artifacts for repositories with no results. [#2736](https://github.com/github/vscode-codeql/pull/2736)
+- Group the extension settings, so that they're easier to find in the Settings UI. [#2706](https://github.com/github/vscode-codeql/pull/2706)
+
+## 1.8.10 - 15 August 2023
+
+- Add a code lens to make the `CodeQL: Open Referenced File` command more discoverable. Click the "Open referenced file" prompt in a `.qlref` file to jump to the referenced `.ql` file. [#2704](https://github.com/github/vscode-codeql/pull/2704)
+
+## 1.8.9 - 3 August 2023
+
+- Remove "last updated" information and sorting from variant analysis results view. [#2637](https://github.com/github/vscode-codeql/pull/2637)
+- Links to code on GitHub now include column numbers as well as line numbers. [#2406](https://github.com/github/vscode-codeql/pull/2406)
+- No longer highlight trailing commas for jump to definition.  [#2615](https://github.com/github/vscode-codeql/pull/2615)
+- Fix a bug where the QHelp preview page was not being refreshed after changes to the underlying `.qhelp` file. [#2660](https://github.com/github/vscode-codeql/pull/2660)
+
+## 1.8.8 - 17 July 2023
+
+- Remove support for CodeQL CLI versions older than 2.9.4. [#2610](https://github.com/github/vscode-codeql/pull/2610)
+- Implement syntax highlighting for the `additional` and `default` keywords. [#2609](https://github.com/github/vscode-codeql/pull/2609)
+
+## 1.8.7 - 29 June 2023
+
+- Show a run button on the file tab for query files, that will start a local query. This button will only show when a local database is selected in the extension. [#2544](https://github.com/github/vscode-codeql/pull/2544)
+- Add a `CodeQL: Quick Evaluation Count` command to generate the count summary statistics of the results set
+  without spending the time to compute locations and strings. [#2475](https://github.com/github/vscode-codeql/pull/2475)
+
+## 1.8.6 - 14 June 2023
+
+- Add repositories to a variant analysis list with GitHub Code Search. [#2439](https://github.com/github/vscode-codeql/pull/2439) and [#2476](https://github.com/github/vscode-codeql/pull/2476)
+
+## 1.8.5 - 6 June 2023
+
+- Add settings `codeQL.variantAnalysis.defaultResultsFilter` and `codeQL.variantAnalysis.defaultResultsSort` for configuring how variant analysis results are filtered and sorted in the results view. The default is to show all repositories, and to sort by the number of results. [#2392](https://github.com/github/vscode-codeql/pull/2392)
+- Fix bug to ensure error messages have complete stack trace in message logs. [#2425](https://github.com/github/vscode-codeql/pull/2425)
+- Fix bug where the `CodeQL: Compare Query` command did not work for comparing quick-eval queries. [#2422](https://github.com/github/vscode-codeql/pull/2422)
+- Update text of copy and export buttons in variant analysis results view to clarify that they only copy/export the selected/filtered results. [#2427](https://github.com/github/vscode-codeql/pull/2427)
+- Add warning when using unsupported CodeQL CLI version. [#2428](https://github.com/github/vscode-codeql/pull/2428)
+- Retry variant analysis results download if connection times out. [#2440](https://github.com/github/vscode-codeql/pull/2440)
+
 ## 1.8.4 - 3 May 2023
 
 - Avoid repeated error messages when unable to monitor a variant analysis. [#2396](https://github.com/github/vscode-codeql/pull/2396)

extensions/ql-vscode/gulpfile.ts/webpack.config.ts

@@ -15,9 +15,6 @@ export const config: webpack.Configuration = {
   devtool: isDevBuild ? "inline-source-map" : "source-map",
   resolve: {
     extensions: [".js", ".ts", ".tsx", ".json"],
-    fallback: {
-      path: require.resolve("path-browserify"),
-    },
   },
   module: {
     rules: [
@@ -62,18 +59,10 @@ export const config: webpack.Configuration = {
       },
       {
         test: /\.(woff(2)?|ttf|eot)$/,
-        use: [
-          {
-            loader: "file-loader",
-            options: {
-              name: "[name].[ext]",
-              outputPath: "fonts/",
-              // We need this to make Webpack use the correct path for the fonts.
-              // Without this, the CSS file will use `url([object Module])`
-              esModule: false,
-            },
-          },
-        ],
+        type: "asset/resource",
+        generator: {
+          filename: "fonts/[hash][ext][query]",
+        },
       },
     ],
   },

extensions/ql-vscode/language-configuration.json

@@ -30,5 +30,5 @@
       "end": "^\\s*//\\s*#?endregion\\b"
     }
   },
-  "wordPattern": "(-?\\d*\\.\\d\\w*)|([^\\~\\!\\@\\#\\%\\^\\&\\*\\(\\)\\-\\=\\+\\[\\{\\]\\}\\\\\\|\\;\\:\\'\\\"\\.\\<\\>\\/\\?\\s]+)"
+  "wordPattern": "(-?\\d*\\.\\d\\w*)|([^\\~\\!\\@\\#\\%\\^\\&\\*\\(\\)\\-\\=\\+\\[\\{\\]\\}\\\\\\|\\;\\:\\'\\\"\\.\\<\\>\\/\\?\\s\\,]+)"
 }

extensions/ql-vscode/media/dark/symbol-misc.svg

@@ -0,0 +1 @@
+<svg width="16" height="16" viewBox="0 0 16 16" xmlns="http://www.w3.org/2000/svg" fill="none"><path fill-rule="evenodd" clip-rule="evenodd" d="M4 2h8v4c.341.035.677.112 1 .23V1H3v8.48l1-1.75V2zm2.14 8L5 8 4 9.75 3.29 11 1 15h8l-2.29-4-.57-1zm-3.42 4l1.72-3L5 10l.56 1 1.72 3H2.72zm6.836-6.41a3.5 3.5 0 1 1 3.888 5.82 3.5 3.5 0 0 1-3.888-5.82zm.555 4.989a2.5 2.5 0 1 0 2.778-4.157 2.5 2.5 0 0 0-2.778 4.157z" fill="#C5C5C5"/></svg>

extensions/ql-vscode/media/light/symbol-misc.svg

@@ -0,0 +1 @@
+<svg width="16" height="16" viewBox="0 0 16 16" xmlns="http://www.w3.org/2000/svg" fill="none"><path fill-rule="evenodd" clip-rule="evenodd" d="M4 2h8v4c.341.035.677.112 1 .23V1H3v8.48l1-1.75V2zm2.14 8L5 8 4 9.75 3.29 11 1 15h8l-2.29-4-.57-1zm-3.42 4l1.72-3L5 10l.56 1 1.72 3H2.72zm6.836-6.41a3.5 3.5 0 1 1 3.888 5.82 3.5 3.5 0 0 1-3.888-5.82zm.555 4.989a2.5 2.5 0 1 0 2.778-4.157 2.5 2.5 0 0 0-2.778 4.157z" fill="#424242"/></svg>

extensions/ql-vscode/patches/jest-runner-vscode+3.0.1.patch

@@ -25,7 +25,7 @@ index 1ac28d5..f91f216 100644
          await super.setup();
          await (0, load_pnp_1.default)();
 diff --git a/node_modules/jest-runner-vscode/dist/child/runner.js b/node_modules/jest-runner-vscode/dist/child/runner.js
-index 0663c5c..4991663 100644
+index 0663c5c..bdf4a8b 100644
 --- a/node_modules/jest-runner-vscode/dist/child/runner.js
 +++ b/node_modules/jest-runner-vscode/dist/child/runner.js
 @@ -18,10 +18,13 @@ async function run() {
@@ -43,6 +43,16 @@ index 0663c5c..4991663 100644
          const options = JSON.parse(PARENT_JEST_OPTIONS);
          const jestOptions = [
              ...options.args,
+@@ -39,6 +42,9 @@ async function run() {
+             ...(argv.projects?.map(project => path_1.default.resolve(project)) || []),
+             options.workspacePath,
+         ]);
++        const testPaths = new Set(argv._.map(testPath => path_1.default.resolve(testPath)));
++        argv._ = [...testPaths];
++
+         await (0, core_1.runCLI)(argv, [...projects]);
+     }
+     catch (error) {
 diff --git a/node_modules/jest-runner-vscode/dist/public-types.d.ts b/node_modules/jest-runner-vscode/dist/public-types.d.ts
 index 57716e5..d8614af 100644
 --- a/node_modules/jest-runner-vscode/dist/public-types.d.ts

extensions/ql-vscode/scripts/add-fields-to-scenarios.ts

@@ -18,15 +18,15 @@ import { Octokit, type RestEndpointMethodTypes } from "@octokit/rest";
 import { throttling } from "@octokit/plugin-throttling";
 
 import { getFiles } from "./util/files";
-import type { GitHubApiRequest } from "../src/variant-analysis/gh-api/mocks/gh-api-request";
-import { isGetVariantAnalysisRequest } from "../src/variant-analysis/gh-api/mocks/gh-api-request";
+import type { GitHubApiRequest } from "../src/common/mock-gh-api/gh-api-request";
+import { isGetVariantAnalysisRequest } from "../src/common/mock-gh-api/gh-api-request";
 import { VariantAnalysis } from "../src/variant-analysis/gh-api/variant-analysis";
 import { RepositoryWithMetadata } from "../src/variant-analysis/gh-api/repository";
 
 const extensionDirectory = resolve(__dirname, "..");
 const scenariosDirectory = resolve(
   extensionDirectory,
-  "src/variant-analysis/gh-api/mocks/scenarios",
+  "src/common/mock-gh-api/scenarios",
 );
 
 // Make sure we don't run into rate limits by automatically waiting until we can

extensions/ql-vscode/scripts/find-deadcode.ts

@@ -0,0 +1,47 @@
+import { basename, join, relative, resolve } from "path";
+import analyzeTsConfig from "ts-unused-exports";
+import { containsPath, pathsEqual } from "../src/common/files";
+import { exit } from "process";
+
+function ignoreFile(file: string): boolean {
+  return (
+    containsPath("gulpfile.ts", file) ||
+    containsPath(join("src", "stories"), file) ||
+    pathsEqual(
+      join("test", "vscode-tests", "jest-runner-installed-extensions.ts"),
+      file,
+    ) ||
+    basename(file) === "jest.config.ts" ||
+    basename(file) === "index.tsx" ||
+    basename(file) === "index.ts"
+  );
+}
+
+function main() {
+  const repositoryRoot = resolve(join(__dirname, ".."));
+
+  const result = analyzeTsConfig("tsconfig.deadcode.json");
+  let foundUnusedExports = false;
+
+  for (const [filepath, exportNameAndLocations] of Object.entries(result)) {
+    const relativeFilepath = relative(repositoryRoot, filepath);
+
+    if (ignoreFile(relativeFilepath)) {
+      continue;
+    }
+
+    foundUnusedExports = true;
+
+    console.log(relativeFilepath);
+    for (const exportNameAndLocation of exportNameAndLocations) {
+      console.log(`    ${exportNameAndLocation.exportName}`);
+    }
+    console.log();
+  }
+
+  if (foundUnusedExports) {
+    exit(1);
+  }
+}
+
+main();

extensions/ql-vscode/scripts/fix-scenario-file-numbering.ts

@@ -22,7 +22,7 @@ const scenarioName = process.argv[2];
 const extensionDirectory = resolve(__dirname, "..");
 const scenariosDirectory = resolve(
   extensionDirectory,
-  "src/variant-analysis/gh-api/mocks/scenarios",
+  "src/common/mock-gh-api/scenarios",
 );
 const scenarioDirectory = resolve(scenariosDirectory, scenarioName);
 

extensions/ql-vscode/scripts/lint-scenarios.ts

@@ -10,7 +10,7 @@ const extensionDirectory = resolve(__dirname, "..");
 const rootDirectory = resolve(extensionDirectory, "../..");
 const scenariosDirectory = resolve(
   extensionDirectory,
-  "src/variant-analysis/gh-api/mocks/scenarios",
+  "src/common/mock-gh-api/scenarios",
 );
 
 const debug = process.env.RUNNER_DEBUG || process.argv.includes("--debug");
@@ -19,7 +19,7 @@ async function lintScenarios() {
   const schema = createGenerator({
     path: resolve(
       extensionDirectory,
-      "src/variant-analysis/gh-api/mocks/gh-api-request.ts",
+      "src/common/mock-gh-api/gh-api-request.ts",
     ),
     tsconfig: resolve(extensionDirectory, "tsconfig.json"),
     type: "GitHubApiRequest",

extensions/ql-vscode/src/code-tour/code-tour.ts

@@ -0,0 +1,55 @@
+import { AppCommandManager } from "../common/commands";
+import { Uri, workspace } from "vscode";
+import { join } from "path";
+import { pathExists } from "fs-extra";
+import { isCodespacesTemplate } from "../config";
+import { showBinaryChoiceDialog } from "../common/vscode/dialog";
+import { extLogger } from "../common/logging/vscode";
+
+/**
+ * Check if the current workspace is the CodeTour and open the workspace folder.
+ * Without this, we can't run the code tour correctly.
+ **/
+export async function prepareCodeTour(
+  commandManager: AppCommandManager,
+): Promise<void> {
+  if (workspace.workspaceFolders?.length) {
+    const currentFolder = workspace.workspaceFolders[0].uri.fsPath;
+
+    const tutorialWorkspacePath = join(
+      currentFolder,
+      "tutorial.code-workspace",
+    );
+    const toursFolderPath = join(currentFolder, ".tours");
+
+    /** We're opening the tutorial workspace, if we detect it.
+     * This will only happen if the following three conditions are met:
+     * - the .tours folder exists
+     * - the tutorial.code-workspace file exists
+     * - the CODESPACES_TEMPLATE setting doesn't exist (it's only set if the user has already opened
+     * the tutorial workspace so it's a good indicator that the user is in the folder but has ignored
+     * the prompt to open the workspace)
+     */
+    if (
+      (await pathExists(tutorialWorkspacePath)) &&
+      (await pathExists(toursFolderPath)) &&
+      !isCodespacesTemplate()
+    ) {
+      const answer = await showBinaryChoiceDialog(
+        "We've detected you're in the CodeQL Tour repo. We will need to open the workspace file to continue. Reload?",
+      );
+
+      if (!answer) {
+        return;
+      }
+
+      const tutorialWorkspaceUri = Uri.file(tutorialWorkspacePath);
+
+      void extLogger.log(
+        `In prepareCodeTour() method, going to open the tutorial workspace file: ${tutorialWorkspacePath}`,
+      );
+
+      await commandManager.execute("vscode.openFolder", tutorialWorkspaceUri);
+    }
+  }
+}

extensions/ql-vscode/src/codeql-cli/cli-version.ts

@@ -1,7 +1,7 @@
 import * as semver from "semver";
 import { runCodeQlCliCommand } from "./cli";
-import { Logger } from "../common";
-import { getErrorMessage } from "../pure/helpers-pure";
+import { Logger } from "../common/logging";
+import { getErrorMessage } from "../common/helpers-pure";
 
 /**
  * Get the version of a CodeQL CLI.

extensions/ql-vscode/src/codeql-cli/cli.ts

@@ -11,7 +11,7 @@ import tk from "tree-kill";
 import { promisify } from "util";
 import { CancellationToken, Disposable, Uri } from "vscode";
 
-import { BQRSInfo, DecodedBqrsChunk } from "../pure/bqrs-cli-types";
+import { BQRSInfo, DecodedBqrsChunk } from "../common/bqrs-cli-types";
 import { allowCanaryQueryServer, CliConfig } from "../config";
 import {
   DistributionProvider,
@@ -21,12 +21,13 @@ import {
   assertNever,
   getErrorMessage,
   getErrorStack,
-} from "../pure/helpers-pure";
-import { QueryMetadata, SortDirection } from "../pure/interface-types";
-import { BaseLogger, Logger, ProgressReporter } from "../common";
-import { CompilationMessage } from "../pure/legacy-messages";
+} from "../common/helpers-pure";
+import { walkDirectory } from "../common/files";
+import { QueryMetadata, SortDirection } from "../common/interface-types";
+import { BaseLogger, Logger } from "../common/logging";
+import { ProgressReporter } from "../common/logging/vscode";
+import { CompilationMessage } from "../query-server/legacy-messages";
 import { sarifParser } from "../common/sarif-parser";
-import { walkDirectory } from "../helpers";
 import { App } from "../common/app";
 import { QueryLanguage } from "../common/query-language";
 
@@ -134,6 +135,11 @@ export interface SourceInfo {
   sourceLocationPrefix: string;
 }
 
+/**
+ * The expected output of `codeql resolve queries`.
+ */
+export type ResolvedQueries = string[];
+
 /**
  * The expected output of `codeql resolve tests`.
  */
@@ -213,7 +219,7 @@ export class CodeQLCliServer implements Disposable {
     private readonly app: App,
     private distributionProvider: DistributionProvider,
     private cliConfig: CliConfig,
-    private logger: Logger,
+    public readonly logger: Logger,
   ) {
     this.commandQueue = [];
     this.commandInProcess = false;
@@ -325,6 +331,7 @@ export class CodeQLCliServer implements Disposable {
     commandArgs: string[],
     description: string,
     onLine?: OnLineCallback,
+    silent?: boolean,
   ): Promise<string> {
     const stderrBuffers: Buffer[] = [];
     if (this.commandInProcess) {
@@ -344,7 +351,12 @@ export class CodeQLCliServer implements Disposable {
       // Compute the full args array
       const args = command.concat(LOGGING_FLAGS).concat(commandArgs);
       const argsString = args.join(" ");
-      void this.logger.log(`${description} using CodeQL CLI: ${argsString}...`);
+      // If we are running silently, we don't want to print anything to the console.
+      if (!silent) {
+        void this.logger.log(
+          `${description} using CodeQL CLI: ${argsString}...`,
+        );
+      }
       try {
         await new Promise<void>((resolve, reject) => {
           // Start listening to stdout
@@ -390,24 +402,30 @@ export class CodeQLCliServer implements Disposable {
         const fullBuffer = Buffer.concat(stdoutBuffers);
         // Make sure we remove the terminator;
         const data = fullBuffer.toString("utf8", 0, fullBuffer.length - 1);
-        void this.logger.log("CLI command succeeded.");
+        if (!silent) {
+          void this.logger.log("CLI command succeeded.");
+        }
         return data;
       } catch (err) {
         // Kill the process if it isn't already dead.
         this.killProcessIfRunning();
-        // Report the error (if there is a stderr then use that otherwise just report the error cod or nodejs error)
+        // Report the error (if there is a stderr then use that otherwise just report the error code or nodejs error)
         const newError =
           stderrBuffers.length === 0
-            ? new Error(`${description} failed: ${err}`)
+            ? new Error(
+                `${description} failed with args:${EOL}    ${argsString}${EOL}${err}`,
+              )
             : new Error(
-                `${description} failed: ${Buffer.concat(stderrBuffers).toString(
-                  "utf8",
-                )}`,
+                `${description} failed with args:${EOL}    ${argsString}${EOL}${Buffer.concat(
+                  stderrBuffers,
+                ).toString("utf8")}`,
               );
         newError.stack += getErrorStack(err);
         throw newError;
       } finally {
-        void this.logger.log(Buffer.concat(stderrBuffers).toString("utf8"));
+        if (!silent) {
+          void this.logger.log(Buffer.concat(stderrBuffers).toString("utf8"));
+        }
         // Remove the listeners we set up.
         process.stdout.removeAllListeners("data");
         process.stderr.removeAllListeners("data");
@@ -544,9 +562,11 @@ export class CodeQLCliServer implements Disposable {
     {
       progressReporter,
       onLine,
+      silent = false,
     }: {
       progressReporter?: ProgressReporter;
       onLine?: OnLineCallback;
+      silent?: boolean;
     } = {},
   ): Promise<string> {
     if (progressReporter) {
@@ -562,6 +582,7 @@ export class CodeQLCliServer implements Disposable {
             commandArgs,
             description,
             onLine,
+            silent,
           ).then(resolve, reject);
         } catch (err) {
           reject(err);
@@ -595,10 +616,12 @@ export class CodeQLCliServer implements Disposable {
       addFormat = true,
       progressReporter,
       onLine,
+      silent = false,
     }: {
       addFormat?: boolean;
       progressReporter?: ProgressReporter;
       onLine?: OnLineCallback;
+      silent?: boolean;
     } = {},
   ): Promise<OutputType> {
     let args: string[] = [];
@@ -609,6 +632,7 @@ export class CodeQLCliServer implements Disposable {
     const result = await this.runCodeQlCliCommand(command, args, description, {
       progressReporter,
       onLine,
+      silent,
     });
     try {
       return JSON.parse(result) as OutputType;
@@ -695,6 +719,7 @@ export class CodeQLCliServer implements Disposable {
   async resolveLibraryPath(
     workspaces: string[],
     queryPath: string,
+    silent = false,
   ): Promise<QuerySetup> {
     const subcommandArgs = [
       "--query",
@@ -705,6 +730,7 @@ export class CodeQLCliServer implements Disposable {
       ["resolve", "library-path"],
       subcommandArgs,
       "Resolving library paths",
+      { silent },
     );
   }
 
@@ -731,6 +757,25 @@ export class CodeQLCliServer implements Disposable {
     );
   }
 
+  /**
+   * Finds all available queries in a given directory.
+   * @param queryDir Root of directory tree to search for queries.
+   * @param silent If true, don't print logs to the CodeQL extension log.
+   * @returns The list of queries that were found.
+   */
+  public async resolveQueries(
+    queryDir: string,
+    silent?: boolean,
+  ): Promise<ResolvedQueries> {
+    const subcommandArgs = [queryDir];
+    return await this.runJsonCodeQlCliCommand<ResolvedQueries>(
+      ["resolve", "queries"],
+      subcommandArgs,
+      "Resolving queries",
+      { silent },
+    );
+  }
+
   /**
    * Finds all available QL tests in a given directory.
    * @param testPath Root of directory tree to search for tests.
@@ -1031,6 +1076,7 @@ export class CodeQLCliServer implements Disposable {
     resultsPath: string,
     interpretedResultsPath: string,
     sourceInfo?: SourceInfo,
+    args?: string[],
   ): Promise<sarif.Log> {
     const additionalArgs = [
       // TODO: This flag means that we don't group interpreted results
@@ -1038,6 +1084,7 @@ export class CodeQLCliServer implements Disposable {
       // interpretation with and without this flag, or do some
       // grouping client-side.
       "--no-group-results",
+      ...(args ?? []),
     ];
 
     await this.runInterpretCommand(
@@ -1381,21 +1428,13 @@ export class CodeQLCliServer implements Disposable {
 
   async packPacklist(dir: string, includeQueries: boolean): Promise<string[]> {
     const args = includeQueries ? [dir] : ["--no-include-queries", dir];
-    // since 2.7.1, packlist returns an object with a "paths" property that is a list of packs.
-    // previous versions return a list of packs.
-    const results: { paths: string[] } | string[] =
-      await this.runJsonCodeQlCliCommand(
-        ["pack", "packlist"],
-        args,
-        "Generating the pack list",
-      );
+    const results: { paths: string[] } = await this.runJsonCodeQlCliCommand(
+      ["pack", "packlist"],
+      args,
+      "Generating the pack list",
+    );
 
-    // Once we no longer need to support 2.7.0 or earlier, we can remove this and assume all versions return an object.
-    if ("paths" in results) {
-      return results.paths;
-    } else {
-      return results;
-    }
+    return results.paths;
   }
 
   async packResolveDependencies(
@@ -1431,9 +1470,9 @@ export class CodeQLCliServer implements Disposable {
         // this._version is only undefined upon config change, so we reset CLI-based context key only when necessary.
         await this.app.commands.execute(
           "setContext",
-          "codeql.supportsEvalLog",
+          "codeql.supportsQuickEvalCount",
           newVersion.compare(
-            CliVersionConstraint.CLI_VERSION_WITH_PER_QUERY_EVAL_LOG,
+            CliVersionConstraint.CLI_VERSION_WITH_QUICK_EVAL_COUNT,
           ) >= 0,
         );
       } catch (e) {
@@ -1525,10 +1564,23 @@ export function spawnServer(
     );
   }
 
+  let lastStdout: any = undefined;
+  child.stdout!.on("data", (data) => {
+    lastStdout = data;
+  });
   // Set up event listeners.
-  child.on("close", (code) =>
-    logger.log(`Child process exited with code ${code}`),
-  );
+  child.on("close", async (code, signal) => {
+    if (code !== null)
+      void logger.log(`Child process exited with code ${code}`);
+    if (signal)
+      void logger.log(
+        `Child process exited due to receipt of signal ${signal}`,
+      );
+    // If the process exited abnormally, log the last stdout message,
+    // It may be from the jvm.
+    if (code !== 0 && lastStdout !== undefined)
+      void logger.log(`Last stdout was "${lastStdout.toString()}"`);
+  });
   child.stderr!.on("data", stderrListener);
   if (stdoutListener !== undefined) {
     child.stdout!.on("data", stdoutListener);
@@ -1699,31 +1751,32 @@ async function logStream(stream: Readable, logger: BaseLogger): Promise<void> {
   }
 }
 
-export function shouldDebugIdeServer() {
+function isEnvTrue(name: string): boolean {
   return (
-    "IDE_SERVER_JAVA_DEBUG" in process.env &&
-    process.env.IDE_SERVER_JAVA_DEBUG !== "0" &&
-    process.env.IDE_SERVER_JAVA_DEBUG?.toLocaleLowerCase() !== "false"
+    name in process.env &&
+    process.env[name] !== "0" &&
+    // Use en-US since we expect the value to be either "false" or "FALSE", not a localized version.
+    process.env[name]?.toLocaleLowerCase("en-US") !== "false"
   );
 }
 
+export function shouldDebugIdeServer() {
+  return isEnvTrue("IDE_SERVER_JAVA_DEBUG");
+}
+
 export function shouldDebugQueryServer() {
-  return (
-    "QUERY_SERVER_JAVA_DEBUG" in process.env &&
-    process.env.QUERY_SERVER_JAVA_DEBUG !== "0" &&
-    process.env.QUERY_SERVER_JAVA_DEBUG?.toLocaleLowerCase() !== "false"
-  );
+  return isEnvTrue("QUERY_SERVER_JAVA_DEBUG");
 }
 
 export function shouldDebugCliServer() {
-  return (
-    "CLI_SERVER_JAVA_DEBUG" in process.env &&
-    process.env.CLI_SERVER_JAVA_DEBUG !== "0" &&
-    process.env.CLI_SERVER_JAVA_DEBUG?.toLocaleLowerCase() !== "false"
-  );
+  return isEnvTrue("CLI_SERVER_JAVA_DEBUG");
 }
 
 export class CliVersionConstraint {
+  // The oldest version of the CLI that we support. This is used to determine
+  // whether to show a warning about the CLI being too old on startup.
+  public static OLDEST_SUPPORTED_CLI_VERSION = new SemVer("2.9.4");
+
   /**
    * CLI version where building QLX packs for remote queries is supported.
    * (The options were _accepted_ by a few earlier versions, but only from
@@ -1739,21 +1792,9 @@ export class CliVersionConstraint {
   );
 
   /**
-   * CLI version where the `--evaluator-log` and related options to the query server were introduced,
-   * on a per-query server basis.
+   * CLI version where the `resolve extensions` subcommand exists.
    */
-  public static CLI_VERSION_WITH_STRUCTURED_EVAL_LOG = new SemVer("2.8.2");
-
-  /**
-   * CLI version that supports rotating structured logs to produce one per query.
-   *
-   * Note that 2.8.4 supports generating the evaluation logs and summaries,
-   * but 2.9.0 includes a new option to produce the end-of-query summary logs to
-   * the query server console. For simplicity we gate all features behind 2.9.0,
-   * but if a user is tied to the 2.8 release, we can enable evaluator logs
-   * and summaries for them.
-   */
-  public static CLI_VERSION_WITH_PER_QUERY_EVAL_LOG = new SemVer("2.9.0");
+  public static CLI_VERSION_WITH_RESOLVE_EXTENSIONS = new SemVer("2.10.2");
 
   /**
    * CLI version that supports the `--sourcemap` option for log generation.
@@ -1782,6 +1823,20 @@ export class CliVersionConstraint {
     "2.12.4",
   );
 
+  public static CLI_VERSION_GLOBAL_CACHE = new SemVer("2.12.4");
+
+  /**
+   * CLI version where the query server supports quick-eval count mode.
+   */
+  public static CLI_VERSION_WITH_QUICK_EVAL_COUNT = new SemVer("2.13.3");
+
+  /**
+   * CLI version where the langauge server supports visisbility change notifications.
+   */
+  public static CLI_VERSION_WITH_VISIBILITY_NOTIFICATIONS = new SemVer(
+    "2.14.0",
+  );
+
   constructor(private readonly cli: CodeQLCliServer) {
     /**/
   }
@@ -1800,15 +1855,9 @@ export class CliVersionConstraint {
     );
   }
 
-  async supportsStructuredEvalLog() {
+  async supportsResolveExtensions() {
     return this.isVersionAtLeast(
-      CliVersionConstraint.CLI_VERSION_WITH_STRUCTURED_EVAL_LOG,
-    );
-  }
-
-  async supportsPerQueryEvalLog() {
-    return this.isVersionAtLeast(
-      CliVersionConstraint.CLI_VERSION_WITH_PER_QUERY_EVAL_LOG,
+      CliVersionConstraint.CLI_VERSION_WITH_RESOLVE_EXTENSIONS,
     );
   }
 
@@ -1851,4 +1900,20 @@ export class CliVersionConstraint {
       CliVersionConstraint.CLI_VERSION_WITH_ADDITIONAL_PACKS_INSTALL,
     );
   }
+
+  async usesGlobalCompilationCache() {
+    return this.isVersionAtLeast(CliVersionConstraint.CLI_VERSION_GLOBAL_CACHE);
+  }
+
+  async supportsVisibilityNotifications() {
+    return this.isVersionAtLeast(
+      CliVersionConstraint.CLI_VERSION_WITH_VISIBILITY_NOTIFICATIONS,
+    );
+  }
+
+  async supportsQuickEvalCount() {
+    return this.isVersionAtLeast(
+      CliVersionConstraint.CLI_VERSION_WITH_QUICK_EVAL_COUNT,
+    );
+  }
 }

extensions/ql-vscode/src/codeql-cli/distribution.ts

@@ -3,16 +3,10 @@ import { pathExists, mkdtemp, createWriteStream, remove } from "fs-extra";
 import { tmpdir } from "os";
 import { delimiter, dirname, join } from "path";
 import * as semver from "semver";
-import { parse } from "url";
+import { URL } from "url";
 import { ExtensionContext, Event } from "vscode";
 import { DistributionConfig } from "../config";
-import {
-  InvocationRateLimiter,
-  InvocationRateLimiterResultKind,
-  showAndLogErrorMessage,
-  showAndLogWarningMessage,
-} from "../helpers";
-import { extLogger } from "../common";
+import { extLogger } from "../common/logging/vscode";
 import { getCodeQlCliVersion } from "./cli-version";
 import {
   ProgressCallback,
@@ -23,7 +17,15 @@ import {
   deprecatedCodeQlLauncherName,
   extractZipArchive,
   getRequiredAssetName,
-} from "../pure/distribution";
+} from "../common/distribution";
+import {
+  InvocationRateLimiter,
+  InvocationRateLimiterResultKind,
+} from "../common/invocation-rate-limiter";
+import {
+  showAndLogErrorMessage,
+  showAndLogWarningMessage,
+} from "../common/logging";
 
 /**
  * distribution.ts
@@ -76,7 +78,7 @@ export class DistributionManager implements DistributionProvider {
         extensionContext,
       );
     this.updateCheckRateLimiter = new InvocationRateLimiter(
-      extensionContext,
+      extensionContext.globalState,
       "extensionSpecificDistributionUpdateCheck",
       () =>
         this.extensionSpecificDistributionManager.checkForUpdatesToDistribution(),
@@ -158,6 +160,7 @@ export class DistributionManager implements DistributionProvider {
     if (this.config.customCodeQlPath) {
       if (!(await pathExists(this.config.customCodeQlPath))) {
         void showAndLogErrorMessage(
+          extLogger,
           `The CodeQL executable path is specified as "${this.config.customCodeQlPath}" ` +
             "by a configuration setting, but a CodeQL executable could not be found at that path. Please check " +
             "that a CodeQL executable exists at the specified path or remove the setting.",
@@ -505,7 +508,7 @@ class ExtensionSpecificDistributionManager {
         0,
       ) || "";
     return join(
-      this.extensionContext.globalStoragePath,
+      this.extensionContext.globalStorageUri.fsPath,
       ExtensionSpecificDistributionManager._currentDistributionFolderBaseName +
         distributionFolderIndex,
     );
@@ -670,7 +673,7 @@ export class ReleasesApiConsumer {
       redirectUrl &&
       redirectCount < ReleasesApiConsumer._maxRedirects
     ) {
-      const parsedRedirectUrl = parse(redirectUrl);
+      const parsedRedirectUrl = new URL(redirectUrl);
       if (parsedRedirectUrl.protocol !== "https:") {
         throw new Error("Encountered a non-https redirect, rejecting");
       }
@@ -715,7 +718,7 @@ export enum DistributionKind {
   PathEnvironmentVariable,
 }
 
-export interface Distribution {
+interface Distribution {
   codeQlPath: string;
   kind: DistributionKind;
 }
@@ -773,22 +776,22 @@ type DistributionUpdateCheckResult =
   | InvalidLocationResult
   | UpdateAvailableResult;
 
-export interface AlreadyCheckedRecentlyResult {
+interface AlreadyCheckedRecentlyResult {
   kind: DistributionUpdateCheckResultKind.AlreadyCheckedRecentlyResult;
 }
 
-export interface AlreadyUpToDateResult {
+interface AlreadyUpToDateResult {
   kind: DistributionUpdateCheckResultKind.AlreadyUpToDate;
 }
 
 /**
  * The distribution could not be installed or updated because it is not managed by the extension.
  */
-export interface InvalidLocationResult {
+interface InvalidLocationResult {
   kind: DistributionUpdateCheckResultKind.InvalidLocation;
 }
 
-export interface UpdateAvailableResult {
+interface UpdateAvailableResult {
   kind: DistributionUpdateCheckResultKind.UpdateAvailable;
   updatedRelease: Release;
 }
@@ -850,6 +853,7 @@ export async function getExecutableFromDirectory(
 
 function warnDeprecatedLauncher() {
   void showAndLogWarningMessage(
+    extLogger,
     `The "${deprecatedCodeQlLauncherName()!}" launcher has been deprecated and will be removed in a future version. ` +
       `Please use "${codeQlLauncherName()}" instead. It is recommended to update to the latest CodeQL binaries.`,
   );
@@ -858,7 +862,7 @@ function warnDeprecatedLauncher() {
 /**
  * A release on GitHub.
  */
-export interface Release {
+interface Release {
   assets: ReleaseAsset[];
 
   /**
@@ -880,7 +884,7 @@ export interface Release {
 /**
  * An asset corresponding to a release on GitHub.
  */
-export interface ReleaseAsset {
+interface ReleaseAsset {
   /**
    * The id associated with the asset on GitHub.
    */
@@ -950,7 +954,10 @@ export interface GithubReleaseAsset {
 }
 
 export class GithubApiError extends Error {
-  constructor(public status: number, public body: string) {
+  constructor(
+    public status: number,
+    public body: string,
+  ) {
     super(`API call failed with status code ${status}, body: ${body}`);
   }
 }

extensions/ql-vscode/src/codeql-cli/query-language.ts

@@ -0,0 +1,80 @@
+import { CodeQLCliServer } from "./cli";
+import { Uri, window } from "vscode";
+import { isQueryLanguage, QueryLanguage } from "../common/query-language";
+import { getOnDiskWorkspaceFolders } from "../common/vscode/workspace-folders";
+import { extLogger } from "../common/logging/vscode";
+import { UserCancellationException } from "../common/vscode/progress";
+import { showAndLogErrorMessage } from "../common/logging";
+
+/**
+ * Finds the language that a query targets.
+ * If it can't be autodetected, prompt the user to specify the language manually.
+ */
+export async function findLanguage(
+  cliServer: CodeQLCliServer,
+  queryUri: Uri | undefined,
+): Promise<QueryLanguage | undefined> {
+  const uri = queryUri || window.activeTextEditor?.document.uri;
+  if (uri !== undefined) {
+    try {
+      const queryInfo = await cliServer.resolveQueryByLanguage(
+        getOnDiskWorkspaceFolders(),
+        uri,
+      );
+      const language = Object.keys(queryInfo.byLanguage)[0];
+      void extLogger.log(`Detected query language: ${language}`);
+
+      if (isQueryLanguage(language)) {
+        return language;
+      }
+
+      void extLogger.log(
+        "Query language is unsupported. Select language manually.",
+      );
+    } catch (e) {
+      void extLogger.log(
+        "Could not autodetect query language. Select language manually.",
+      );
+    }
+  }
+
+  // will be undefined if user cancels the quick pick.
+  return await askForLanguage(cliServer, false);
+}
+
+export async function askForLanguage(
+  cliServer: CodeQLCliServer,
+  throwOnEmpty = true,
+): Promise<QueryLanguage | undefined> {
+  const language = await window.showQuickPick(
+    await cliServer.getSupportedLanguages(),
+    {
+      placeHolder: "Select target language for your query",
+      ignoreFocusOut: true,
+    },
+  );
+  if (!language) {
+    // This only happens if the user cancels the quick pick.
+    if (throwOnEmpty) {
+      throw new UserCancellationException("Cancelled.");
+    } else {
+      void showAndLogErrorMessage(
+        extLogger,
+        "Language not found. Language must be specified manually.",
+      );
+    }
+    return undefined;
+  }
+
+  if (!isQueryLanguage(language)) {
+    void showAndLogErrorMessage(
+      extLogger,
+      `Language '${language}' is not supported. Only languages ${Object.values(
+        QueryLanguage,
+      ).join(", ")} are supported.`,
+    );
+    return undefined;
+  }
+
+  return language;
+}

extensions/ql-vscode/src/codeql-cli/query-metadata.ts

@@ -0,0 +1,22 @@
+import { CodeQLCliServer } from "./cli";
+import { QueryMetadata } from "../common/interface-types";
+import { extLogger } from "../common/logging/vscode";
+
+/**
+ * Gets metadata for a query, if it exists.
+ * @param cliServer The CLI server.
+ * @param queryPath The path to the query.
+ * @returns A promise that resolves to the query metadata, if available.
+ */
+export async function tryGetQueryMetadata(
+  cliServer: CodeQLCliServer,
+  queryPath: string,
+): Promise<QueryMetadata | undefined> {
+  try {
+    return await cliServer.resolveMetadata(queryPath);
+  } catch (e) {
+    // Ignore errors and provide no metadata.
+    void extLogger.log(`Couldn't resolve metadata for ${queryPath}: ${e}`);
+    return;
+  }
+}

extensions/ql-vscode/src/common/app.ts

@@ -1,14 +1,16 @@
 import { Credentials } from "./authentication";
-import { Disposable } from "../pure/disposable-object";
+import { Disposable } from "./disposable-object";
 import { AppEventEmitter } from "./events";
-import { Logger } from "./logging";
+import { NotificationLogger } from "./logging";
 import { Memento } from "./memento";
 import { AppCommandManager } from "./commands";
+import { AppTelemetry } from "./telemetry";
 
 export interface App {
   createEventEmitter<T>(): AppEventEmitter<T>;
   readonly mode: AppMode;
-  readonly logger: Logger;
+  readonly logger: NotificationLogger;
+  readonly telemetry?: AppTelemetry;
   readonly subscriptions: Disposable[];
   readonly extensionPath: string;
   readonly globalStoragePath: string;
@@ -16,6 +18,7 @@ export interface App {
   readonly workspaceState: Memento;
   readonly credentials: Credentials;
   readonly commands: AppCommandManager;
+  readonly environment: EnvironmentContext;
 }
 
 export enum AppMode {
@@ -23,3 +26,7 @@ export enum AppMode {
   Development = 2,
   Test = 3,
 }
+
+export interface EnvironmentContext {
+  language: string;
+}

extensions/ql-vscode/src/common/bqrs-cli-types.ts

@@ -1,5 +1,3 @@
-export const PAGE_SIZE = 1000;
-
 /**
  * The single-character codes used in the bqrs format for the the kind
  * of a result column. This namespace is intentionally not an enum, see
@@ -15,7 +13,7 @@ export namespace ColumnKindCode {
   export const ENTITY = "e";
 }
 
-export type ColumnKind =
+type ColumnKind =
   | typeof ColumnKindCode.FLOAT
   | typeof ColumnKindCode.INTEGER
   | typeof ColumnKindCode.STRING
@@ -46,7 +44,7 @@ export function getResultSetSchema(
   }
   return undefined;
 }
-export interface PaginationInfo {
+interface PaginationInfo {
   "step-size": number;
   offsets: number[];
 }
@@ -115,7 +113,7 @@ export type BqrsKind =
   | "Entity";
 
 interface BqrsColumn {
-  name: string;
+  name?: string;
   kind: BqrsKind;
 }
 export interface DecodedBqrsChunk {

extensions/ql-vscode/src/common/bqrs-utils.ts

@@ -4,7 +4,7 @@ import {
   LineColumnLocation,
   WholeFileLocation,
 } from "./bqrs-cli-types";
-import { createRemoteFileRef } from "./location-link-utils";
+import { createRemoteFileRef } from "../common/location-link-utils";
 
 /**
  * The CodeQL filesystem libraries use this pattern in `getURL()` predicates
@@ -142,5 +142,7 @@ export function tryGetRemoteLocation(
     fileLink,
     resolvableLocation.startLine,
     resolvableLocation.endLine,
+    resolvableLocation.startColumn,
+    resolvableLocation.endColumn,
   );
 }

extensions/ql-vscode/src/common/commands.ts

@@ -4,7 +4,6 @@ import type { AstItem } from "../language-support";
 import type { DbTreeViewItem } from "../databases/ui/db-tree-view-item";
 import type { DatabaseItem } from "../databases/local-databases";
 import type { QueryHistoryInfo } from "../query-history/query-history-info";
-import type { RepositoriesFilterSortStateWithIds } from "../pure/variant-analysis-filter-sort";
 import type { TestTreeNode } from "../query-testing/test-tree-node";
 import type {
   VariantAnalysis,
@@ -12,6 +11,8 @@ import type {
   VariantAnalysisScannedRepositoryResult,
 } from "../variant-analysis/shared/variant-analysis";
 import type { QLDebugConfiguration } from "../debugger/debug-configuration";
+import type { QueryTreeViewItem } from "../queries-panel/query-tree-view-item";
+import type { Usage } from "../model-editor/method";
 
 // A command function matching the signature that VS Code calls when
 // a command is invoked from a context menu on a TreeView with
@@ -55,10 +56,11 @@ export type ExplorerSelectionCommandFunction<Item> = (
 
 // Builtin commands where the implementation is provided by VS Code and not by this extension.
 // See https://code.visualstudio.com/api/references/commands
-export type BuiltInVsCodeCommands = {
+type BuiltInVsCodeCommands = {
   // The codeQLDatabases.focus command is provided by VS Code because we've registered the custom view
   "codeQLDatabases.focus": () => Promise<void>;
   "markdown.showPreviewToSide": (uri: Uri) => Promise<void>;
+  "workbench.action.closeActiveEditor": () => Promise<void>;
   revealFileInOS: (uri: Uri) => Promise<void>;
   setContext: (
     key: `${"codeql" | "codeQL"}${string}`,
@@ -115,6 +117,10 @@ export type QueryEditorCommands = {
     selectedQuery: Uri,
   ) => Promise<void>;
   "codeQL.previewQueryHelp": (selectedQuery: Uri) => Promise<void>;
+  "codeQL.previewQueryHelpContextEditor": (selectedQuery: Uri) => Promise<void>;
+  "codeQL.previewQueryHelpContextExplorer": (
+    selectedQuery: Uri,
+  ) => Promise<void>;
 };
 
 // Commands used for running local queries
@@ -125,8 +131,15 @@ export type LocalQueryCommands = {
   "codeQL.runQueryOnMultipleDatabasesContextEditor": (
     uri?: Uri,
   ) => Promise<void>;
+  "codeQLQueries.runLocalQueryFromQueriesPanel": TreeViewContextSingleSelectionCommandFunction<QueryTreeViewItem>;
+  "codeQLQueries.runLocalQueryContextMenu": TreeViewContextSingleSelectionCommandFunction<QueryTreeViewItem>;
+  "codeQLQueries.runLocalQueriesContextMenu": TreeViewContextSingleSelectionCommandFunction<QueryTreeViewItem>;
+  "codeQLQueries.runLocalQueriesFromPanel": TreeViewContextSingleSelectionCommandFunction<QueryTreeViewItem>;
+  "codeQLQueries.createQuery": () => Promise<void>;
+  "codeQL.runLocalQueryFromFileTab": (uri: Uri) => Promise<void>;
   "codeQL.runQueries": ExplorerSelectionCommandFunction<Uri>;
   "codeQL.quickEval": (uri: Uri) => Promise<void>;
+  "codeQL.quickEvalCount": (uri: Uri) => Promise<void>;
   "codeQL.quickEvalContextEditor": (uri: Uri) => Promise<void>;
   "codeQL.codeLensQuickEval": (uri: Uri, range: Range) => Promise<void>;
   "codeQL.quickQuery": () => Promise<void>;
@@ -233,10 +246,6 @@ export type VariantAnalysisCommands = {
     scannedRepo: VariantAnalysisScannedRepository,
     variantAnalysisSummary: VariantAnalysis,
   ) => Promise<void>;
-  "codeQL.copyVariantAnalysisRepoList": (
-    variantAnalysisId: number,
-    filterSort?: RepositoriesFilterSortStateWithIds,
-  ) => Promise<void>;
   "codeQL.loadVariantAnalysisRepoResults": (
     variantAnalysisId: number,
     repositoryFullName: string,
@@ -247,6 +256,9 @@ export type VariantAnalysisCommands = {
   "codeQL.monitorRehydratedVariantAnalysis": (
     variantAnalysis: VariantAnalysis,
   ) => Promise<void>;
+  "codeQL.monitorReauthenticatedVariantAnalysis": (
+    variantAnalysis: VariantAnalysis,
+  ) => Promise<void>;
   "codeQL.openVariantAnalysisLogs": (
     variantAnalysisId: number,
   ) => Promise<void>;
@@ -255,6 +267,7 @@ export type VariantAnalysisCommands = {
   ) => Promise<void>;
   "codeQL.runVariantAnalysis": (uri?: Uri) => Promise<void>;
   "codeQL.runVariantAnalysisContextEditor": (uri?: Uri) => Promise<void>;
+  "codeQLQueries.runVariantAnalysisContextMenu": TreeViewContextSingleSelectionCommandFunction<QueryTreeViewItem>;
 };
 
 export type DatabasePanelCommands = {
@@ -268,6 +281,7 @@ export type DatabasePanelCommands = {
   "codeQLVariantAnalysisRepositories.openOnGitHubContextMenu": TreeViewContextSingleSelectionCommandFunction<DbTreeViewItem>;
   "codeQLVariantAnalysisRepositories.renameItemContextMenu": TreeViewContextSingleSelectionCommandFunction<DbTreeViewItem>;
   "codeQLVariantAnalysisRepositories.removeItemContextMenu": TreeViewContextSingleSelectionCommandFunction<DbTreeViewItem>;
+  "codeQLVariantAnalysisRepositories.importFromCodeSearch": TreeViewContextSingleSelectionCommandFunction<DbTreeViewItem>;
 };
 
 export type AstCfgCommands = {
@@ -289,8 +303,12 @@ export type PackagingCommands = {
   "codeQL.downloadPacks": () => Promise<void>;
 };
 
-export type DataExtensionsEditorCommands = {
-  "codeQL.openDataExtensionsEditor": () => Promise<void>;
+export type ModelEditorCommands = {
+  "codeQL.openModelEditor": () => Promise<void>;
+  "codeQLModelEditor.jumpToUsageLocation": (
+    usage: Usage,
+    databaseItem: DatabaseItem,
+  ) => Promise<void>;
 };
 
 export type EvalLogViewerCommands = {
@@ -299,6 +317,7 @@ export type EvalLogViewerCommands = {
 
 export type SummaryLanguageSupportCommands = {
   "codeQL.gotoQL": () => Promise<void>;
+  "codeQL.gotoQLContextEditor": () => Promise<void>;
 };
 
 export type TestUICommands = {
@@ -329,7 +348,7 @@ export type AllExtensionCommands = BaseCommands &
   AstCfgCommands &
   AstViewerCommands &
   PackagingCommands &
-  DataExtensionsEditorCommands &
+  ModelEditorCommands &
   EvalLogViewerCommands &
   SummaryLanguageSupportCommands &
   Partial<TestUICommands> &

extensions/ql-vscode/src/common/discovery.ts

@@ -1,25 +1,38 @@
-import { DisposableObject } from "../pure/disposable-object";
-import { extLogger } from "../common";
-import { getErrorMessage } from "../pure/helpers-pure";
+import { DisposableObject } from "./disposable-object";
+import { getErrorMessage } from "./helpers-pure";
+import { Logger } from "./logging";
 
 /**
  * Base class for "discovery" operations, which scan the file system to find specific kinds of
  * files. This class automatically prevents more than one discovery operation from running at the
  * same time.
  */
-export abstract class Discovery<T> extends DisposableObject {
-  private retry = false;
-  private discoveryInProgress = false;
+export abstract class Discovery extends DisposableObject {
+  private restartWhenFinished = false;
+  private currentDiscoveryPromise: Promise<void> | undefined;
 
-  constructor(private readonly name: string) {
+  constructor(
+    protected readonly name: string,
+    private readonly logger: Logger,
+  ) {
     super();
   }
 
+  /**
+   * Returns the promise of the currently running refresh operation, if one is in progress.
+   * Otherwise returns a promise that resolves immediately.
+   */
+  public waitForCurrentRefresh(): Promise<void> {
+    return this.currentDiscoveryPromise ?? Promise.resolve();
+  }
+
   /**
    * Force the discovery process to run. Normally invoked by the derived class when a relevant file
    * system change is detected.
+   *
+   * Returns a promise that resolves when the refresh is complete, including any retries.
    */
-  public refresh(): void {
+  public refresh(): Promise<void> {
     // We avoid having multiple discovery operations in progress at the same time. Otherwise, if we
     // got a storm of refresh requests due to, say, the copying or deletion of a large directory
     // tree, we could potentially spawn a separate simultaneous discovery operation for each
@@ -36,14 +49,16 @@ export abstract class Discovery<T> extends DisposableObject {
     // other change notifications that might be coming along. However, this would create more
     // latency in the common case, in order to save a bit of latency in the uncommon case.
 
-    if (this.discoveryInProgress) {
+    if (this.currentDiscoveryPromise !== undefined) {
       // There's already a discovery operation in progress. Tell it to restart when it's done.
-      this.retry = true;
+      this.restartWhenFinished = true;
     } else {
       // No discovery in progress, so start one now.
-      this.discoveryInProgress = true;
-      this.launchDiscovery();
+      this.currentDiscoveryPromise = this.launchDiscovery().finally(() => {
+        this.currentDiscoveryPromise = undefined;
+      });
     }
+    return this.currentDiscoveryPromise;
   }
 
   /**
@@ -51,46 +66,28 @@ export abstract class Discovery<T> extends DisposableObject {
    * discovery operation completes, the `update` function will be invoked with the results of the
    * discovery.
    */
-  private launchDiscovery(): void {
-    const discoveryPromise = this.discover();
-    discoveryPromise
-      .then((results) => {
-        if (!this.retry) {
-          // Update any listeners with the results of the discovery.
-          this.discoveryInProgress = false;
-          this.update(results);
-        }
-      })
+  private async launchDiscovery(): Promise<void> {
+    try {
+      await this.discover();
+    } catch (err) {
+      void this.logger.log(
+        `${this.name} failed. Reason: ${getErrorMessage(err)}`,
+      );
+    }
 
-      .catch((err: unknown) => {
-        void extLogger.log(
-          `${this.name} failed. Reason: ${getErrorMessage(err)}`,
-        );
-      })
-
-      .finally(() => {
-        if (this.retry) {
-          // Another refresh request came in while we were still running a previous discovery
-          // operation. Since the discovery results we just computed are now stale, we'll launch
-          // another discovery operation instead of updating.
-          // Note that by doing this inside of `finally`, we will relaunch discovery even if the
-          // initial discovery operation failed.
-          this.retry = false;
-          this.launchDiscovery();
-        }
-      });
+    if (this.restartWhenFinished) {
+      // Another refresh request came in while we were still running a previous discovery
+      // operation. Since the discovery results we just computed are now stale, we'll launch
+      // another discovery operation instead of updating.
+      // We want to relaunch discovery regardless of if the initial discovery operation
+      // succeeded or failed.
+      this.restartWhenFinished = false;
+      await this.launchDiscovery();
+    }
   }
 
   /**
    * Overridden by the derived class to spawn the actual discovery operation, returning the results.
    */
-  protected abstract discover(): Promise<T>;
-
-  /**
-   * Overridden by the derived class to atomically update the `Discovery` object with the results of
-   * the discovery operation, and to notify any listeners that the discovery results may have
-   * changed.
-   * @param results The discovery results returned by the `discover` function.
-   */
-  protected abstract update(results: T): void;
+  protected abstract discover(): Promise<void>;
 }

extensions/ql-vscode/src/common/events.ts

@@ -1,10 +1,10 @@
-import { Disposable } from "../pure/disposable-object";
+import { Disposable } from "./disposable-object";
 
 export interface AppEvent<T> {
   (listener: (event: T) => void): Disposable;
 }
 
-export interface AppEventEmitter<T> {
+export interface AppEventEmitter<T> extends Disposable {
   event: AppEvent<T>;
   fire(data: T): void;
 }

extensions/ql-vscode/src/common/file-tree-nodes.ts

@@ -0,0 +1,122 @@
+import { basename, dirname, join } from "path";
+import { EnvironmentContext } from "./app";
+
+/**
+ * A node in the tree of files. This will be either a `FileTreeDirectory` or a `FileTreeLeaf`.
+ */
+export abstract class FileTreeNode<T = undefined> {
+  constructor(
+    private _path: string,
+    private _name: string,
+    private _data?: T,
+  ) {}
+
+  public get path(): string {
+    return this._path;
+  }
+
+  public get name(): string {
+    return this._name;
+  }
+
+  public get data(): T | undefined {
+    return this._data;
+  }
+
+  public abstract get children(): ReadonlyArray<FileTreeNode<T>>;
+
+  public abstract finish(): void;
+}
+
+/**
+ * A directory containing one or more files or other directories.
+ */
+export class FileTreeDirectory<T = undefined> extends FileTreeNode<T> {
+  constructor(
+    _path: string,
+    _name: string,
+    protected readonly env: EnvironmentContext,
+    private _children: Array<FileTreeNode<T>> = [],
+  ) {
+    super(_path, _name);
+  }
+
+  public get children(): ReadonlyArray<FileTreeNode<T>> {
+    return this._children;
+  }
+
+  public addChild(child: FileTreeNode<T>): void {
+    this._children.push(child);
+  }
+
+  public createDirectory(relativePath: string): FileTreeDirectory<T> {
+    if (relativePath === ".") {
+      return this;
+    }
+    const dirName = dirname(relativePath);
+    if (dirName === ".") {
+      return this.createChildDirectory(relativePath);
+    } else {
+      const parent = this.createDirectory(dirName);
+      return parent.createDirectory(basename(relativePath));
+    }
+  }
+
+  public finish(): void {
+    // remove empty directories
+    this._children.filter(
+      (child) => child instanceof FileTreeLeaf || child.children.length > 0,
+    );
+    this._children.sort((a, b) =>
+      a.name.localeCompare(b.name, this.env.language),
+    );
+    this._children.forEach((child, i) => {
+      child.finish();
+      if (
+        child.children?.length === 1 &&
+        child.children[0] instanceof FileTreeDirectory
+      ) {
+        // collapse children
+        const replacement = new FileTreeDirectory<T>(
+          child.children[0].path,
+          `${child.name} / ${child.children[0].name}`,
+          this.env,
+          Array.from(child.children[0].children),
+        );
+        this._children[i] = replacement;
+      }
+    });
+  }
+
+  private createChildDirectory(name: string): FileTreeDirectory<T> {
+    const existingChild = this._children.find((child) => child.name === name);
+    if (existingChild !== undefined) {
+      return existingChild as FileTreeDirectory<T>;
+    } else {
+      const newChild = new FileTreeDirectory<T>(
+        join(this.path, name),
+        name,
+        this.env,
+      );
+      this.addChild(newChild);
+      return newChild;
+    }
+  }
+}
+
+/**
+ * A single file.
+ */
+export class FileTreeLeaf<T = undefined> extends FileTreeNode<T> {
+  constructor(_path: string, _name: string, _data?: T) {
+    super(_path, _name, _data);
+  }
+
+  public get children(): ReadonlyArray<FileTreeNode<T>> {
+    return [];
+  }
+
+  public finish(): void {
+    /**/
+  }
+}

extensions/ql-vscode/src/common/files.ts

@@ -0,0 +1,129 @@
+import { pathExists, stat, readdir, opendir } from "fs-extra";
+import { isAbsolute, join, relative, resolve } from "path";
+import { tmpdir as osTmpdir } from "os";
+
+/**
+ * Recursively finds all .ql files in this set of Uris.
+ *
+ * @param paths The list of Uris to search through
+ *
+ * @returns list of ql files and a boolean describing whether or not a directory was found/
+ */
+export async function gatherQlFiles(
+  paths: string[],
+): Promise<[string[], boolean]> {
+  const gatheredUris: Set<string> = new Set();
+  let dirFound = false;
+  for (const nextPath of paths) {
+    if ((await pathExists(nextPath)) && (await stat(nextPath)).isDirectory()) {
+      dirFound = true;
+      const subPaths = await readdir(nextPath);
+      const fullPaths = subPaths.map((p) => join(nextPath, p));
+      const nestedFiles = (await gatherQlFiles(fullPaths))[0];
+      nestedFiles.forEach((nested) => gatheredUris.add(nested));
+    } else if (nextPath.endsWith(".ql")) {
+      gatheredUris.add(nextPath);
+    }
+  }
+  return [Array.from(gatheredUris), dirFound];
+}
+
+/**
+ * Lists the names of directories inside the given path.
+ * @param path The path to the directory to read.
+ * @returns the names of the directories inside the given path.
+ */
+export async function getDirectoryNamesInsidePath(
+  path: string,
+): Promise<string[]> {
+  if (!(await pathExists(path))) {
+    throw Error(`Path does not exist: ${path}`);
+  }
+  if (!(await stat(path)).isDirectory()) {
+    throw Error(`Path is not a directory: ${path}`);
+  }
+
+  const dirItems = await readdir(path, { withFileTypes: true });
+
+  const dirNames = dirItems
+    .filter((dirent) => dirent.isDirectory())
+    .map((dirent) => dirent.name);
+
+  return dirNames;
+}
+
+export function normalizePath(path: string): string {
+  // On Windows, "C:/", "C:\", and "c:/" are all equivalent. We need
+  // to normalize the paths to ensure they all get resolved to the
+  // same format. On Windows, we also need to do the comparison
+  // case-insensitively.
+  path = resolve(path);
+  if (process.platform === "win32") {
+    path = path.toLowerCase();
+  }
+  return path;
+}
+
+export function pathsEqual(path1: string, path2: string): boolean {
+  return normalizePath(path1) === normalizePath(path2);
+}
+
+/**
+ * Returns true if `parent` contains `child`, or if they are equal.
+ */
+export function containsPath(parent: string, child: string): boolean {
+  const relativePath = relative(parent, child);
+  return (
+    !relativePath.startsWith("..") &&
+    // On windows, if the two paths are in different drives, then the
+    // relative path will be an absolute path to the other drive.
+    !isAbsolute(relativePath)
+  );
+}
+
+export async function readDirFullPaths(path: string): Promise<string[]> {
+  const baseNames = await readdir(path);
+  return baseNames.map((baseName) => join(path, baseName));
+}
+
+/**
+ * Recursively walk a directory and return the full path to all files found.
+ * Symbolic links are ignored.
+ *
+ * @param dir the directory to walk
+ *
+ * @return An iterator of the full path to all files recursively found in the directory.
+ */
+export async function* walkDirectory(
+  dir: string,
+): AsyncIterableIterator<string> {
+  const seenFiles = new Set<string>();
+  for await (const d of await opendir(dir)) {
+    const entry = join(dir, d.name);
+    seenFiles.add(entry);
+    if (d.isDirectory()) {
+      yield* walkDirectory(entry);
+    } else if (d.isFile()) {
+      yield entry;
+    }
+  }
+}
+
+/**
+ * Error thrown from methods from the `fs` module.
+ *
+ * In practice, any error matching this is likely an instance of `NodeJS.ErrnoException`.
+ * If desired in the future, we could model more fields or use `NodeJS.ErrnoException` directly.
+ */
+export interface IOError {
+  readonly code: string;
+}
+
+export function isIOError(e: any): e is IOError {
+  return e.code !== undefined && typeof e.code === "string";
+}
+
+// This function is a wrapper around `os.tmpdir()` to make it easier to mock in tests.
+export function tmpdir(): string {
+  return osTmpdir();
+}

extensions/ql-vscode/src/common/github-url-identifier-helper.ts

@@ -1,4 +1,4 @@
-import { OWNER_REGEX, REPO_REGEX } from "../pure/helpers-pure";
+import { OWNER_REGEX, REPO_REGEX } from "./helpers-pure";
 
 /**
  * Checks if a string is a valid GitHub NWO.

extensions/ql-vscode/src/common/index.ts

@@ -1 +0,0 @@
-export * from "./logging";

extensions/ql-vscode/src/common/interface-types.ts

@@ -5,18 +5,22 @@ import {
   ResultSetSchema,
   Column,
   ResolvableLocationValue,
-} from "./bqrs-cli-types";
+} from "../common/bqrs-cli-types";
 import {
   VariantAnalysis,
   VariantAnalysisScannedRepositoryResult,
   VariantAnalysisScannedRepositoryState,
 } from "../variant-analysis/shared/variant-analysis";
-import { RepositoriesFilterSortStateWithIds } from "./variant-analysis-filter-sort";
-import { ErrorLike } from "./errors";
+import {
+  RepositoriesFilterSortState,
+  RepositoriesFilterSortStateWithIds,
+} from "../variant-analysis/shared/variant-analysis-filter-sort";
+import { ErrorLike } from "../common/errors";
 import { DataFlowPaths } from "../variant-analysis/shared/data-flow-paths";
-import { ExternalApiUsage } from "../data-extensions-editor/external-api-usage";
-import { ModeledMethod } from "../data-extensions-editor/modeled-method";
-import { DataExtensionEditorViewState } from "../data-extensions-editor/shared/view-state";
+import { Method, Usage } from "../model-editor/method";
+import { ModeledMethod } from "../model-editor/modeled-method";
+import { ModelEditorViewState } from "../model-editor/shared/view-state";
+import { Mode } from "../model-editor/shared/mode";
 
 /**
  * This module contains types and code that are shared between
@@ -72,11 +76,9 @@ export type GraphInterpretationData = {
   dot: string[];
 };
 
-export type InterpretationData =
-  | SarifInterpretationData
-  | GraphInterpretationData;
+type InterpretationData = SarifInterpretationData | GraphInterpretationData;
 
-export interface InterpretationT<T> {
+interface InterpretationT<T> {
   sourceLocationPrefix: string;
   numTruncatedResults: number;
   numTotalResults: number;
@@ -102,7 +104,7 @@ export type SortedResultsMap = { [resultSet: string]: SortedResultSetInfo };
  *
  * As a result of receiving this message, listeners might want to display a loading indicator.
  */
-export interface ResultsUpdatingMsg {
+interface ResultsUpdatingMsg {
   t: "resultsUpdating";
 }
 
@@ -110,7 +112,7 @@ export interface ResultsUpdatingMsg {
  * Message to set the initial state of the results view with a new
  * query.
  */
-export interface SetStateMsg {
+interface SetStateMsg {
   t: "setState";
   resultsPath: string;
   origResultsPaths: ResultsPaths;
@@ -139,7 +141,7 @@ export interface SetStateMsg {
  * Message indicating that the results view should display interpreted
  * results.
  */
-export interface ShowInterpretedPageMsg {
+interface ShowInterpretedPageMsg {
   t: "showInterpretedPage";
   interpretation: Interpretation;
   database: DatabaseInfo;
@@ -169,7 +171,7 @@ export interface NavigateMsg {
  * A message indicating that the results view should untoggle the
  * "Show results in Problems view" checkbox.
  */
-export interface UntoggleShowProblemsMsg {
+interface UntoggleShowProblemsMsg {
   t: "untoggleShowProblems";
 }
 
@@ -199,7 +201,7 @@ export type FromResultsViewMsg =
  * Message from the results view to open a database source
  * file at the provided location.
  */
-export interface ViewSourceFileMsg {
+interface ViewSourceFileMsg {
   t: "viewSourceFile";
   loc: ResolvableLocationValue;
   databaseUri: string;
@@ -208,7 +210,7 @@ export interface ViewSourceFileMsg {
 /**
  * Message from the results view to open a file in an editor.
  */
-export interface OpenFileMsg {
+interface OpenFileMsg {
   t: "openFile";
   /* Full path to the file to open. */
   filePath: string;
@@ -270,7 +272,7 @@ export interface RawResultsSortState {
   sortDirection: SortDirection;
 }
 
-export type InterpretedResultsSortColumn = "alert-message";
+type InterpretedResultsSortColumn = "alert-message";
 
 export interface InterpretedResultsSortState {
   sortBy: InterpretedResultsSortColumn;
@@ -314,7 +316,7 @@ export type FromCompareViewMessage =
 /**
  * Message from the compare view to request opening a query.
  */
-export interface OpenQueryMessage {
+interface OpenQueryMessage {
   readonly t: "openQuery";
   readonly kind: "from" | "to";
 }
@@ -402,63 +404,69 @@ export interface ParsedResultSets {
   resultSet: ResultSet;
 }
 
-export interface SetVariantAnalysisMessage {
+interface SetVariantAnalysisMessage {
   t: "setVariantAnalysis";
   variantAnalysis: VariantAnalysis;
 }
 
+interface SetFilterSortStateMessage {
+  t: "setFilterSortState";
+  filterSortState: RepositoriesFilterSortState;
+}
+
 export type VariantAnalysisState = {
   variantAnalysisId: number;
 };
 
-export interface SetRepoResultsMessage {
+interface SetRepoResultsMessage {
   t: "setRepoResults";
   repoResults: VariantAnalysisScannedRepositoryResult[];
 }
 
-export interface SetRepoStatesMessage {
+interface SetRepoStatesMessage {
   t: "setRepoStates";
   repoStates: VariantAnalysisScannedRepositoryState[];
 }
 
-export interface RequestRepositoryResultsMessage {
+interface RequestRepositoryResultsMessage {
   t: "requestRepositoryResults";
   repositoryFullName: string;
 }
 
-export interface OpenQueryFileMessage {
+interface OpenQueryFileMessage {
   t: "openQueryFile";
 }
 
-export interface OpenQueryTextMessage {
+interface OpenQueryTextMessage {
   t: "openQueryText";
 }
 
-export interface CopyRepositoryListMessage {
+interface CopyRepositoryListMessage {
   t: "copyRepositoryList";
   filterSort?: RepositoriesFilterSortStateWithIds;
 }
 
-export interface ExportResultsMessage {
+interface ExportResultsMessage {
   t: "exportResults";
   filterSort?: RepositoriesFilterSortStateWithIds;
 }
 
-export interface OpenLogsMessage {
+interface OpenLogsMessage {
   t: "openLogs";
 }
 
-export interface CancelVariantAnalysisMessage {
+interface CancelVariantAnalysisMessage {
   t: "cancelVariantAnalysis";
 }
 
-export interface ShowDataFlowPathsMessage {
+interface ShowDataFlowPathsMessage {
   t: "showDataFlowPaths";
   dataFlowPaths: DataFlowPaths;
 }
 
 export type ToVariantAnalysisMessage =
   | SetVariantAnalysisMessage
+  | SetFilterSortStateMessage
   | SetRepoResultsMessage
   | SetRepoStatesMessage;
 
@@ -473,7 +481,7 @@ export type FromVariantAnalysisMessage =
   | CancelVariantAnalysisMessage
   | ShowDataFlowPathsMessage;
 
-export interface SetDataFlowPathsMessage {
+interface SetDataFlowPathsMessage {
   t: "setDataFlowPaths";
   dataFlowPaths: DataFlowPaths;
 }
@@ -482,69 +490,114 @@ export type ToDataFlowPathsMessage = SetDataFlowPathsMessage;
 
 export type FromDataFlowPathsMessage = CommonFromViewMessages;
 
-export interface SetExtensionPackStateMessage {
-  t: "setDataExtensionEditorViewState";
-  viewState: DataExtensionEditorViewState;
+interface SetExtensionPackStateMessage {
+  t: "setModelEditorViewState";
+  viewState: ModelEditorViewState;
 }
 
-export interface SetExternalApiUsagesMessage {
-  t: "setExternalApiUsages";
-  externalApiUsages: ExternalApiUsage[];
+interface SetMethodsMessage {
+  t: "setMethods";
+  methods: Method[];
 }
 
-export interface ShowProgressMessage {
-  t: "showProgress";
-  step: number;
-  maxStep: number;
-  message: string;
+interface LoadModeledMethodsMessage {
+  t: "loadModeledMethods";
+  modeledMethods: Record<string, ModeledMethod>;
 }
 
-export interface AddModeledMethodsMessage {
+interface AddModeledMethodsMessage {
   t: "addModeledMethods";
   modeledMethods: Record<string, ModeledMethod>;
-
-  /**
-   * If true, then any existing modeled methods set to "none" will be
-   * overwritten by the new modeled methods. Otherwise, the "none" modeled
-   * methods will not be overwritten, even if the new modeled methods
-   * contain a better model.
-   */
-  overrideNone?: boolean;
 }
 
-export interface JumpToUsageMessage {
+interface SetInProgressMethodsMessage {
+  t: "setInProgressMethods";
+  packageName: string;
+  inProgressMethods: string[];
+}
+
+interface SwitchModeMessage {
+  t: "switchMode";
+  mode: Mode;
+}
+
+interface JumpToUsageMessage {
   t: "jumpToUsage";
-  location: ResolvableLocationValue;
+  method: Method;
+  usage: Usage;
 }
 
-export interface OpenExtensionPackMessage {
+interface OpenDatabaseMessage {
+  t: "openDatabase";
+}
+
+interface OpenExtensionPackMessage {
   t: "openExtensionPack";
 }
 
-export interface OpenModelFileMessage {
-  t: "openModelFile";
+interface RefreshMethods {
+  t: "refreshMethods";
 }
 
-export interface SaveModeledMethods {
+interface SaveModeledMethods {
   t: "saveModeledMethods";
-  externalApiUsages: ExternalApiUsage[];
+  methods: Method[];
   modeledMethods: Record<string, ModeledMethod>;
 }
 
-export interface GenerateExternalApiMessage {
-  t: "generateExternalApi";
+interface GenerateMethodMessage {
+  t: "generateMethod";
 }
 
-export type ToDataExtensionsEditorMessage =
-  | SetExtensionPackStateMessage
-  | SetExternalApiUsagesMessage
-  | ShowProgressMessage
-  | AddModeledMethodsMessage;
+interface GenerateMethodsFromLlmMessage {
+  t: "generateMethodsFromLlm";
+  packageName: string;
+  methods: Method[];
+  modeledMethods: Record<string, ModeledMethod>;
+}
 
-export type FromDataExtensionsEditorMessage =
+interface StopGeneratingMethodsFromLlmMessage {
+  t: "stopGeneratingMethodsFromLlm";
+  packageName: string;
+}
+
+interface ModelDependencyMessage {
+  t: "modelDependency";
+}
+
+interface HideModeledApisMessage {
+  t: "hideModeledApis";
+  hideModeledApis: boolean;
+}
+
+export type ToModelEditorMessage =
+  | SetExtensionPackStateMessage
+  | SetMethodsMessage
+  | LoadModeledMethodsMessage
+  | AddModeledMethodsMessage
+  | SetInProgressMethodsMessage;
+
+export type FromModelEditorMessage =
   | ViewLoadedMsg
-  | OpenModelFileMessage
+  | SwitchModeMessage
+  | RefreshMethods
+  | OpenDatabaseMessage
   | OpenExtensionPackMessage
   | JumpToUsageMessage
   | SaveModeledMethods
-  | GenerateExternalApiMessage;
+  | GenerateMethodMessage
+  | GenerateMethodsFromLlmMessage
+  | StopGeneratingMethodsFromLlmMessage
+  | ModelDependencyMessage
+  | HideModeledApisMessage;
+
+export type FromMethodModelingMessage =
+  | TelemetryMessage
+  | UnhandledErrorMessage;
+
+interface SetMethodMessage {
+  t: "setMethod";
+  method: Method;
+}
+
+export type ToMethodModelingMessage = SetMethodMessage;

extensions/ql-vscode/src/common/invocation-rate-limiter.ts

@@ -0,0 +1,89 @@
+import { Memento } from "./memento";
+
+/**
+ * Provides a utility method to invoke a function only if a minimum time interval has elapsed since
+ * the last invocation of that function.
+ */
+export class InvocationRateLimiter<T> {
+  constructor(
+    private readonly globalState: Memento,
+    private readonly funcIdentifier: string,
+    private readonly func: () => Promise<T>,
+    private readonly createDate: (dateString?: string) => Date = (s) =>
+      s ? new Date(s) : new Date(),
+  ) {}
+
+  /**
+   * Invoke the function if `minSecondsSinceLastInvocation` seconds have elapsed since the last invocation.
+   */
+  public async invokeFunctionIfIntervalElapsed(
+    minSecondsSinceLastInvocation: number,
+  ): Promise<InvocationRateLimiterResult<T>> {
+    const updateCheckStartDate = this.createDate();
+    const lastInvocationDate = this.getLastInvocationDate();
+    if (
+      minSecondsSinceLastInvocation &&
+      lastInvocationDate &&
+      lastInvocationDate <= updateCheckStartDate &&
+      lastInvocationDate.getTime() + minSecondsSinceLastInvocation * 1000 >
+        updateCheckStartDate.getTime()
+    ) {
+      return createRateLimitedResult();
+    }
+    const result = await this.func();
+    await this.setLastInvocationDate(updateCheckStartDate);
+    return createInvokedResult(result);
+  }
+
+  private getLastInvocationDate(): Date | undefined {
+    const maybeDateString: string | undefined = this.globalState.get(
+      InvocationRateLimiter._invocationRateLimiterPrefix + this.funcIdentifier,
+    );
+    return maybeDateString ? this.createDate(maybeDateString) : undefined;
+  }
+
+  private async setLastInvocationDate(date: Date): Promise<void> {
+    return await this.globalState.update(
+      InvocationRateLimiter._invocationRateLimiterPrefix + this.funcIdentifier,
+      date,
+    );
+  }
+
+  private static readonly _invocationRateLimiterPrefix =
+    "invocationRateLimiter_lastInvocationDate_";
+}
+
+export enum InvocationRateLimiterResultKind {
+  Invoked,
+  RateLimited,
+}
+
+/**
+ * The function was invoked and returned the value `result`.
+ */
+interface InvokedResult<T> {
+  kind: InvocationRateLimiterResultKind.Invoked;
+  result: T;
+}
+
+/**
+ * The function was not invoked as the minimum interval since the last invocation had not elapsed.
+ */
+interface RateLimitedResult {
+  kind: InvocationRateLimiterResultKind.RateLimited;
+}
+
+type InvocationRateLimiterResult<T> = InvokedResult<T> | RateLimitedResult;
+
+function createInvokedResult<T>(result: T): InvokedResult<T> {
+  return {
+    kind: InvocationRateLimiterResultKind.Invoked,
+    result,
+  };
+}
+
+function createRateLimitedResult(): RateLimitedResult {
+  return {
+    kind: InvocationRateLimiterResultKind.RateLimited,
+  };
+}

extensions/ql-vscode/src/common/location-link-utils.ts

@@ -0,0 +1,27 @@
+import { FileLink } from "../variant-analysis/shared/analysis-result";
+
+export function createRemoteFileRef(
+  fileLink: FileLink,
+  startLine?: number,
+  endLine?: number,
+  startColumn?: number,
+  endColumn?: number,
+): string {
+  if (
+    startColumn &&
+    endColumn &&
+    startLine &&
+    endLine &&
+    // Verify that location information is valid; otherwise highlighting might be broken
+    ((startLine === endLine && startColumn < endColumn) || startLine < endLine)
+  ) {
+    // This relies on column highlighting of new code view on GitHub
+    return `${fileLink.fileLinkPrefix}/${fileLink.filePath}#L${startLine}C${startColumn}-L${endLine}C${endColumn}`;
+  } else if (startLine && endLine && startLine < endLine) {
+    return `${fileLink.fileLinkPrefix}/${fileLink.filePath}#L${startLine}-L${endLine}`;
+  } else if (startLine) {
+    return `${fileLink.fileLinkPrefix}/${fileLink.filePath}#L${startLine}`;
+  } else {
+    return `${fileLink.fileLinkPrefix}/${fileLink.filePath}`;
+  }
+}

extensions/ql-vscode/src/common/logging/index.ts

@@ -1,4 +1,4 @@
 export * from "./logger";
+export * from "./notification-logger";
+export * from "./notifications";
 export * from "./tee-logger";
-export * from "./vscode/loggers";
-export * from "./vscode/output-channel-logger";

extensions/ql-vscode/src/common/logging/notification-logger.ts

@@ -0,0 +1,7 @@
+import { Logger } from "./logger";
+
+export interface NotificationLogger extends Logger {
+  showErrorMessage(message: string): Promise<void>;
+  showWarningMessage(message: string): Promise<void>;
+  showInformationMessage(message: string): Promise<void>;
+}

extensions/ql-vscode/src/common/logging/notifications.ts

@@ -0,0 +1,116 @@
+import { NotificationLogger } from "./notification-logger";
+import { AppTelemetry } from "../telemetry";
+import { RedactableError } from "../errors";
+
+interface ShowAndLogOptions {
+  /**
+   * An alternate message that is added to the log, but not displayed in the popup.
+   * This is useful for adding extra detail to the logs that would be too noisy for the popup.
+   */
+  fullMessage?: string;
+}
+
+/**
+ * Show an error message and log it to the console
+ *
+ * @param logger The logger that will receive the message.
+ * @param message The message to show.
+ * @param options? See individual fields on `ShowAndLogOptions` type.
+ *
+ * @return A promise that resolves to the selected item or undefined when being dismissed.
+ */
+export async function showAndLogErrorMessage(
+  logger: NotificationLogger,
+  message: string,
+  options?: ShowAndLogOptions,
+): Promise<void> {
+  return internalShowAndLog(
+    logger,
+    dropLinesExceptInitial(message),
+    logger.showErrorMessage,
+    { fullMessage: message, ...options },
+  );
+}
+
+function dropLinesExceptInitial(message: string, n = 2) {
+  return message.toString().split(/\r?\n/).slice(0, n).join("\n");
+}
+
+/**
+ * Show a warning message and log it to the console
+ *
+ * @param logger The logger that will receive the message.
+ * @param message The message to show.
+ * @param options? See individual fields on `ShowAndLogOptions` type.
+ *
+ * @return A promise that resolves to the selected item or undefined when being dismissed.
+ */
+export async function showAndLogWarningMessage(
+  logger: NotificationLogger,
+  message: string,
+  options?: ShowAndLogOptions,
+): Promise<void> {
+  return internalShowAndLog(
+    logger,
+    message,
+    logger.showWarningMessage,
+    options,
+  );
+}
+
+/**
+ * Show an information message and log it to the console
+ *
+ * @param logger The logger that will receive the message.
+ * @param message The message to show.
+ * @param options? See individual fields on `ShowAndLogOptions` type.
+ *
+ * @return A promise that resolves to the selected item or undefined when being dismissed.
+ */
+export async function showAndLogInformationMessage(
+  logger: NotificationLogger,
+  message: string,
+  options?: ShowAndLogOptions,
+): Promise<void> {
+  return internalShowAndLog(
+    logger,
+    message,
+    logger.showInformationMessage,
+    options,
+  );
+}
+
+async function internalShowAndLog(
+  logger: NotificationLogger,
+  message: string,
+  fn: (message: string) => Promise<void>,
+  { fullMessage }: ShowAndLogOptions = {},
+): Promise<void> {
+  void logger.log(fullMessage || message);
+  await fn.bind(logger)(message);
+}
+
+interface ShowAndLogExceptionOptions extends ShowAndLogOptions {
+  /** Custom properties to include in the telemetry report. */
+  extraTelemetryProperties?: { [key: string]: string };
+}
+
+/**
+ * Show an error message, log it to the console, and emit redacted information as telemetry
+ *
+ * @param logger The logger that will receive the message.
+ * @param telemetry The telemetry instance to use for reporting.
+ * @param error The error to show. Only redacted information will be included in the telemetry.
+ * @param options See individual fields on `ShowAndLogExceptionOptions` type.
+ *
+ * @return A promise that resolves to the selected item or undefined when being dismissed.
+ */
+export async function showAndLogExceptionWithTelemetry(
+  logger: NotificationLogger,
+  telemetry: AppTelemetry | undefined,
+  error: RedactableError,
+  options: ShowAndLogExceptionOptions = {},
+): Promise<void> {
+  telemetry?.sendError(error, options.extraTelemetryProperties);
+  return showAndLogErrorMessage(logger, error.fullMessage, options);
+}

extensions/ql-vscode/src/common/logging/tee-logger.ts

@@ -1,6 +1,6 @@
 import { appendFile, ensureFile } from "fs-extra";
 import { isAbsolute } from "path";
-import { getErrorMessage } from "../../pure/helpers-pure";
+import { getErrorMessage } from "../helpers-pure";
 import { Logger, LogOptions } from "./logger";
 
 /**

extensions/ql-vscode/src/common/logging/vscode/index.ts

@@ -0,0 +1,2 @@
+export * from "./loggers";
+export * from "./output-channel-logger";

extensions/ql-vscode/src/common/logging/vscode/output-channel-logger.ts

@@ -1,11 +1,15 @@
 import { window as Window, OutputChannel, Progress } from "vscode";
 import { Logger, LogOptions } from "../logger";
-import { DisposableObject } from "../../../pure/disposable-object";
+import { DisposableObject } from "../../disposable-object";
+import { NotificationLogger } from "../notification-logger";
 
 /**
  * A logger that writes messages to an output channel in the VS Code Output tab.
  */
-export class OutputChannelLogger extends DisposableObject implements Logger {
+export class OutputChannelLogger
+  extends DisposableObject
+  implements Logger, NotificationLogger
+{
   public readonly outputChannel: OutputChannel;
   isCustomLogDirectory: boolean;
 
@@ -42,6 +46,30 @@ export class OutputChannelLogger extends DisposableObject implements Logger {
   show(preserveFocus?: boolean): void {
     this.outputChannel.show(preserveFocus);
   }
+
+  async showErrorMessage(message: string): Promise<void> {
+    await this.showMessage(message, Window.showErrorMessage);
+  }
+
+  async showInformationMessage(message: string): Promise<void> {
+    await this.showMessage(message, Window.showInformationMessage);
+  }
+
+  async showWarningMessage(message: string): Promise<void> {
+    await this.showMessage(message, Window.showWarningMessage);
+  }
+
+  private async showMessage(
+    message: string,
+    show: (message: string, ...items: string[]) => Thenable<string | undefined>,
+  ): Promise<void> {
+    const label = "Show Log";
+    const result = await show(message, label);
+
+    if (result === label) {
+      this.show();
+    }
+  }
 }
 
 export type ProgressReporter = Progress<{ message: string }>;

extensions/ql-vscode/src/common/mock-gh-api/gh-api-request.ts

@@ -1,5 +1,8 @@
-import { Repository } from "../repository";
-import { VariantAnalysis, VariantAnalysisRepoTask } from "../variant-analysis";
+import { Repository } from "../../variant-analysis/gh-api/repository";
+import {
+  VariantAnalysis,
+  VariantAnalysisRepoTask,
+} from "../../variant-analysis/gh-api/variant-analysis";
 
 // Types that represent requests/responses from the GitHub API
 // that we need to mock.
@@ -10,13 +13,15 @@ export enum RequestKind {
   GetVariantAnalysis = "getVariantAnalysis",
   GetVariantAnalysisRepo = "getVariantAnalysisRepo",
   GetVariantAnalysisRepoResult = "getVariantAnalysisRepoResult",
+  CodeSearch = "codeSearch",
+  AutoModel = "autoModel",
 }
 
-export interface BasicErorResponse {
+interface BasicErorResponse {
   message: string;
 }
 
-export interface GetRepoRequest {
+interface GetRepoRequest {
   request: {
     kind: RequestKind.GetRepo;
   };
@@ -26,7 +31,7 @@ export interface GetRepoRequest {
   };
 }
 
-export interface SubmitVariantAnalysisRequest {
+interface SubmitVariantAnalysisRequest {
   request: {
     kind: RequestKind.SubmitVariantAnalysis;
   };
@@ -36,7 +41,7 @@ export interface SubmitVariantAnalysisRequest {
   };
 }
 
-export interface GetVariantAnalysisRequest {
+interface GetVariantAnalysisRequest {
   request: {
     kind: RequestKind.GetVariantAnalysis;
   };
@@ -46,7 +51,7 @@ export interface GetVariantAnalysisRequest {
   };
 }
 
-export interface GetVariantAnalysisRepoRequest {
+interface GetVariantAnalysisRepoRequest {
   request: {
     kind: RequestKind.GetVariantAnalysisRepo;
     repositoryId: number;
@@ -69,12 +74,47 @@ export interface GetVariantAnalysisRepoResultRequest {
   };
 }
 
+interface CodeSearchRequest {
+  request: {
+    kind: RequestKind.CodeSearch;
+    query: string;
+  };
+  response: {
+    status: number;
+    body?: {
+      total_count?: number;
+      items?: Array<{
+        repository: Repository;
+      }>;
+    };
+    message?: string;
+  };
+}
+
+interface AutoModelRequest {
+  request: {
+    kind: RequestKind.AutoModel;
+    body?: {
+      candidates: string;
+    };
+  };
+  response: {
+    status: number;
+    body?: {
+      models: string;
+    };
+    message?: string;
+  };
+}
+
 export type GitHubApiRequest =
   | GetRepoRequest
   | SubmitVariantAnalysisRequest
   | GetVariantAnalysisRequest
   | GetVariantAnalysisRepoRequest
-  | GetVariantAnalysisRepoResultRequest;
+  | GetVariantAnalysisRepoResultRequest
+  | CodeSearchRequest
+  | AutoModelRequest;
 
 export const isGetRepoRequest = (
   request: GitHubApiRequest,
@@ -99,3 +139,13 @@ export const isGetVariantAnalysisRepoResultRequest = (
   request: GitHubApiRequest,
 ): request is GetVariantAnalysisRepoResultRequest =>
   request.request.kind === RequestKind.GetVariantAnalysisRepoResult;
+
+export const isCodeSearchRequest = (
+  request: GitHubApiRequest,
+): request is CodeSearchRequest =>
+  request.request.kind === RequestKind.CodeSearch;
+
+export const isAutoModelRequest = (
+  request: GitHubApiRequest,
+): request is AutoModelRequest =>
+  request.request.kind === RequestKind.AutoModel;

extensions/ql-vscode/src/common/mock-gh-api/mock-gh-api-server.ts

@@ -2,11 +2,11 @@ import { join, resolve } from "path";
 import { pathExists } from "fs-extra";
 import { setupServer, SetupServer } from "msw/node";
 
-import { DisposableObject } from "../../../pure/disposable-object";
+import { DisposableObject } from "../disposable-object";
 
 import { Recorder } from "./recorder";
 import { createRequestHandlers } from "./request-handlers";
-import { getDirectoryNamesInsidePath } from "../../../pure/files";
+import { getDirectoryNamesInsidePath } from "../files";
 
 /**
  * Enables mocking of the GitHub API server via HTTP interception, using msw.
@@ -129,11 +129,11 @@ export class MockGitHubApiServer extends DisposableObject {
 
   public async getDefaultScenariosPath(): Promise<string | undefined> {
     // This should be the directory where package.json is located
-    const rootDirectory = resolve(__dirname, "../../../..");
+    const rootDirectory = resolve(__dirname, "../../..");
 
     const scenariosPath = resolve(
       rootDirectory,
-      "src/variant-analysis/gh-api/mocks/scenarios",
+      "src/common/mock-gh-api/scenarios",
     );
     if (await pathExists(scenariosPath)) {
       return scenariosPath;

extensions/ql-vscode/src/common/mock-gh-api/recorder.ts

@@ -8,7 +8,7 @@ import { IsomorphicResponse } from "@mswjs/interceptors";
 import { Headers } from "headers-polyfill";
 import fetch from "node-fetch";
 
-import { DisposableObject } from "../../../pure/disposable-object";
+import { DisposableObject } from "../disposable-object";
 
 import {
   GetVariantAnalysisRepoResultRequest,
@@ -245,6 +245,35 @@ async function createGitHubApiRequest(
     };
   }
 
+  const codeSearchMatch = url.match(/\/search\/code\?q=(?<query>.*)$/);
+  if (codeSearchMatch?.groups?.query) {
+    return {
+      request: {
+        kind: RequestKind.CodeSearch,
+        query: codeSearchMatch?.groups?.query,
+      },
+      response: {
+        status,
+        body: JSON.parse(body),
+      },
+    };
+  }
+
+  const autoModelMatch = url.match(
+    /\/repos\/github\/codeql\/code-scanning\/codeql\/auto-model/,
+  );
+  if (autoModelMatch) {
+    return {
+      request: {
+        kind: RequestKind.AutoModel,
+      },
+      response: {
+        status,
+        body: JSON.parse(body),
+      },
+    };
+  }
+
   return undefined;
 }
 

extensions/ql-vscode/src/common/mock-gh-api/request-handlers.ts

@@ -3,6 +3,8 @@ import { readdir, readJson, readFile } from "fs-extra";
 import { DefaultBodyType, MockedRequest, rest, RestHandler } from "msw";
 import {
   GitHubApiRequest,
+  isAutoModelRequest,
+  isCodeSearchRequest,
   isGetRepoRequest,
   isGetVariantAnalysisRepoRequest,
   isGetVariantAnalysisRepoResultRequest,
@@ -12,7 +14,7 @@ import {
 
 const baseUrl = "https://api.github.com";
 
-export type RequestHandler = RestHandler<MockedRequest<DefaultBodyType>>;
+type RequestHandler = RestHandler<MockedRequest<DefaultBodyType>>;
 
 export async function createRequestHandlers(
   scenarioDirPath: string,
@@ -25,6 +27,8 @@ export async function createRequestHandlers(
     createGetVariantAnalysisRequestHandler(requests),
     createGetVariantAnalysisRepoRequestHandler(requests),
     createGetVariantAnalysisRepoResultRequestHandler(requests),
+    createCodeSearchRequestHandler(requests),
+    createAutoModelRequestHandler(requests),
   ];
 
   return handlers;
@@ -193,3 +197,54 @@ function createGetVariantAnalysisRepoResultRequestHandler(
     },
   );
 }
+
+function createCodeSearchRequestHandler(
+  requests: GitHubApiRequest[],
+): RequestHandler {
+  const codeSearchRequests = requests.filter(isCodeSearchRequest);
+  let requestIndex = 0;
+
+  // During a code search, there are multiple request to get pages of results. We
+  // need to return different responses for each request, so keep an index of the
+  // request and return the appropriate response.
+  return rest.get(`${baseUrl}/search/code?q=*`, (_req, res, ctx) => {
+    const request = codeSearchRequests[requestIndex];
+
+    if (requestIndex < codeSearchRequests.length - 1) {
+      // If there are more requests to come, increment the index.
+      requestIndex++;
+    }
+
+    return res(
+      ctx.status(request.response.status),
+      ctx.json(request.response.body),
+    );
+  });
+}
+
+function createAutoModelRequestHandler(
+  requests: GitHubApiRequest[],
+): RequestHandler {
+  const autoModelRequests = requests.filter(isAutoModelRequest);
+  let requestIndex = 0;
+
+  // During automodeling there can be multiple API requests for each batch
+  // of candidates we want to model. We need to return different responses for each request,
+  // so keep an index of the request and return the appropriate response.
+  return rest.post(
+    `${baseUrl}/repos/github/codeql/code-scanning/codeql/auto-model`,
+    (_req, res, ctx) => {
+      const request = autoModelRequests[requestIndex];
+
+      if (requestIndex < autoModelRequests.length - 1) {
+        // If there are more requests to come, increment the index.
+        requestIndex++;
+      }
+
+      return res(
+        ctx.status(request.response.status),
+        ctx.json(request.response.body),
+      );
+    },
+  );
+}

extensions/ql-vscode/src/common/mock-gh-api/scenarios/auto-model-success/0-autoModel.json

@@ -0,0 +1,11 @@
+{
+  "request": {
+    "kind": "autoModel"
+  },
+  "response": {
+    "status": 200,
+    "body": {
+      "models": "extensions:\n- addsTo: {extensible: sinkModel, pack: codeql/java-all}\n  data:\n  - [javax.servlet.http, HttpServletResponse, true, sendRedirect, (String), '', 'Argument[this]',\n    request-forgery, ai-generated]\n  - [javax.servlet.http, HttpServletResponse, true, sendRedirect, (String), '', 'Argument[0]',\n    request-forgery, ai-generated]\n"
+    }
+  }
+}

extensions/ql-vscode/src/common/mock-gh-api/scenarios/auto-model-success/1-autoModel.json

@@ -0,0 +1,11 @@
+{
+  "request": {
+    "kind": "autoModel"
+  },
+  "response": {
+    "status": 200,
+    "body": {
+      "models": "extensions:\n- addsTo: {extensible: sinkModel, pack: codeql/java-all}\n  data:\n  - [javax.servlet, MultipartConfigElement, true, MultipartConfigElement, (String),\n    '', 'Argument[0]', request-forgery, ai-generated]\n"
+    }
+  }
+}

extensions/ql-vscode/src/common/mock-gh-api/scenarios/auto-model-success/README.md

@@ -0,0 +1 @@
+This scenario is best when modeling the `javax.servlet-api` package.

extensions/ql-vscode/src/common/mock-gh-api/scenarios/code-search-success/10-codeSearch.json

@@ -0,0 +1,13 @@
+{
+  "request": {
+    "kind": "codeSearch",
+    "query": "org%3Adotnet+project+language%3Acsharp&per_page=100&page=10"
+  },
+  "response": {
+    "status": 403,
+    "body": {
+      "message": "API rate limit exceeded for user ID 311693.",
+      "documentation_url": "https://docs.github.com/rest/overview/resources-in-the-rest-api#rate-limiting"
+    }
+  }
+}

extensions/ql-vscode/src/common/mock-gh-api/scenarios/code-search-success/9-codeSearch.json

@@ -0,0 +1,13 @@
+{
+  "request": {
+    "kind": "codeSearch",
+    "query": "org%3Adotnet+project+language%3Acsharp&per_page=100&page=10"
+  },
+  "response": {
+    "status": 403,
+    "body": {
+      "message": "API rate limit exceeded for user ID 311693.",
+      "documentation_url": "https://docs.github.com/rest/overview/resources-in-the-rest-api#rate-limiting"
+    }
+  }
+}

extensions/ql-vscode/src/common/mock-gh-api/scenarios/mrva-problem-query-success/19-getVariantAnalysisRepoResult.json

@@ -5,7 +5,7 @@
   },
   "response": {
     "status": 200,
-    "body": "file:20-getVariantAnalysisRepoResult.body.zip",
+    "body": "file:19-getVariantAnalysisRepoResult.body.zip",
     "contentType": "application/zip"
   }
 }