Merge remote-tracking branch 'origin/main' into dbartol/save-before-start

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

@@ -2,9 +2,8 @@
  * @name Unwanted dependency on vscode API
  * @kind path-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".
+ * @id vscode-codeql/assert-no-vscode-dependency
+ * @description The modules stored under `common` should not have dependencies on the VS Code API
  */
 
 import javascript
@@ -13,12 +12,9 @@ class VSCodeImport extends ImportDeclaration {
   VSCodeImport() { this.getImportedPath().getValue() = "vscode" }
 }
 
-class PureFile extends File {
-  PureFile() {
-    (
-      this.getRelativePath().regexpMatch(".*/src/pure/.*") or
-      this.getRelativePath().regexpMatch(".*/src/common/.*")
-    ) and
+class CommonFile extends File {
+  CommonFile() {
+    this.getRelativePath().regexpMatch(".*/src/common/.*") and
     not this.getRelativePath().regexpMatch(".*/vscode/.*")
   }
 }
@@ -34,7 +30,8 @@ query predicate edges(AstNode a, AstNode b) {
 
 from Module m, VSCodeImport v
 where
-  m.getFile() instanceof PureFile and
+  m.getFile() instanceof CommonFile and
   edges+(m, v)
 select m, m, v,
-  "This module is not pure: it has a transitive dependency on the vscode API imported $@", v, "here"
+  "This module is in the 'common' directory but has a transitive dependency on the vscode API imported $@",
+  v, "here"

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

@@ -26,7 +26,7 @@ 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 "../pure/legacy-messages";
+import { CompilationMessage } from "../query-server/legacy-messages";
 import { sarifParser } from "../common/sarif-parser";
 import { App } from "../common/app";
 import { QueryLanguage } from "../common/query-language";

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

@@ -4,7 +4,7 @@ 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 { RepositoriesFilterSortStateWithIds } from "../variant-analysis/shared/variant-analysis-filter-sort";
 import type { TestTreeNode } from "../query-testing/test-tree-node";
 import type {
   VariantAnalysis,

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

@@ -1,5 +1,6 @@
 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.
@@ -121,3 +122,8 @@ export interface IOError {
 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/interface-types.ts

@@ -14,7 +14,7 @@ import {
 import {
   RepositoriesFilterSortState,
   RepositoriesFilterSortStateWithIds,
-} from "../pure/variant-analysis-filter-sort";
+} 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";

extensions/ql-vscode/src/config.ts

@@ -14,7 +14,7 @@ import {
   FilterKey,
   SortKey,
   defaultFilterSortState,
-} from "./pure/variant-analysis-filter-sort";
+} from "./variant-analysis/shared/variant-analysis-filter-sort";
 
 export const ALL_SETTINGS: Setting[] = [];
 
@@ -731,7 +731,15 @@ export function showQueriesPanel(): boolean {
 
 const DATA_EXTENSIONS = new Setting("dataExtensions", ROOT_SETTING);
 const LLM_GENERATION = new Setting("llmGeneration", DATA_EXTENSIONS);
+const DISABLE_AUTO_NAME_EXTENSION_PACK = new Setting(
+  "disableAutoNameExtensionPack",
+  DATA_EXTENSIONS,
+);
 
 export function showLlmGeneration(): boolean {
   return !!LLM_GENERATION.getValue<boolean>();
 }
+
+export function disableAutoNameExtensionPack(): boolean {
+  return !!DISABLE_AUTO_NAME_EXTENSION_PACK.getValue<boolean>();
+}

extensions/ql-vscode/src/data-extensions-editor/extension-pack-name.ts

@@ -0,0 +1,93 @@
+const packNamePartRegex = /[a-z0-9](?:[a-z0-9-]*[a-z0-9])?/;
+const packNameRegex = new RegExp(
+  `^(?<scope>${packNamePartRegex.source})/(?<name>${packNamePartRegex.source})$`,
+);
+const packNameLength = 128;
+
+export interface ExtensionPackName {
+  scope: string;
+  name: string;
+}
+
+export function formatPackName(packName: ExtensionPackName): string {
+  return `${packName.scope}/${packName.name}`;
+}
+
+export function autoNameExtensionPack(
+  name: string,
+  language: string,
+): ExtensionPackName | undefined {
+  let packName = `${name}-${language}`;
+  if (!packName.includes("/")) {
+    packName = `pack/${packName}`;
+  }
+
+  const parts = packName.split("/");
+  const sanitizedParts = parts.map((part) => sanitizeExtensionPackName(part));
+
+  // If the scope is empty (e.g. if the given name is "-/b"), then we need to still set a scope
+  if (sanitizedParts[0].length === 0) {
+    sanitizedParts[0] = "pack";
+  }
+
+  return {
+    scope: sanitizedParts[0],
+    // This will ensure there's only 1 slash
+    name: sanitizedParts.slice(1).join("-"),
+  };
+}
+
+function sanitizeExtensionPackName(name: string) {
+  // Lowercase everything
+  name = name.toLowerCase();
+
+  // Replace all spaces, dots, and underscores with hyphens
+  name = name.replaceAll(/[\s._]+/g, "-");
+
+  // Replace all characters which are not allowed by empty strings
+  name = name.replaceAll(/[^a-z0-9-]/g, "");
+
+  // Remove any leading or trailing hyphens
+  name = name.replaceAll(/^-|-$/g, "");
+
+  // Remove any duplicate hyphens
+  name = name.replaceAll(/-{2,}/g, "-");
+
+  return name;
+}
+
+export function parsePackName(packName: string): ExtensionPackName | undefined {
+  const matches = packNameRegex.exec(packName);
+  if (!matches?.groups) {
+    return;
+  }
+
+  const scope = matches.groups.scope;
+  const name = matches.groups.name;
+
+  return {
+    scope,
+    name,
+  };
+}
+
+export function validatePackName(name: string): string | undefined {
+  if (!name) {
+    return "Pack name must not be empty";
+  }
+
+  if (name.length > packNameLength) {
+    return `Pack name must be no longer than ${packNameLength} characters`;
+  }
+
+  const matches = packNameRegex.exec(name);
+  if (!matches?.groups) {
+    if (!name.includes("/")) {
+      return "Invalid package name: a pack name must contain a slash to separate the scope from the pack name";
+    }
+
+    return "Invalid package name: a pack name must contain only lowercase ASCII letters, ASCII digits, and hyphens";
+  }
+
+  return undefined;
+}

extensions/ql-vscode/src/data-extensions-editor/extension-pack-picker.ts

@@ -3,11 +3,8 @@ import { outputFile, pathExists, readFile } from "fs-extra";
 import { dump as dumpYaml, load as loadYaml } from "js-yaml";
 import { minimatch } from "minimatch";
 import { CancellationToken, window } from "vscode";
-import { CodeQLCliServer } from "../codeql-cli/cli";
-import {
-  getOnDiskWorkspaceFolders,
-  getOnDiskWorkspaceFoldersObjects,
-} from "../common/vscode/workspace-folders";
+import { CodeQLCliServer, QlpacksInfo } from "../codeql-cli/cli";
+import { getOnDiskWorkspaceFolders } from "../common/vscode/workspace-folders";
 import { ProgressCallback } from "../common/vscode/progress";
 import { DatabaseItem } from "../databases/local-databases";
 import { getQlPackPath, QLPACK_FILENAMES } from "../common/ql";
@@ -15,15 +12,21 @@ import { getErrorMessage } from "../common/helpers-pure";
 import { ExtensionPack, ExtensionPackModelFile } from "./shared/extension-pack";
 import { NotificationLogger, showAndLogErrorMessage } from "../common/logging";
 import { containsPath } from "../common/files";
+import { disableAutoNameExtensionPack } from "../config";
+import {
+  autoNameExtensionPack,
+  ExtensionPackName,
+  formatPackName,
+  parsePackName,
+  validatePackName,
+} from "./extension-pack-name";
+import {
+  askForWorkspaceFolder,
+  autoPickExtensionsDirectory,
+} from "./extensions-workspace-folder";
 
 const maxStep = 3;
 
-const packNamePartRegex = /[a-z0-9](?:[a-z0-9-]*[a-z0-9])?/;
-const packNameRegex = new RegExp(
-  `^(?<scope>${packNamePartRegex.source})/(?<name>${packNamePartRegex.source})$`,
-);
-const packNameLength = 128;
-
 export async function pickExtensionPackModelFile(
   cliServer: Pick<CodeQLCliServer, "resolveQlpacks" | "resolveExtensions">,
   databaseItem: Pick<DatabaseItem, "name" | "language">,
@@ -79,6 +82,21 @@ async function pickExtensionPack(
     true,
   );
 
+  if (!disableAutoNameExtensionPack()) {
+    progress({
+      message: "Creating extension pack...",
+      step: 2,
+      maxStep,
+    });
+
+    return autoCreateExtensionPack(
+      databaseItem.name,
+      databaseItem.language,
+      extensionPacksInfo,
+      logger,
+    );
+  }
+
   if (Object.keys(extensionPacksInfo).length === 0) {
     return pickNewExtensionPack(databaseItem, token);
   }
@@ -239,51 +257,35 @@ async function pickNewExtensionPack(
   databaseItem: Pick<DatabaseItem, "name" | "language">,
   token: CancellationToken,
 ): Promise<ExtensionPack | undefined> {
-  const workspaceFolders = getOnDiskWorkspaceFoldersObjects();
-  const workspaceFolderOptions = workspaceFolders.map((folder) => ({
-    label: folder.name,
-    detail: folder.uri.fsPath,
-    path: folder.uri.fsPath,
-  }));
-
-  // We're not using window.showWorkspaceFolderPick because that also includes the database source folders while
-  // we only want to include on-disk workspace folders.
-  const workspaceFolder = await window.showQuickPick(workspaceFolderOptions, {
-    title: "Select workspace folder to create extension pack in",
-  });
+  const workspaceFolder = await askForWorkspaceFolder();
   if (!workspaceFolder) {
     return undefined;
   }
 
-  let examplePackName = `${databaseItem.name}-extensions`;
-  if (!examplePackName.includes("/")) {
-    examplePackName = `pack/${examplePackName}`;
-  }
+  const examplePackName = autoNameExtensionPack(
+    databaseItem.name,
+    databaseItem.language,
+  );
 
-  const packName = await window.showInputBox(
+  const name = await window.showInputBox(
     {
       title: "Create new extension pack",
       prompt: "Enter name of extension pack",
-      placeHolder: `e.g. ${examplePackName}`,
+      placeHolder: examplePackName
+        ? `e.g. ${formatPackName(examplePackName)}`
+        : "",
       validateInput: async (value: string): Promise<string | undefined> => {
-        if (!value) {
-          return "Pack name must not be empty";
+        const message = validatePackName(value);
+        if (message) {
+          return message;
         }
 
-        if (value.length > packNameLength) {
-          return `Pack name must be no longer than ${packNameLength} characters`;
+        const packName = parsePackName(value);
+        if (!packName) {
+          return "Invalid pack name";
         }
 
-        const matches = packNameRegex.exec(value);
-        if (!matches?.groups) {
-          if (!value.includes("/")) {
-            return "Invalid package name: a pack name must contain a slash to separate the scope from the pack name";
-          }
-
-          return "Invalid package name: a pack name must contain only lowercase ASCII letters, ASCII digits, and hyphens";
-        }
-
-        const packPath = join(workspaceFolder.path, matches.groups.name);
+        const packPath = join(workspaceFolder.uri.fsPath, packName.name);
         if (await pathExists(packPath)) {
           return `A pack already exists at ${packPath}`;
         }
@@ -293,31 +295,121 @@ async function pickNewExtensionPack(
     },
     token,
   );
+  if (!name) {
+    return undefined;
+  }
+
+  const packName = parsePackName(name);
   if (!packName) {
     return undefined;
   }
 
-  const matches = packNameRegex.exec(packName);
-  if (!matches?.groups) {
-    return;
-  }
-
-  const name = matches.groups.name;
-  const packPath = join(workspaceFolder.path, name);
+  const packPath = join(workspaceFolder.uri.fsPath, packName.name);
 
   if (await pathExists(packPath)) {
     return undefined;
   }
 
+  return writeExtensionPack(packPath, packName, databaseItem.language);
+}
+
+async function autoCreateExtensionPack(
+  name: string,
+  language: string,
+  extensionPacksInfo: QlpacksInfo,
+  logger: NotificationLogger,
+): Promise<ExtensionPack | undefined> {
+  // Get the extensions directory to create the extension pack in
+  const extensionsDirectory = await autoPickExtensionsDirectory();
+  if (!extensionsDirectory) {
+    return undefined;
+  }
+
+  // Generate the name of the extension pack
+  const packName = autoNameExtensionPack(name, language);
+  if (!packName) {
+    void showAndLogErrorMessage(
+      logger,
+      `Could not automatically name extension pack for database ${name}`,
+    );
+
+    return undefined;
+  }
+
+  // Find any existing locations of this extension pack
+  const existingExtensionPackPaths =
+    extensionPacksInfo[formatPackName(packName)];
+
+  // If there is already an extension pack with this name, use it if it is valid
+  if (existingExtensionPackPaths?.length === 1) {
+    let extensionPack: ExtensionPack;
+    try {
+      extensionPack = await readExtensionPack(existingExtensionPackPaths[0]);
+    } catch (e: unknown) {
+      void showAndLogErrorMessage(
+        logger,
+        `Could not read extension pack ${formatPackName(packName)}`,
+        {
+          fullMessage: `Could not read extension pack ${formatPackName(
+            packName,
+          )} at ${existingExtensionPackPaths[0]}: ${getErrorMessage(e)}`,
+        },
+      );
+
+      return undefined;
+    }
+
+    return extensionPack;
+  }
+
+  // If there is already an existing extension pack with this name, but it resolves
+  // to multiple paths, then we can't use it
+  if (existingExtensionPackPaths?.length > 1) {
+    void showAndLogErrorMessage(
+      logger,
+      `Extension pack ${formatPackName(packName)} resolves to multiple paths`,
+      {
+        fullMessage: `Extension pack ${formatPackName(
+          packName,
+        )} resolves to multiple paths: ${existingExtensionPackPaths.join(
+          ", ",
+        )}`,
+      },
+    );
+
+    return undefined;
+  }
+
+  const packPath = join(extensionsDirectory.fsPath, packName.name);
+
+  if (await pathExists(packPath)) {
+    void showAndLogErrorMessage(
+      logger,
+      `Directory ${packPath} already exists for extension pack ${formatPackName(
+        packName,
+      )}`,
+    );
+
+    return undefined;
+  }
+
+  return writeExtensionPack(packPath, packName, language);
+}
+
+async function writeExtensionPack(
+  packPath: string,
+  packName: ExtensionPackName,
+  language: string,
+): Promise<ExtensionPack> {
   const packYamlPath = join(packPath, "codeql-pack.yml");
 
   const extensionPack: ExtensionPack = {
     path: packPath,
     yamlPath: packYamlPath,
-    name: packName,
+    name: formatPackName(packName),
     version: "0.0.0",
     extensionTargets: {
-      [`codeql/${databaseItem.language}-all`]: "*",
+      [`codeql/${language}-all`]: "*",
     },
     dataExtensions: ["models/**/*.yml"],
   };

extensions/ql-vscode/src/data-extensions-editor/extensions-workspace-folder.ts

@@ -0,0 +1,224 @@
+import { FileType, Uri, window, workspace, WorkspaceFolder } from "vscode";
+import { getOnDiskWorkspaceFoldersObjects } from "../common/vscode/workspace-folders";
+import { extLogger } from "../common/logging/vscode";
+import { tmpdir } from "../common/files";
+
+/**
+ * Returns the ancestors of this path in order from furthest to closest (i.e. root of filesystem to parent directory)
+ */
+function getAncestors(uri: Uri): Uri[] {
+  const ancestors: Uri[] = [];
+  let current = uri;
+  while (current.fsPath !== Uri.joinPath(current, "..").fsPath) {
+    ancestors.push(current);
+    current = Uri.joinPath(current, "..");
+  }
+
+  // The ancestors are now in order from closest to furthest, so reverse them
+  ancestors.reverse();
+
+  return ancestors;
+}
+
+async function getRootWorkspaceDirectory(): Promise<Uri | undefined> {
+  // If there is a valid workspace file, just use its directory as the directory for the extensions
+  const workspaceFile = workspace.workspaceFile;
+  if (workspaceFile?.scheme === "file") {
+    return Uri.joinPath(workspaceFile, "..");
+  }
+
+  const allWorkspaceFolders = getOnDiskWorkspaceFoldersObjects();
+
+  // Get the system temp directory and convert it to a URI so it's normalized
+  const systemTmpdir = Uri.file(tmpdir());
+
+  const workspaceFolders = allWorkspaceFolders.filter((folder) => {
+    // Never use a workspace folder that is in the system temp directory
+    return !folder.uri.fsPath.startsWith(systemTmpdir.fsPath);
+  });
+
+  // Find the common root directory of all workspace folders by finding the longest common prefix
+  const commonRoot = workspaceFolders.reduce((commonRoot, folder) => {
+    const folderUri = folder.uri;
+    const ancestors = getAncestors(folderUri);
+
+    const minLength = Math.min(commonRoot.length, ancestors.length);
+    let commonLength = 0;
+    for (let i = 0; i < minLength; i++) {
+      if (commonRoot[i].fsPath === ancestors[i].fsPath) {
+        commonLength++;
+      } else {
+        break;
+      }
+    }
+
+    return commonRoot.slice(0, commonLength);
+  }, getAncestors(workspaceFolders[0].uri));
+
+  if (commonRoot.length === 0) {
+    return await findGitFolder(workspaceFolders);
+  }
+
+  // The path closest to the workspace folders is the last element of the common root
+  const commonRootUri = commonRoot[commonRoot.length - 1];
+
+  // If we are at the root of the filesystem, we can't go up any further and there's something
+  // wrong, so just return undefined
+  if (commonRootUri.fsPath === Uri.joinPath(commonRootUri, "..").fsPath) {
+    return await findGitFolder(workspaceFolders);
+  }
+
+  return commonRootUri;
+}
+
+async function findGitFolder(
+  workspaceFolders: WorkspaceFolder[],
+): Promise<Uri | undefined> {
+  // Go through all workspace folders one-by-one and try to find the closest .git folder for each one
+  const folders = await Promise.all(
+    workspaceFolders.map(async (folder) => {
+      const ancestors = getAncestors(folder.uri);
+
+      // Reverse the ancestors so we're going from closest to furthest
+      ancestors.reverse();
+
+      const gitFoldersExists = await Promise.all(
+        ancestors.map(async (uri) => {
+          const gitFolder = Uri.joinPath(uri, ".git");
+          try {
+            const stat = await workspace.fs.stat(gitFolder);
+            // Check whether it's a directory
+            return (stat.type & FileType.Directory) !== 0;
+          } catch (e) {
+            return false;
+          }
+        }),
+      );
+
+      // Find the first ancestor that has a .git folder
+      const ancestorIndex = gitFoldersExists.findIndex((exists) => exists);
+
+      if (ancestorIndex === -1) {
+        return undefined;
+      }
+
+      return [ancestorIndex, ancestors[ancestorIndex]];
+    }),
+  );
+
+  const validFolders = folders.filter(
+    (folder): folder is [number, Uri] => folder !== undefined,
+  );
+  if (validFolders.length === 0) {
+    return undefined;
+  }
+
+  // Find the .git folder which is closest to a workspace folder
+  const closestFolder = validFolders.reduce((closestFolder, folder) => {
+    if (folder[0] < closestFolder[0]) {
+      return folder;
+    }
+    return closestFolder;
+  }, validFolders[0]);
+
+  return closestFolder?.[1];
+}
+
+/**
+ * Finds a suitable directory for extension packs to be created in. This will
+ * always be a path ending in `.github/codeql/extensions`. The parent directory
+ * will be determined heuristically based on the on-disk workspace folders.
+ *
+ * The heuristic is as follows (`.github/codeql/extensions` is added automatically unless
+ * otherwise specified):
+ * 1. If there is only 1 workspace folder, use that folder
+ * 2. If there is a workspace folder for which the path ends in `.github/codeql/extensions`, use that folder
+ *   - If there are multiple such folders, use the first one
+ *   - Does not append `.github/codeql/extensions` to the path
+ * 3. If there is a workspace file (`<basename>.code-workspace`), use the directory containing that file
+ * 4. If there is a common root directory for all workspace folders, use that directory
+ *   - Workspace folders in the system temp directory are ignored
+ *   - If the common root directory is the root of the filesystem, then it's not used
+ * 5. If there is a .git directory in any workspace folder, use the directory containing that .git directory
+ *    for which the .git directory is closest to a workspace folder
+ * 6. If none of the above apply, return `undefined`
+ */
+export async function autoPickExtensionsDirectory(): Promise<Uri | undefined> {
+  const workspaceFolders = getOnDiskWorkspaceFoldersObjects();
+
+  // If there's only 1 workspace folder, use the `.github/codeql/extensions` directory in that folder
+  if (workspaceFolders.length === 1) {
+    return Uri.joinPath(
+      workspaceFolders[0].uri,
+      ".github",
+      "codeql",
+      "extensions",
+    );
+  }
+
+  // Now try to find a workspace folder for which the path ends in `.github/codeql/extensions`
+  const workspaceFolderForExtensions = workspaceFolders.find((folder) =>
+    // Using path instead of fsPath because path always uses forward slashes
+    folder.uri.path.endsWith(".github/codeql/extensions"),
+  );
+  if (workspaceFolderForExtensions) {
+    return workspaceFolderForExtensions.uri;
+  }
+
+  // Get the root workspace directory, i.e. the common root directory of all workspace folders
+  const rootDirectory = await getRootWorkspaceDirectory();
+  if (!rootDirectory) {
+    void extLogger.log("Unable to determine root workspace directory");
+
+    return undefined;
+  }
+
+  // We'll create a new workspace folder for the extensions in the root workspace directory
+  // at `.github/codeql/extensions`
+  const extensionsUri = Uri.joinPath(
+    rootDirectory,
+    ".github",
+    "codeql",
+    "extensions",
+  );
+
+  if (
+    !workspace.updateWorkspaceFolders(
+      workspace.workspaceFolders?.length ?? 0,
+      0,
+      {
+        name: "CodeQL Extension Packs",
+        uri: extensionsUri,
+      },
+    )
+  ) {
+    void extLogger.log(
+      `Failed to add workspace folder for extensions at ${extensionsUri.fsPath}`,
+    );
+    return undefined;
+  }
+
+  return extensionsUri;
+}
+
+export async function askForWorkspaceFolder(): Promise<
+  WorkspaceFolder | undefined
+> {
+  const workspaceFolders = getOnDiskWorkspaceFoldersObjects();
+  const workspaceFolderOptions = workspaceFolders.map((folder) => ({
+    label: folder.name,
+    detail: folder.uri.fsPath,
+    folder,
+  }));
+
+  // We're not using window.showWorkspaceFolderPick because that also includes the database source folders while
+  // we only want to include on-disk workspace folders.
+  const workspaceFolder = await window.showQuickPick(workspaceFolderOptions, {
+    title: "Select workspace folder to create extension pack in",
+  });
+  if (!workspaceFolder) {
+    return undefined;
+  }
+
+  return workspaceFolder.folder;
+}

extensions/ql-vscode/src/data-extensions-editor/external-api-usage-query.ts

@@ -11,7 +11,7 @@ import { CodeQLCliServer } from "../codeql-cli/cli";
 import { DatabaseItem } from "../databases/local-databases";
 import { ProgressCallback } from "../common/vscode/progress";
 import { fetchExternalApiQueries } from "./queries";
-import { QueryResultType } from "../pure/new-messages";
+import { QueryResultType } from "../query-server/new-messages";
 import { join } from "path";
 import { redactableError } from "../common/errors";
 import { telemetryListener } from "../common/vscode/telemetry";

extensions/ql-vscode/src/data-extensions-editor/generate-flow-model.ts

@@ -13,7 +13,7 @@ import {
   ModeledMethodWithSignature,
 } from "./modeled-method";
 import { redactableError } from "../common/errors";
-import { QueryResultType } from "../pure/new-messages";
+import { QueryResultType } from "../query-server/new-messages";
 import { file } from "tmp-promise";
 import { writeFile } from "fs-extra";
 import { dump } from "js-yaml";

extensions/ql-vscode/src/data-extensions-editor/queries/csharp.ts

@@ -75,6 +75,16 @@ class ExternalApi extends DotNet::Callable {
     not isUninteresting(this)
   }
 
+  /**
+   * Gets the unbound type, name and parameter types of this API.
+   */
+  bindingset[this]
+  private string getSignature() {
+    result =
+      this.getDeclaringType().getUnboundDeclaration() + "." + this.getName() + "(" +
+        parameterQualifiedTypeNamesToString(this) + ")"
+  }
+
   /**
    * Gets the namespace of this API.
    */
@@ -85,8 +95,7 @@ class ExternalApi extends DotNet::Callable {
    * Gets the namespace and signature of this API.
    */
   bindingset[this]
-  string getApiName() { result = this.getNamespace() + "." + this.getDeclaringType().getUnboundDeclaration() + "#" + this.getName() + "(" +
-  parameterQualifiedTypeNamesToString(this) + ")" }
+  string getApiName() { result = this.getNamespace() + "#" + this.getSignature() }
 
   /** Gets a node that is an input to a call to this API. */
   private ArgumentNode getAnInput() {
@@ -146,7 +155,7 @@ class ExternalApi extends DotNet::Callable {
 int resultLimit() { result = 1000 }
 
 /**
- * Holds if it is relevant to count usages of "api".
+ * Holds if it is relevant to count usages of \`api\`.
  */
 signature predicate relevantApi(ExternalApi api);
 
@@ -174,7 +183,7 @@ module Results<relevantApi/1 getRelevantUsages> {
   }
 
   /**
-   * Holds if there exists an API with "apiName" that is being used "usages" times
+   * Holds if there exists an API with \`apiName\` that is being used \`usages\` times
    * and if it is in the top results (guarded by resultLimit).
    */
   predicate restrict(string apiName, int usages) {

extensions/ql-vscode/src/data-extensions-editor/queries/java.ts

@@ -41,31 +41,7 @@ private import semmle.code.java.dataflow.FlowSummary
 private import semmle.code.java.dataflow.internal.DataFlowPrivate
 private import semmle.code.java.dataflow.internal.FlowSummaryImpl as FlowSummaryImpl
 private import semmle.code.java.dataflow.TaintTracking
-
-pragma[nomagic]
-private predicate isTestPackage(Package p) {
-  p.getName()
-      .matches([
-          "org.junit%", "junit.%", "org.mockito%", "org.assertj%",
-          "com.github.tomakehurst.wiremock%", "org.hamcrest%", "org.springframework.test.%",
-          "org.springframework.mock.%", "org.springframework.boot.test.%", "reactor.test%",
-          "org.xmlunit%", "org.testcontainers.%", "org.opentest4j%", "org.mockserver%",
-          "org.powermock%", "org.skyscreamer.jsonassert%", "org.rnorth.visibleassertions",
-          "org.openqa.selenium%", "com.gargoylesoftware.htmlunit%", "org.jboss.arquillian.testng%",
-          "org.testng%"
-        ])
-}
-
-/**
- * A test library.
- */
-private class TestLibrary extends RefType {
-  TestLibrary() { isTestPackage(this.getPackage()) }
-}
-
-private string containerAsJar(Container container) {
-  if container instanceof JarFile then result = container.getBaseName() else result = "rt.jar"
-}
+private import semmle.code.java.dataflow.internal.ModelExclusions
 
 /** Holds if the given callable is not worth supporting. */
 private predicate isUninteresting(Callable c) {
@@ -88,10 +64,18 @@ class ExternalApi extends Callable {
         "#" + this.getName() + paramsString(this)
   }
 
+  private string getJarName() {
+    result = this.getCompilationUnit().getParentContainer*().(JarFile).getBaseName()
+  }
+
   /**
    * Gets the jar file containing this API. Normalizes the Java Runtime to "rt.jar" despite the presence of modules.
    */
-  string jarContainer() { result = containerAsJar(this.getCompilationUnit().getParentContainer*()) }
+  string jarContainer() {
+    result = this.getJarName()
+    or
+    not exists(this.getJarName()) and result = "rt.jar"
+  }
 
   /** Gets a node that is an input to a call to this API. */
   private DataFlow::Node getAnInput() {

extensions/ql-vscode/src/debugger/debug-protocol.ts

@@ -1,5 +1,5 @@
 import { DebugProtocol } from "@vscode/debugprotocol";
-import { QueryResultType } from "../pure/new-messages";
+import { QueryResultType } from "../query-server/new-messages";
 import { QuickEvalContext } from "../run-queries-shared";
 
 // Events

extensions/ql-vscode/src/debugger/debug-session.ts

@@ -14,7 +14,7 @@ import { Disposable } from "vscode";
 import { CancellationTokenSource } from "vscode-jsonrpc";
 import { BaseLogger, LogOptions } from "../common/logging";
 import { queryServerLogger } from "../common/logging/vscode";
-import { QueryResultType } from "../pure/new-messages";
+import { QueryResultType } from "../query-server/new-messages";
 import { CoreQueryResults, CoreQueryRun, QueryRunner } from "../query-server";
 import * as CodeQLProtocol from "./debug-protocol";
 import { QuickEvalContext } from "../run-queries-shared";

extensions/ql-vscode/src/language-support/contextual/location-finder.ts

@@ -20,7 +20,7 @@ import {
 import { CancellationToken, LocationLink, Uri } from "vscode";
 import { QueryOutputDir } from "../../run-queries-shared";
 import { QueryRunner } from "../../query-server";
-import { QueryResultType } from "../../pure/new-messages";
+import { QueryResultType } from "../../query-server/new-messages";
 import { fileRangeFromURI } from "./file-range-from-uri";
 
 export const SELECT_QUERY_NAME = "#select";

extensions/ql-vscode/src/local-queries/local-query-run.ts

@@ -19,7 +19,7 @@ import {
 import { CompletedLocalQueryInfo, LocalQueryInfo } from "../query-results";
 import { WebviewReveal } from "./webview";
 import { CodeQLCliServer } from "../codeql-cli/cli";
-import { QueryResultType } from "../pure/new-messages";
+import { QueryResultType } from "../query-server/new-messages";
 import { redactableError } from "../common/errors";
 import { LocalQueries } from "./local-queries";
 import { tryGetQueryMetadata } from "../codeql-cli/query-metadata";

extensions/ql-vscode/src/query-evaluation-logging/eval-log-tree-builder.ts

@@ -1,5 +1,5 @@
 import { ChildEvalLogTreeItem, EvalLogTreeItem } from "./eval-log-viewer";
-import { EvalLogData as EvalLogData } from "../pure/log-summary-parser";
+import { EvalLogData as EvalLogData } from "../log-insights/log-summary-parser";
 
 /** Builds the tree data for the evaluator log viewer for a single query run. */
 export class EvalLogTreeBuilder {

extensions/ql-vscode/src/query-history/query-history-manager.ts

@@ -40,7 +40,10 @@ import { CliVersionConstraint } from "../codeql-cli/cli";
 import { HistoryItemLabelProvider } from "./history-item-label-provider";
 import { ResultsView, WebviewReveal } from "../local-queries";
 import { EvalLogTreeBuilder, EvalLogViewer } from "../query-evaluation-logging";
-import { EvalLogData, parseViewerData } from "../pure/log-summary-parser";
+import {
+  EvalLogData,
+  parseViewerData,
+} from "../log-insights/log-summary-parser";
 import { QueryWithResults } from "../run-queries-shared";
 import { QueryRunner } from "../query-server";
 import { VariantAnalysisManager } from "../variant-analysis/variant-analysis-manager";

extensions/ql-vscode/src/query-results.ts

@@ -1,7 +1,7 @@
 import { CancellationTokenSource, env } from "vscode";
 
-import * as messages from "./pure/messages-shared";
-import * as legacyMessages from "./pure/legacy-messages";
+import * as messages from "./query-server/messages-shared";
+import * as legacyMessages from "./query-server/legacy-messages";
 import * as cli from "./codeql-cli/cli";
 import { pathExists } from "fs-extra";
 import { basename } from "path";

extensions/ql-vscode/src/query-server/legacy/legacy-query-runner.ts

@@ -7,7 +7,7 @@ import {
   Dataset,
   deregisterDatabases,
   registerDatabases,
-} from "../../pure/legacy-messages";
+} from "../legacy-messages";
 import {
   CoreQueryResults,
   CoreQueryTarget,

extensions/ql-vscode/src/query-server/legacy/query-server-client.ts

@@ -13,7 +13,7 @@ import {
   progress,
   ProgressMessage,
   WithProgressId,
-} from "../../pure/legacy-messages";
+} from "../legacy-messages";
 import { ProgressCallback, ProgressTask } from "../../common/vscode/progress";
 import { ServerProcess } from "../server-process";
 import { App } from "../../common/app";

extensions/ql-vscode/src/query-server/legacy/run-queries.ts

@@ -18,15 +18,15 @@ import {
   showAndLogExceptionWithTelemetry,
   showAndLogWarningMessage,
 } from "../../common/logging";
-import * as messages from "../../pure/legacy-messages";
-import * as newMessages from "../../pure/new-messages";
+import * as messages from "../legacy-messages";
+import * as newMessages from "../new-messages";
 import * as qsClient from "./query-server-client";
 import { asError, getErrorMessage } from "../../common/helpers-pure";
 import { compileDatabaseUpgradeSequence } from "./upgrades";
 import { QueryEvaluationInfo, QueryOutputDir } from "../../run-queries-shared";
 import { redactableError } from "../../common/errors";
 import { CoreQueryResults, CoreQueryTarget } from "../query-runner";
-import { Position } from "../../pure/messages-shared";
+import { Position } from "../messages-shared";
 import { ensureDirSync } from "fs-extra";
 import { telemetryListener } from "../../common/vscode/telemetry";
 

extensions/ql-vscode/src/query-server/legacy/upgrades.ts

@@ -7,7 +7,7 @@ import {
 } from "../../common/vscode/progress";
 import { extLogger } from "../../common/logging/vscode";
 import { showAndLogExceptionWithTelemetry } from "../../common/logging";
-import * as messages from "../../pure/legacy-messages";
+import * as messages from "../legacy-messages";
 import * as qsClient from "./query-server-client";
 import * as tmp from "tmp-promise";
 import { dirname } from "path";

extensions/ql-vscode/src/query-server/new-query-runner.ts

@@ -11,7 +11,7 @@ import {
   deregisterDatabases,
   registerDatabases,
   upgradeDatabase,
-} from "../pure/new-messages";
+} from "./new-messages";
 import { CoreQueryResults, CoreQueryTarget, QueryRunner } from "./query-runner";
 import { QueryServerClient } from "./query-server-client";
 import { compileAndRunQueryAgainstDatabaseCore } from "./run-queries";

extensions/ql-vscode/src/query-server/query-runner.ts

@@ -3,7 +3,7 @@ import { CodeQLCliServer } from "../codeql-cli/cli";
 import { ProgressCallback } from "../common/vscode/progress";
 import { DatabaseItem } from "../databases/local-databases";
 import { QueryOutputDir } from "../run-queries-shared";
-import { Position, QueryResultType } from "../pure/new-messages";
+import { Position, QueryResultType } from "./new-messages";
 import { BaseLogger, Logger } from "../common/logging";
 import { basename, join } from "path";
 import { nanoid } from "nanoid";

extensions/ql-vscode/src/query-server/query-server-client.ts

@@ -7,11 +7,7 @@ import * as cli from "../codeql-cli/cli";
 import { QueryServerConfig } from "../config";
 import { Logger, showAndLogErrorMessage } from "../common/logging";
 import { extLogger, ProgressReporter } from "../common/logging/vscode";
-import {
-  progress,
-  ProgressMessage,
-  WithProgressId,
-} from "../pure/new-messages";
+import { progress, ProgressMessage, WithProgressId } from "./new-messages";
 import {
   ProgressCallback,
   ProgressTask,

extensions/ql-vscode/src/query-server/run-queries.ts

@@ -1,6 +1,6 @@
 import { CancellationToken } from "vscode";
 import { ProgressCallback } from "../common/vscode/progress";
-import * as messages from "../pure/new-messages";
+import * as messages from "./new-messages";
 import { QueryOutputDir } from "../run-queries-shared";
 import * as qsClient from "./query-server-client";
 import { CoreQueryResults, CoreQueryTarget } from "./query-runner";

extensions/ql-vscode/src/run-queries-shared.ts

@@ -1,5 +1,5 @@
-import * as messages from "./pure/messages-shared";
-import * as legacyMessages from "./pure/legacy-messages";
+import * as messages from "./query-server/messages-shared";
+import * as legacyMessages from "./query-server/legacy-messages";
 import { DatabaseInfo, QueryMetadata } from "./common/interface-types";
 import { join, parse, dirname, basename } from "path";
 import { Range, TextEditor, Uri, window, workspace } from "vscode";

extensions/ql-vscode/src/stories/variant-analysis/RepositoriesFilter.stories.tsx

@@ -4,7 +4,7 @@ import { useState } from "react";
 import { ComponentMeta } from "@storybook/react";
 
 import { RepositoriesFilter as RepositoriesFilterComponent } from "../../view/variant-analysis/RepositoriesFilter";
-import { FilterKey } from "../../pure/variant-analysis-filter-sort";
+import { FilterKey } from "../../variant-analysis/shared/variant-analysis-filter-sort";
 
 export default {
   title: "Variant Analysis/Repositories Filter",

extensions/ql-vscode/src/stories/variant-analysis/RepositoriesSearchSortRow.stories.tsx

@@ -4,7 +4,7 @@ import { useState } from "react";
 import { ComponentMeta } from "@storybook/react";
 
 import { RepositoriesSearchSortRow as RepositoriesSearchSortRowComponent } from "../../view/variant-analysis/RepositoriesSearchSortRow";
-import { defaultFilterSortState } from "../../pure/variant-analysis-filter-sort";
+import { defaultFilterSortState } from "../../variant-analysis/shared/variant-analysis-filter-sort";
 
 export default {
   title: "Variant Analysis/Repositories Search and Sort Row",

extensions/ql-vscode/src/stories/variant-analysis/RepositoriesSort.stories.tsx

@@ -4,7 +4,7 @@ import { useState } from "react";
 import { ComponentMeta } from "@storybook/react";
 
 import { RepositoriesSort as RepositoriesSortComponent } from "../../view/variant-analysis/RepositoriesSort";
-import { SortKey } from "../../pure/variant-analysis-filter-sort";
+import { SortKey } from "../../variant-analysis/shared/variant-analysis-filter-sort";
 
 export default {
   title: "Variant Analysis/Repositories Sort",

extensions/ql-vscode/src/stories/variant-analysis/VariantAnalysisOutcomePanels.stories.tsx

@@ -15,7 +15,7 @@ import { createMockRepositoryWithMetadata } from "../../../test/factories/varian
 import {
   defaultFilterSortState,
   RepositoriesFilterSortState,
-} from "../../pure/variant-analysis-filter-sort";
+} from "../../variant-analysis/shared/variant-analysis-filter-sort";
 
 export default {
   title: "Variant Analysis/Variant Analysis Outcome Panels",

extensions/ql-vscode/src/variant-analysis/export-results.ts

@@ -26,7 +26,7 @@ import {
 import {
   filterAndSortRepositoriesWithResults,
   RepositoriesFilterSortStateWithIds,
-} from "../pure/variant-analysis-filter-sort";
+} from "./shared/variant-analysis-filter-sort";
 import { Credentials } from "../common/authentication";
 import { AppCommandManager } from "../common/commands";
 

extensions/ql-vscode/src/variant-analysis/shared/variant-analysis-filter-sort.ts

@@ -1,9 +1,6 @@
-import {
-  Repository,
-  RepositoryWithMetadata,
-} from "../variant-analysis/shared/repository";
-import { parseDate } from "../common/date";
-import { assertNever } from "../common/helpers-pure";
+import { Repository, RepositoryWithMetadata } from "./repository";
+import { parseDate } from "../../common/date";
+import { assertNever } from "../../common/helpers-pure";
 
 export enum FilterKey {
   All = "all",

extensions/ql-vscode/src/variant-analysis/variant-analysis-manager.ts

@@ -57,7 +57,7 @@ import {
   defaultFilterSortState,
   filterAndSortRepositoriesWithResults,
   RepositoriesFilterSortStateWithIds,
-} from "../pure/variant-analysis-filter-sort";
+} from "./shared/variant-analysis-filter-sort";
 import { URLSearchParams } from "url";
 import { DbManager } from "../databases/db-manager";
 import { App } from "../common/app";

extensions/ql-vscode/src/variant-analysis/variant-analysis-view-manager.ts

@@ -3,7 +3,7 @@ import {
   VariantAnalysisScannedRepositoryState,
 } from "./shared/variant-analysis";
 import { AppCommandManager } from "../common/commands";
-import { RepositoriesFilterSortStateWithIds } from "../pure/variant-analysis-filter-sort";
+import { RepositoriesFilterSortStateWithIds } from "./shared/variant-analysis-filter-sort";
 
 export interface VariantAnalysisViewInterface {
   variantAnalysisId: number;

extensions/ql-vscode/src/view/results/alert-table.tsx

@@ -1,7 +1,7 @@
 import { basename } from "path";
 import * as React from "react";
 import * as Sarif from "sarif";
-import * as Keys from "../../pure/result-keys";
+import * as Keys from "./result-keys";
 import { chevronDown, chevronRight, info, listUnordered } from "./octicons";
 import {
   className,

extensions/ql-vscode/src/view/variant-analysis/RepositoriesFilter.tsx

@@ -3,7 +3,7 @@ import { useCallback } from "react";
 import styled from "styled-components";
 import { VSCodeDropdown, VSCodeOption } from "@vscode/webview-ui-toolkit/react";
 import { Codicon } from "../common";
-import { FilterKey } from "../../pure/variant-analysis-filter-sort";
+import { FilterKey } from "../../variant-analysis/shared/variant-analysis-filter-sort";
 
 const Dropdown = styled(VSCodeDropdown)`
   width: 100%;

extensions/ql-vscode/src/view/variant-analysis/RepositoriesSearchSortRow.tsx

@@ -5,7 +5,7 @@ import {
   FilterKey,
   RepositoriesFilterSortState,
   SortKey,
-} from "../../pure/variant-analysis-filter-sort";
+} from "../../variant-analysis/shared/variant-analysis-filter-sort";
 import { RepositoriesSearch } from "./RepositoriesSearch";
 import { RepositoriesSort } from "./RepositoriesSort";
 import { RepositoriesFilter } from "./RepositoriesFilter";

extensions/ql-vscode/src/view/variant-analysis/RepositoriesSort.tsx

@@ -2,7 +2,7 @@ import * as React from "react";
 import { useCallback } from "react";
 import styled from "styled-components";
 import { VSCodeDropdown, VSCodeOption } from "@vscode/webview-ui-toolkit/react";
-import { SortKey } from "../../pure/variant-analysis-filter-sort";
+import { SortKey } from "../../variant-analysis/shared/variant-analysis-filter-sort";
 import { Codicon } from "../common";
 
 const Dropdown = styled(VSCodeDropdown)`

extensions/ql-vscode/src/view/variant-analysis/VariantAnalysis.tsx

@@ -12,7 +12,7 @@ import { VariantAnalysisOutcomePanels } from "./VariantAnalysisOutcomePanels";
 import { VariantAnalysisLoading } from "./VariantAnalysisLoading";
 import { ToVariantAnalysisMessage } from "../../common/interface-types";
 import { vscode } from "../vscode-api";
-import { defaultFilterSortState } from "../../pure/variant-analysis-filter-sort";
+import { defaultFilterSortState } from "../../variant-analysis/shared/variant-analysis-filter-sort";
 import { sendTelemetry, useTelemetryOnChange } from "../common/telemetry";
 
 export type VariantAnalysisProps = {

extensions/ql-vscode/src/view/variant-analysis/VariantAnalysisAnalyzedRepos.tsx

@@ -10,7 +10,7 @@ import {
 import {
   filterAndSortRepositoriesWithResultsByName,
   RepositoriesFilterSortState,
-} from "../../pure/variant-analysis-filter-sort";
+} from "../../variant-analysis/shared/variant-analysis-filter-sort";
 
 const Container = styled.div`
   display: flex;

extensions/ql-vscode/src/view/variant-analysis/VariantAnalysisHeader.tsx

@@ -19,7 +19,7 @@ import {
   defaultFilterSortState,
   filterAndSortRepositoriesWithResults,
   RepositoriesFilterSortState,
-} from "../../pure/variant-analysis-filter-sort";
+} from "../../variant-analysis/shared/variant-analysis-filter-sort";
 
 export type VariantAnalysisHeaderProps = {
   variantAnalysis: VariantAnalysis;

extensions/ql-vscode/src/view/variant-analysis/VariantAnalysisOutcomePanels.tsx

@@ -17,7 +17,7 @@ import {
 import { VariantAnalysisAnalyzedRepos } from "./VariantAnalysisAnalyzedRepos";
 import { Alert } from "../common";
 import { VariantAnalysisSkippedRepositoriesTab } from "./VariantAnalysisSkippedRepositoriesTab";
-import { RepositoriesFilterSortState } from "../../pure/variant-analysis-filter-sort";
+import { RepositoriesFilterSortState } from "../../variant-analysis/shared/variant-analysis-filter-sort";
 import { RepositoriesSearchSortRow } from "./RepositoriesSearchSortRow";
 import { FailureReasonAlert } from "./FailureReasonAlert";
 

extensions/ql-vscode/src/view/variant-analysis/VariantAnalysisSkippedRepositoriesTab.tsx

@@ -8,7 +8,7 @@ import {
   compareRepository,
   matchesFilter,
   RepositoriesFilterSortState,
-} from "../../pure/variant-analysis-filter-sort";
+} from "../../variant-analysis/shared/variant-analysis-filter-sort";
 
 export type VariantAnalysisSkippedRepositoriesTabProps = {
   alertTitle: string;

extensions/ql-vscode/src/view/variant-analysis/__tests__/VariantAnalysis.spec.tsx

@@ -7,7 +7,10 @@ import {
 import { VariantAnalysis, VariantAnalysisProps } from "../VariantAnalysis";
 import { createMockVariantAnalysis } from "../../../../test/factories/variant-analysis/shared/variant-analysis";
 import { ToVariantAnalysisMessage } from "../../../common/interface-types";
-import { FilterKey, SortKey } from "../../../pure/variant-analysis-filter-sort";
+import {
+  FilterKey,
+  SortKey,
+} from "../../../variant-analysis/shared/variant-analysis-filter-sort";
 import { postMessage } from "../../common/post-message";
 
 describe(VariantAnalysis.name, () => {

extensions/ql-vscode/src/view/variant-analysis/__tests__/VariantAnalysisAnalyzedRepos.spec.tsx

@@ -13,7 +13,7 @@ import {
 import { createMockVariantAnalysis } from "../../../../test/factories/variant-analysis/shared/variant-analysis";
 import { createMockRepositoryWithMetadata } from "../../../../test/factories/variant-analysis/shared/repository";
 import { createMockScannedRepo } from "../../../../test/factories/variant-analysis/shared/scanned-repositories";
-import { SortKey } from "../../../pure/variant-analysis-filter-sort";
+import { SortKey } from "../../../variant-analysis/shared/variant-analysis-filter-sort";
 import { permissiveFilterSortState } from "../../../../test/unit-tests/variant-analysis-filter-sort.test";
 
 describe(VariantAnalysisAnalyzedRepos.name, () => {

extensions/ql-vscode/src/view/variant-analysis/__tests__/VariantAnalysisOutcomePanels.spec.tsx

@@ -16,7 +16,7 @@ import {
   createMockScannedRepo,
   createMockScannedRepos,
 } from "../../../../test/factories/variant-analysis/shared/scanned-repositories";
-import { defaultFilterSortState } from "../../../pure/variant-analysis-filter-sort";
+import { defaultFilterSortState } from "../../../variant-analysis/shared/variant-analysis-filter-sort";
 
 describe(VariantAnalysisOutcomePanels.name, () => {
   const defaultVariantAnalysis = {

extensions/ql-vscode/src/view/variant-analysis/__tests__/VariantAnalysisSkippedRepositoriesTab.spec.tsx

@@ -4,7 +4,7 @@ import {
   VariantAnalysisSkippedRepositoriesTab,
   VariantAnalysisSkippedRepositoriesTabProps,
 } from "../VariantAnalysisSkippedRepositoriesTab";
-import { SortKey } from "../../../pure/variant-analysis-filter-sort";
+import { SortKey } from "../../../variant-analysis/shared/variant-analysis-filter-sort";
 import { permissiveFilterSortState } from "../../../../test/unit-tests/variant-analysis-filter-sort.test";
 
 describe(VariantAnalysisSkippedRepositoriesTab.name, () => {

extensions/ql-vscode/test/factories/query-history/local-query-history-item.ts

@@ -5,7 +5,7 @@ import {
   QueryWithResults,
 } from "../../../src/run-queries-shared";
 import { CancellationTokenSource } from "vscode";
-import { QueryResultType } from "../../../src/pure/legacy-messages";
+import { QueryResultType } from "../../../src/query-server/legacy-messages";
 import { QueryMetadata } from "../../../src/common/interface-types";
 
 export function createMockLocalQueryInfo({

extensions/ql-vscode/test/unit-tests/command-lint.test.ts

@@ -49,7 +49,7 @@ describe("commands declared in package.json", () => {
       expect(title).toBeDefined();
       commandTitles[command] = title!;
     } else {
-      fail(`Unexpected command name ${command}`);
+      throw new Error(`Unexpected command name ${command}`);
     }
   });
 

extensions/ql-vscode/test/unit-tests/common/helpers-pure.test.ts

@@ -13,7 +13,7 @@ describe("helpers-pure", () => {
 
     try {
       await asyncFilter([1, 2, 3], rejects);
-      fail("Should have thrown");
+      throw new Error("Should have thrown");
     } catch (e) {
       expect(getErrorMessage(e)).toBe("opps");
     }

extensions/ql-vscode/test/unit-tests/data-extensions-editor/extension-pack-name.test.ts

@@ -0,0 +1,88 @@
+import {
+  autoNameExtensionPack,
+  formatPackName,
+  parsePackName,
+  validatePackName,
+} from "../../../src/data-extensions-editor/extension-pack-name";
+
+describe("autoNameExtensionPack", () => {
+  const testCases: Array<{
+    name: string;
+    language: string;
+    expected: string;
+  }> = [
+    {
+      name: "github/vscode-codeql",
+      language: "javascript",
+      expected: "github/vscode-codeql-javascript",
+    },
+    {
+      name: "vscode-codeql",
+      language: "a",
+      expected: "pack/vscode-codeql-a",
+    },
+    {
+      name: "b",
+      language: "java",
+      expected: "pack/b-java",
+    },
+    {
+      name: "a/b",
+      language: "csharp",
+      expected: "a/b-csharp",
+    },
+    {
+      name: "-/b",
+      language: "csharp",
+      expected: "pack/b-csharp",
+    },
+    {
+      name: "a/b/c/d",
+      language: "csharp",
+      expected: "a/b-c-d-csharp",
+    },
+    {
+      name: "JAVA/CodeQL",
+      language: "csharp",
+      expected: "java/codeql-csharp",
+    },
+    {
+      name: "my new pack",
+      language: "swift",
+      expected: "pack/my-new-pack-swift",
+    },
+    {
+      name: "gïthub/vscode-codeql",
+      language: "javascript",
+      expected: "gthub/vscode-codeql-javascript",
+    },
+    {
+      name: "a/b-",
+      language: "csharp",
+      expected: "a/b-csharp",
+    },
+    {
+      name: "-a-/b",
+      language: "ruby",
+      expected: "a/b-ruby",
+    },
+    {
+      name: "a/b--d--e-d-",
+      language: "csharp",
+      expected: "a/b-d-e-d-csharp",
+    },
+  ];
+
+  test.each(testCases)(
+    "$name with $language = $expected",
+    ({ name, language, expected }) => {
+      const result = autoNameExtensionPack(name, language);
+      expect(result).not.toBeUndefined();
+      if (!result) {
+        return;
+      }
+      expect(validatePackName(formatPackName(result))).toBeUndefined();
+      expect(result).toEqual(parsePackName(expected));
+    },
+  );
+});

extensions/ql-vscode/test/unit-tests/log-insights/log-summary-parser.test.ts

@@ -1,6 +1,6 @@
 import { join } from "path";
 
-import { parseViewerData } from "../../../src/pure/log-summary-parser";
+import { parseViewerData } from "../../../src/log-insights/log-summary-parser";
 
 describe("Evaluator log summary tests", () => {
   describe("for a valid summary text", () => {

extensions/ql-vscode/test/unit-tests/variant-analysis-filter-sort.test.ts

@@ -6,7 +6,7 @@ import {
   FilterKey,
   matchesFilter,
   SortKey,
-} from "../../src/pure/variant-analysis-filter-sort";
+} from "../../src/variant-analysis/shared/variant-analysis-filter-sort";
 
 /** A filterSortState that matches everything */
 export const permissiveFilterSortState = {

extensions/ql-vscode/test/vscode-tests/activated-extension/variant-analysis/variant-analysis-manager.test.ts

@@ -36,7 +36,7 @@ import {
 import { createTimestampFile } from "../../../../src/run-queries-shared";
 import { createMockVariantAnalysisRepoTask } from "../../../factories/variant-analysis/gh-api/variant-analysis-repo-task";
 import { VariantAnalysisRepoTask } from "../../../../src/variant-analysis/gh-api/variant-analysis";
-import { SortKey } from "../../../../src/pure/variant-analysis-filter-sort";
+import { SortKey } from "../../../../src/variant-analysis/shared/variant-analysis-filter-sort";
 import { DbManager } from "../../../../src/databases/db-manager";
 import { App } from "../../../../src/common/app";
 import { ExtensionApp } from "../../../../src/common/vscode/vscode-app";

extensions/ql-vscode/test/vscode-tests/cli-integration/debugger/debug-controller.ts

@@ -9,7 +9,7 @@ import {
 } from "vscode";
 import * as CodeQLProtocol from "../../../../src/debugger/debug-protocol";
 import { DisposableObject } from "../../../../src/common/disposable-object";
-import { QueryResultType } from "../../../../src/pure/legacy-messages";
+import { QueryResultType } from "../../../../src/query-server/legacy-messages";
 import { CoreCompletedQuery } from "../../../../src/query-server/query-runner";
 import { QueryOutputDir } from "../../../../src/run-queries-shared";
 import {
@@ -310,11 +310,7 @@ export class DebugController
    */
   private async nextEvent(): Promise<AnyDebugEvent> {
     if (this.resolver !== undefined) {
-      const error = new Error(
-        "Attempt to wait for multiple debugger events at once.",
-      );
-      fail(error);
-      throw error;
+      throw new Error("Attempt to wait for multiple debugger events at once.");
     } else {
       if (this.nextEventIndex < this.eventQueue.length) {
         // No need to wait.

extensions/ql-vscode/test/vscode-tests/cli-integration/legacy-query.test.ts

@@ -3,7 +3,7 @@ import { join, basename } from "path";
 import { dirSync } from "tmp";
 import { pathToFileURL } from "url";
 import { CancellationTokenSource } from "vscode-jsonrpc";
-import * as messages from "../../../src/pure/legacy-messages";
+import * as messages from "../../../src/query-server/legacy-messages";
 import * as qsClient from "../../../src/query-server/legacy/query-server-client";
 import * as cli from "../../../src/codeql-cli/cli";
 import { CellValue } from "../../../src/common/bqrs-cli-types";

extensions/ql-vscode/test/vscode-tests/cli-integration/new-query.test.ts

@@ -1,7 +1,7 @@
 import { join, basename } from "path";
 import { dirSync } from "tmp";
 import { CancellationTokenSource } from "vscode-jsonrpc";
-import * as messages from "../../../src/pure/new-messages";
+import * as messages from "../../../src/query-server/new-messages";
 import * as qsClient from "../../../src/query-server/query-server-client";
 import * as cli from "../../../src/codeql-cli/cli";
 import { CellValue } from "../../../src/common/bqrs-cli-types";
@@ -11,7 +11,7 @@ import {
   extLogger,
   ProgressReporter,
 } from "../../../src/common/logging/vscode";
-import { QueryResultType } from "../../../src/pure/new-messages";
+import { QueryResultType } from "../../../src/query-server/new-messages";
 import { ensureTestDatabase, getActivatedExtension } from "../global.helper";
 import { createMockApp } from "../../__mocks__/appMock";
 

extensions/ql-vscode/test/vscode-tests/cli-integration/queries.test.ts

@@ -29,7 +29,7 @@ import {
 } from "../../../src/query-server/query-runner";
 import { SELECT_QUERY_NAME } from "../../../src/language-support";
 import { LocalQueries, QuickEvalType } from "../../../src/local-queries";
-import { QueryResultType } from "../../../src/pure/new-messages";
+import { QueryResultType } from "../../../src/query-server/new-messages";
 import { createVSCodeCommandManager } from "../../../src/common/vscode/commands";
 import {
   AllCommands,

extensions/ql-vscode/test/vscode-tests/no-workspace/data-extensions-editor/extension-pack-picker.test.ts

@@ -1,4 +1,11 @@
-import { CancellationTokenSource, QuickPickItem, window } from "vscode";
+import {
+  CancellationTokenSource,
+  QuickPickItem,
+  Uri,
+  window,
+  workspace,
+  WorkspaceFolder,
+} from "vscode";
 import { dump as dumpYaml, load as loadYaml } from "js-yaml";
 import { outputFile, readFile } from "fs-extra";
 import { join } from "path";
@@ -8,6 +15,8 @@ import {
   ResolveExtensionsResult,
 } from "../../../../src/codeql-cli/cli";
 
+import * as config from "../../../../src/config";
+
 import { pickExtensionPackModelFile } from "../../../../src/data-extensions-editor/extension-pack-picker";
 import { ExtensionPack } from "../../../../src/data-extensions-editor/shared/extension-pack";
 import { createMockLogger } from "../../../__mocks__/loggerMock";
@@ -16,8 +25,10 @@ describe("pickExtensionPackModelFile", () => {
   let tmpDir: string;
   let extensionPackPath: string;
   let anotherExtensionPackPath: string;
+  let autoExtensionPackPath: string;
   let extensionPack: ExtensionPack;
   let anotherExtensionPack: ExtensionPack;
+  let autoExtensionPack: ExtensionPack;
 
   let qlPacks: QlpacksInfo;
   let extensions: ResolveExtensionsResult;
@@ -32,6 +43,12 @@ describe("pickExtensionPackModelFile", () => {
   const progress = jest.fn();
   let showQuickPickSpy: jest.SpiedFunction<typeof window.showQuickPick>;
   let showInputBoxSpy: jest.SpiedFunction<typeof window.showInputBox>;
+  let disableAutoNameExtensionPackSpy: jest.SpiedFunction<
+    typeof config.disableAutoNameExtensionPack
+  >;
+  let workspaceFoldersSpy: jest.SpyInstance;
+  let additionalPacks: string[];
+  let workspaceFolder: WorkspaceFolder;
 
   const logger = createMockLogger();
 
@@ -42,12 +59,17 @@ describe("pickExtensionPackModelFile", () => {
       })
     ).path;
 
-    extensionPackPath = join(tmpDir, "my-extension-pack");
-    anotherExtensionPackPath = join(tmpDir, "another-extension-pack");
+    // Uri.file(...).fsPath normalizes the filenames so we can properly compare them on Windows
+    extensionPackPath = Uri.file(join(tmpDir, "my-extension-pack")).fsPath;
+    anotherExtensionPackPath = Uri.file(
+      join(tmpDir, "another-extension-pack"),
+    ).fsPath;
+    autoExtensionPackPath = Uri.file(join(tmpDir, "vscode-codeql-java")).fsPath;
 
     qlPacks = {
       "my-extension-pack": [extensionPackPath],
       "another-extension-pack": [anotherExtensionPackPath],
+      "github/vscode-codeql-java": [autoExtensionPackPath],
     };
     extensions = {
       models: [],
@@ -59,6 +81,13 @@ describe("pickExtensionPackModelFile", () => {
             predicate: "sinkModel",
           },
         ],
+        [autoExtensionPackPath]: [
+          {
+            file: join(autoExtensionPackPath, "models", "model.yml"),
+            index: 0,
+            predicate: "sinkModel",
+          },
+        ],
       },
     };
 
@@ -70,6 +99,10 @@ describe("pickExtensionPackModelFile", () => {
       anotherExtensionPackPath,
       "another-extension-pack",
     );
+    autoExtensionPack = await createMockExtensionPack(
+      autoExtensionPackPath,
+      "github/vscode-codeql-java",
+    );
 
     showQuickPickSpy = jest
       .spyOn(window, "showQuickPick")
@@ -77,6 +110,19 @@ describe("pickExtensionPackModelFile", () => {
     showInputBoxSpy = jest
       .spyOn(window, "showInputBox")
       .mockRejectedValue(new Error("Unexpected call to showInputBox"));
+    disableAutoNameExtensionPackSpy = jest
+      .spyOn(config, "disableAutoNameExtensionPack")
+      .mockReturnValue(true);
+
+    workspaceFolder = {
+      uri: Uri.file(tmpDir),
+      name: "codeql-custom-queries-java",
+      index: 0,
+    };
+    additionalPacks = [Uri.file(tmpDir).fsPath];
+    workspaceFoldersSpy = jest
+      .spyOn(workspace, "workspaceFolders", "get")
+      .mockReturnValue([workspaceFolder]);
   });
 
   it("allows choosing an existing extension pack and model file", async () => {
@@ -120,6 +166,12 @@ describe("pickExtensionPackModelFile", () => {
           detail: anotherExtensionPackPath,
           extensionPack: anotherExtensionPack,
         },
+        {
+          label: "github/vscode-codeql-java",
+          description: "0.0.0",
+          detail: autoExtensionPackPath,
+          extensionPack: autoExtensionPack,
+        },
         {
           label: expect.stringMatching(/create/i),
           extensionPack: null,
@@ -147,11 +199,14 @@ describe("pickExtensionPackModelFile", () => {
       token,
     );
     expect(cliServer.resolveQlpacks).toHaveBeenCalledTimes(1);
-    expect(cliServer.resolveQlpacks).toHaveBeenCalledWith([], true);
+    expect(cliServer.resolveQlpacks).toHaveBeenCalledWith(
+      additionalPacks,
+      true,
+    );
     expect(cliServer.resolveExtensions).toHaveBeenCalledTimes(1);
     expect(cliServer.resolveExtensions).toHaveBeenCalledWith(
       extensionPackPath,
-      [],
+      additionalPacks,
     );
   });
 
@@ -190,14 +245,160 @@ describe("pickExtensionPackModelFile", () => {
       token,
     );
     expect(cliServer.resolveQlpacks).toHaveBeenCalledTimes(1);
-    expect(cliServer.resolveQlpacks).toHaveBeenCalledWith([], true);
+    expect(cliServer.resolveQlpacks).toHaveBeenCalledWith(
+      additionalPacks,
+      true,
+    );
     expect(cliServer.resolveExtensions).toHaveBeenCalledTimes(1);
     expect(cliServer.resolveExtensions).toHaveBeenCalledWith(
       extensionPackPath,
-      [],
+      additionalPacks,
     );
   });
 
+  it("automatically selects an extension pack and allows selecting an existing model file", async () => {
+    disableAutoNameExtensionPackSpy.mockReturnValue(false);
+
+    const modelPath = join(autoExtensionPackPath, "models", "model.yml");
+
+    const cliServer = mockCliServer(qlPacks, extensions);
+
+    showQuickPickSpy.mockResolvedValueOnce({
+      label: "models/model.yml",
+      file: modelPath,
+    } as QuickPickItem);
+
+    expect(
+      await pickExtensionPackModelFile(
+        cliServer,
+        databaseItem,
+        logger,
+        progress,
+        token,
+      ),
+    ).toEqual({
+      filename: modelPath,
+      extensionPack: autoExtensionPack,
+    });
+    expect(showQuickPickSpy).toHaveBeenCalledTimes(1);
+    expect(showQuickPickSpy).toHaveBeenCalledWith(
+      [
+        {
+          label: "models/model.yml",
+          file: modelPath,
+        },
+        {
+          label: expect.stringMatching(/create/i),
+          file: null,
+        },
+      ],
+      {
+        title: expect.any(String),
+      },
+      token,
+    );
+    expect(cliServer.resolveQlpacks).toHaveBeenCalledTimes(1);
+    expect(cliServer.resolveQlpacks).toHaveBeenCalledWith(
+      additionalPacks,
+      true,
+    );
+    expect(cliServer.resolveExtensions).toHaveBeenCalledTimes(1);
+    expect(cliServer.resolveExtensions).toHaveBeenCalledWith(
+      autoExtensionPackPath,
+      additionalPacks,
+    );
+  });
+
+  it("automatically creates an extension pack and allows creating a new model file", async () => {
+    disableAutoNameExtensionPackSpy.mockReturnValue(false);
+
+    const tmpDir = await dir({
+      unsafeCleanup: true,
+    });
+
+    workspaceFoldersSpy.mockReturnValue([
+      {
+        uri: Uri.file("/b/a/c"),
+        name: "my-workspace",
+        index: 0,
+      },
+      {
+        uri: Uri.file("/a/b/c"),
+        name: "codeql-custom-queries-csharp",
+        index: 1,
+      },
+      {
+        uri: Uri.joinPath(Uri.file(tmpDir.path), "codeql-custom-queries-java"),
+        name: "codeql-custom-queries-java",
+        index: 2,
+      },
+    ]);
+    jest
+      .spyOn(workspace, "workspaceFile", "get")
+      .mockReturnValue(
+        Uri.joinPath(Uri.file(tmpDir.path), "workspace.code-workspace"),
+      );
+    jest.spyOn(workspace, "updateWorkspaceFolders").mockReturnValue(true);
+
+    const newPackDir = join(
+      Uri.file(tmpDir.path).fsPath,
+      ".github",
+      "codeql",
+      "extensions",
+      "vscode-codeql-java",
+    );
+
+    const cliServer = mockCliServer({}, { models: [], data: {} });
+
+    showInputBoxSpy.mockResolvedValue("models/my-model.yml");
+
+    expect(
+      await pickExtensionPackModelFile(
+        cliServer,
+        databaseItem,
+        logger,
+        progress,
+        token,
+      ),
+    ).toEqual({
+      filename: join(newPackDir, "models", "my-model.yml"),
+      extensionPack: {
+        path: newPackDir,
+        yamlPath: join(newPackDir, "codeql-pack.yml"),
+        name: "github/vscode-codeql-java",
+        version: "0.0.0",
+        extensionTargets: {
+          "codeql/java-all": "*",
+        },
+        dataExtensions: ["models/**/*.yml"],
+      },
+    });
+    expect(showQuickPickSpy).not.toHaveBeenCalled();
+    expect(showInputBoxSpy).toHaveBeenCalledTimes(1);
+    expect(showInputBoxSpy).toHaveBeenCalledWith(
+      {
+        title: expect.stringMatching(/model file/),
+        value: "models/github.vscode-codeql.model.yml",
+        validateInput: expect.any(Function),
+      },
+      token,
+    );
+    expect(cliServer.resolveQlpacks).toHaveBeenCalled();
+    expect(cliServer.resolveExtensions).toHaveBeenCalled();
+
+    expect(
+      loadYaml(await readFile(join(newPackDir, "codeql-pack.yml"), "utf8")),
+    ).toEqual({
+      name: "github/vscode-codeql-java",
+      version: "0.0.0",
+      library: true,
+      extensionTargets: {
+        "codeql/java-all": "*",
+      },
+      dataExtensions: ["models/**/*.yml"],
+    });
+  });
+
   it("allows cancelling the extension pack prompt", async () => {
     const cliServer = mockCliServer(qlPacks, extensions);
 
@@ -223,11 +424,15 @@ describe("pickExtensionPackModelFile", () => {
       unsafeCleanup: true,
     });
 
-    const newPackDir = join(tmpDir.path, "new-extension-pack");
+    const newPackDir = join(Uri.file(tmpDir.path).fsPath, "new-extension-pack");
 
     showQuickPickSpy.mockResolvedValueOnce({
       label: "codeql-custom-queries-java",
-      path: tmpDir.path,
+      folder: {
+        uri: Uri.file(tmpDir.path),
+        name: "codeql-custom-queries-java",
+        index: 0,
+      },
     } as QuickPickItem);
     showInputBoxSpy.mockResolvedValueOnce("pack/new-extension-pack");
     showInputBoxSpy.mockResolvedValue("models/my-model.yml");
@@ -259,7 +464,7 @@ describe("pickExtensionPackModelFile", () => {
       {
         title: expect.stringMatching(/extension pack/i),
         prompt: expect.stringMatching(/extension pack/i),
-        placeHolder: expect.stringMatching(/github\/vscode-codeql-extensions/),
+        placeHolder: expect.stringMatching(/github\/vscode-codeql-java/),
         validateInput: expect.any(Function),
       },
       token,
@@ -295,11 +500,15 @@ describe("pickExtensionPackModelFile", () => {
       unsafeCleanup: true,
     });
 
-    const newPackDir = join(tmpDir.path, "new-extension-pack");
+    const newPackDir = join(Uri.file(tmpDir.path).fsPath, "new-extension-pack");
 
     showQuickPickSpy.mockResolvedValueOnce({
       label: "codeql-custom-queries-java",
-      path: tmpDir.path,
+      folder: {
+        uri: Uri.file(tmpDir.path),
+        name: "codeql-custom-queries-java",
+        index: 0,
+      },
     } as QuickPickItem);
     showInputBoxSpy.mockResolvedValueOnce("pack/new-extension-pack");
     showInputBoxSpy.mockResolvedValue("models/my-model.yml");
@@ -334,7 +543,7 @@ describe("pickExtensionPackModelFile", () => {
       {
         title: expect.stringMatching(/extension pack/i),
         prompt: expect.stringMatching(/extension pack/i),
-        placeHolder: expect.stringMatching(/github\/vscode-codeql-extensions/),
+        placeHolder: expect.stringMatching(/github\/vscode-codeql-csharp/),
         validateInput: expect.any(Function),
       },
       token,
@@ -388,7 +597,11 @@ describe("pickExtensionPackModelFile", () => {
 
     showQuickPickSpy.mockResolvedValueOnce({
       label: "codeql-custom-queries-java",
-      path: "/a/b/c",
+      folder: {
+        uri: Uri.file("/a/b/c"),
+        name: "codeql-custom-queries-java",
+        index: 0,
+      },
     } as QuickPickItem);
     showInputBoxSpy.mockResolvedValueOnce(undefined);
 
@@ -777,7 +990,11 @@ describe("pickExtensionPackModelFile", () => {
 
     showQuickPickSpy.mockResolvedValueOnce({
       label: "a",
-      path: "/a/b/c",
+      folder: {
+        uri: Uri.file("/a/b/c"),
+        name: "a",
+        index: 0,
+      },
     } as QuickPickItem);
     showInputBoxSpy.mockResolvedValue(undefined);
 
@@ -1014,7 +1231,10 @@ describe("pickExtensionPackModelFile", () => {
       token,
     );
     expect(cliServer.resolveQlpacks).toHaveBeenCalledTimes(1);
-    expect(cliServer.resolveQlpacks).toHaveBeenCalledWith([], true);
+    expect(cliServer.resolveQlpacks).toHaveBeenCalledWith(
+      additionalPacks,
+      true,
+    );
     expect(cliServer.resolveExtensions).not.toHaveBeenCalled();
   });
 });

extensions/ql-vscode/test/vscode-tests/no-workspace/data-extensions-editor/extensions-workspace-folder.test.ts

@@ -0,0 +1,214 @@
+import { Uri, workspace, WorkspaceFolder } from "vscode";
+import { dir, DirectoryResult } from "tmp-promise";
+import { join } from "path";
+import { autoPickExtensionsDirectory } from "../../../../src/data-extensions-editor/extensions-workspace-folder";
+import * as files from "../../../../src/common/files";
+import { mkdirp } from "fs-extra";
+
+describe("autoPickExtensionsDirectory", () => {
+  let tmpDir: DirectoryResult;
+  let rootDirectory: Uri;
+  let extensionsDirectory: Uri;
+
+  let workspaceFoldersSpy: jest.SpyInstance<
+    readonly WorkspaceFolder[] | undefined,
+    []
+  >;
+  let workspaceFileSpy: jest.SpyInstance<Uri | undefined, []>;
+  let updateWorkspaceFoldersSpy: jest.SpiedFunction<
+    typeof workspace.updateWorkspaceFolders
+  >;
+  let mockedTmpDirUri: Uri;
+
+  beforeEach(async () => {
+    tmpDir = await dir({
+      unsafeCleanup: true,
+    });
+
+    rootDirectory = Uri.joinPath(Uri.file(tmpDir.path), "root");
+    extensionsDirectory = Uri.joinPath(
+      rootDirectory,
+      ".github",
+      "codeql",
+      "extensions",
+    );
+
+    const mockedTmpDir = join(tmpDir.path, ".tmp", "tmp");
+    mockedTmpDirUri = Uri.file(mockedTmpDir);
+
+    workspaceFoldersSpy = jest
+      .spyOn(workspace, "workspaceFolders", "get")
+      .mockReturnValue([]);
+    workspaceFileSpy = jest
+      .spyOn(workspace, "workspaceFile", "get")
+      .mockReturnValue(undefined);
+    updateWorkspaceFoldersSpy = jest
+      .spyOn(workspace, "updateWorkspaceFolders")
+      .mockReturnValue(true);
+
+    jest.spyOn(files, "tmpdir").mockReturnValue(mockedTmpDir);
+  });
+
+  afterEach(async () => {
+    await tmpDir.cleanup();
+  });
+
+  it("when a workspace folder with the correct path exists", async () => {
+    workspaceFoldersSpy.mockReturnValue([
+      {
+        uri: Uri.joinPath(rootDirectory, "codeql-custom-queries-java"),
+        name: "codeql-custom-queries-java",
+        index: 0,
+      },
+      {
+        uri: Uri.joinPath(rootDirectory, "codeql-custom-queries-python"),
+        name: "codeql-custom-queries-python",
+        index: 1,
+      },
+      {
+        uri: extensionsDirectory,
+        name: "CodeQL Extension Packs",
+        index: 2,
+      },
+    ]);
+
+    expect(await autoPickExtensionsDirectory()).toEqual(extensionsDirectory);
+    expect(updateWorkspaceFoldersSpy).not.toHaveBeenCalled();
+  });
+
+  it("when a workspace file exists", async () => {
+    workspaceFoldersSpy.mockReturnValue([
+      {
+        uri: Uri.file("/a/b/c"),
+        name: "codeql-custom-queries-java",
+        index: 0,
+      },
+      {
+        uri: Uri.joinPath(rootDirectory, "codeql-custom-queries-python"),
+        name: "codeql-custom-queries-python",
+        index: 1,
+      },
+    ]);
+
+    workspaceFileSpy.mockReturnValue(
+      Uri.joinPath(rootDirectory, "workspace.code-workspace"),
+    );
+
+    expect(await autoPickExtensionsDirectory()).toEqual(extensionsDirectory);
+    expect(updateWorkspaceFoldersSpy).toHaveBeenCalledWith(2, 0, {
+      name: "CodeQL Extension Packs",
+      uri: extensionsDirectory,
+    });
+  });
+
+  it("when updating the workspace folders fails", async () => {
+    updateWorkspaceFoldersSpy.mockReturnValue(false);
+
+    workspaceFoldersSpy.mockReturnValue([
+      {
+        uri: Uri.file("/a/b/c"),
+        name: "codeql-custom-queries-java",
+        index: 0,
+      },
+      {
+        uri: Uri.joinPath(rootDirectory, "codeql-custom-queries-python"),
+        name: "codeql-custom-queries-python",
+        index: 1,
+      },
+    ]);
+
+    workspaceFileSpy.mockReturnValue(
+      Uri.joinPath(rootDirectory, "workspace.code-workspace"),
+    );
+
+    expect(await autoPickExtensionsDirectory()).toEqual(undefined);
+  });
+
+  it("when a workspace file does not exist and there is a common root directory", async () => {
+    workspaceFoldersSpy.mockReturnValue([
+      {
+        uri: Uri.joinPath(rootDirectory, "codeql-custom-queries-java"),
+        name: "codeql-custom-queries-java",
+        index: 0,
+      },
+      {
+        uri: Uri.joinPath(rootDirectory, "codeql-custom-queries-python"),
+        name: "codeql-custom-queries-python",
+        index: 1,
+      },
+    ]);
+
+    expect(await autoPickExtensionsDirectory()).toEqual(extensionsDirectory);
+    expect(updateWorkspaceFoldersSpy).toHaveBeenCalledWith(2, 0, {
+      name: "CodeQL Extension Packs",
+      uri: extensionsDirectory,
+    });
+  });
+
+  it("when a workspace file does not exist and there is a temp dir as workspace folder", async () => {
+    workspaceFoldersSpy.mockReturnValue([
+      {
+        uri: Uri.joinPath(rootDirectory, "codeql-custom-queries-java"),
+        name: "codeql-custom-queries-java",
+        index: 0,
+      },
+      {
+        uri: Uri.joinPath(rootDirectory, "codeql-custom-queries-python"),
+        name: "codeql-custom-queries-python",
+        index: 1,
+      },
+      {
+        uri: Uri.joinPath(mockedTmpDirUri, "quick-queries"),
+        name: "quick-queries",
+        index: 2,
+      },
+    ]);
+
+    expect(await autoPickExtensionsDirectory()).toEqual(extensionsDirectory);
+    expect(updateWorkspaceFoldersSpy).toHaveBeenCalledWith(3, 0, {
+      name: "CodeQL Extension Packs",
+      uri: extensionsDirectory,
+    });
+  });
+
+  it("when a workspace file does not exist and there is no common root directory", async () => {
+    workspaceFoldersSpy.mockReturnValue([
+      {
+        uri: Uri.joinPath(rootDirectory, "codeql-custom-queries-java"),
+        name: "codeql-custom-queries-java",
+        index: 0,
+      },
+      {
+        uri: Uri.file("/a/b/c"),
+        name: "codeql-custom-queries-python",
+        index: 1,
+      },
+    ]);
+
+    expect(await autoPickExtensionsDirectory()).toEqual(undefined);
+    expect(updateWorkspaceFoldersSpy).not.toHaveBeenCalled();
+  });
+
+  it("when a workspace file does not exist and there is a .git folder", async () => {
+    await mkdirp(join(rootDirectory.fsPath, ".git"));
+
+    workspaceFoldersSpy.mockReturnValue([
+      {
+        uri: Uri.joinPath(rootDirectory, "codeql-custom-queries-java"),
+        name: "codeql-custom-queries-java",
+        index: 0,
+      },
+      {
+        uri: Uri.file("/a/b/c"),
+        name: "codeql-custom-queries-python",
+        index: 1,
+      },
+    ]);
+
+    expect(await autoPickExtensionsDirectory()).toEqual(extensionsDirectory);
+    expect(updateWorkspaceFoldersSpy).toHaveBeenCalledWith(2, 0, {
+      name: "CodeQL Extension Packs",
+      uri: extensionsDirectory,
+    });
+  });
+});

extensions/ql-vscode/test/vscode-tests/no-workspace/data-extensions-editor/external-api-usage-query.test.ts

@@ -6,7 +6,7 @@ import { createMockLogger } from "../../../__mocks__/loggerMock";
 import type { Uri } from "vscode";
 import { DatabaseKind } from "../../../../src/databases/local-databases";
 import { file } from "tmp-promise";
-import { QueryResultType } from "../../../../src/pure/new-messages";
+import { QueryResultType } from "../../../../src/query-server/new-messages";
 import { readdir, readFile } from "fs-extra";
 import { load } from "js-yaml";
 import { dirname, join } from "path";

extensions/ql-vscode/test/vscode-tests/no-workspace/query-evaluation-logging/eval-log-tree-builder.test.ts

@@ -1,5 +1,5 @@
 import { EvalLogTreeBuilder } from "../../../../src/query-evaluation-logging";
-import { EvalLogData } from "../../../../src/pure/log-summary-parser";
+import { EvalLogData } from "../../../../src/log-insights/log-summary-parser";
 
 describe("EvalLogTreeBuilder", () => {
   it("should build the log tree roots", async () => {

extensions/ql-vscode/test/vscode-tests/no-workspace/query-history/store/query-history-store.test.ts

@@ -12,7 +12,7 @@ import { QueryWithResults } from "../../../../../src/run-queries-shared";
 import { DatabaseInfo } from "../../../../../src/common/interface-types";
 import { CancellationTokenSource, Uri } from "vscode";
 import { tmpDir } from "../../../../../src/tmp-dir";
-import { QueryResultType } from "../../../../../src/pure/legacy-messages";
+import { QueryResultType } from "../../../../../src/query-server/legacy-messages";
 import { QueryInProgress } from "../../../../../src/query-server/legacy";
 import { VariantAnalysisHistoryItem } from "../../../../../src/query-history/variant-analysis-history-item";
 import { QueryHistoryInfo } from "../../../../../src/query-history/query-history-info";

extensions/ql-vscode/test/vscode-tests/no-workspace/query-results.test.ts

@@ -28,7 +28,7 @@ import {
 import {
   EvaluationResult,
   QueryResultType,
-} from "../../../src/pure/legacy-messages";
+} from "../../../src/query-server/legacy-messages";
 import { sleep } from "../../../src/common/time";
 import { mockedObject } from "../utils/mocking.helpers";
 

extensions/ql-vscode/test/vscode-tests/no-workspace/run-queries.test.ts

@@ -7,7 +7,7 @@ import {
   compileQuery,
   registerDatabases,
   deregisterDatabases,
-} from "../../../src/pure/legacy-messages";
+} from "../../../src/query-server/legacy-messages";
 import * as config from "../../../src/config";
 import { tmpDir } from "../../../src/tmp-dir";
 import { CodeQLCliServer } from "../../../src/codeql-cli/cli";