Do not set --expect-discarded-cache on "cleanup-level: overlay"

When a user specifies "cleanup-level: overlay", it suggests that the
user wishes to preserve the evaluation cache for future use. So in this
case we should not set --expect-discarded-cache when running queries.

src/analyze-action.ts

@@ -295,12 +295,16 @@ async function run() {
       logger,
     );
 
+    const cleanupLevel =
+      actionsUtil.getOptionalInput("cleanup-level") || "brutal";
+
     if (actionsUtil.getRequiredInput("skip-queries") !== "true") {
       runStats = await runQueries(
         outputDir,
         memory,
         util.getAddSnippetsFlag(actionsUtil.getRequiredInput("add-snippets")),
         threads,
+        cleanupLevel,
         diffRangePackDir,
         actionsUtil.getOptionalInput("category"),
         config,
@@ -309,12 +313,8 @@ async function run() {
       );
     }
 
-    if (actionsUtil.getOptionalInput("cleanup-level") !== "none") {
-      await runCleanup(
-        config,
-        actionsUtil.getOptionalInput("cleanup-level") || "brutal",
-        logger,
-      );
+    if (cleanupLevel !== "none") {
+      await runCleanup(config, cleanupLevel, logger);
     }
 
     const dbLocations: { [lang: string]: string } = {};

src/analyze.test.ts

@@ -101,6 +101,7 @@ test("status report fields", async (t) => {
         memoryFlag,
         addSnippetsFlag,
         threadsFlag,
+        "brutal",
         undefined,
         undefined,
         config,

src/analyze.ts

@@ -548,6 +548,7 @@ export async function runQueries(
   memoryFlag: string,
   addSnippetsFlag: string,
   threadsFlag: string,
+  cleanupLevel: string,
   diffRangePackDir: string | undefined,
   automationDetailsId: string | undefined,
   config: configUtils.Config,
@@ -555,20 +556,22 @@ export async function runQueries(
   features: FeatureEnablement,
 ): Promise<QueriesStatusReport> {
   const statusReport: QueriesStatusReport = {};
+  const queryFlags = [memoryFlag, threadsFlag];
+
+  if (cleanupLevel !== "overlay") {
+    queryFlags.push("--expect-discarded-cache");
+  }
 
   statusReport.analysis_is_diff_informed = diffRangePackDir !== undefined;
-  const dataExtensionFlags = diffRangePackDir
-    ? [
-        `--additional-packs=${diffRangePackDir}`,
-        "--extension-packs=codeql-action/pr-diff-range",
-      ]
-    : [];
+  if (diffRangePackDir) {
+    queryFlags.push(`--additional-packs=${diffRangePackDir}`);
+    queryFlags.push("--extension-packs=codeql-action/pr-diff-range");
+  }
   const sarifRunPropertyFlag = diffRangePackDir
     ? "--sarif-run-property=incrementalMode=diff-informed"
     : undefined;
 
   const codeql = await getCodeQL(config.codeQLCmd);
-  const queryFlags = [memoryFlag, threadsFlag, ...dataExtensionFlags];
 
   for (const language of config.languages) {
     try {

src/codeql.test.ts

@@ -957,7 +957,7 @@ test("runTool recognizes fatal internal errors", async (t) => {
       await codeqlObject.databaseRunQueries(stubConfig.dbLocation, []),
     {
       instanceOf: CliError,
-      message: `Encountered a fatal error while running "codeql-for-testing database run-queries  --expect-discarded-cache --intra-layer-parallelism --min-disk-free=1024 -v". Exit code was 1 and error was: Oops! A fatal internal error occurred. Details:
+      message: `Encountered a fatal error while running "codeql-for-testing database run-queries  --intra-layer-parallelism --min-disk-free=1024 -v". Exit code was 1 and error was: Oops! A fatal internal error occurred. Details:
     com.semmle.util.exception.CatastrophicError: An error occurred while evaluating ControlFlowGraph::ControlFlow::Root.isRootOf/1#dispred#f610e6ed/2@86282cc8
     Severe disk cache trouble (corruption or out of space) at /home/runner/work/_temp/codeql_databases/go/db-go/default/cache/pages/28/33.pack: Failed to write item to disk. See the logs for more details.`,
     },

src/codeql.ts

@@ -805,7 +805,6 @@ export async function getCodeQLForCmd(
         "run-queries",
         ...flags,
         databasePath,
-        "--expect-discarded-cache",
         "--intra-layer-parallelism",
         "--min-disk-free=1024", // Try to leave at least 1GB free
         "-v",