Design 1: Populate query_results_cache from database_analyze results

Add cacheDatabaseAnalyzeResults() to auto-cache SARIF output from
database_analyze into the query results cache. Update README with
new enableAnnotationTools setting documentation.

Agent-Logs-Url: https://github.com/advanced-security/codeql-development-mcp-server/sessions/0d52c27d-21be-49ea-bf90-c8fb6f50a3da

Co-authored-by: data-douser <70299490+data-douser@users.noreply.github.com>

Author: Copilot

extensions/vscode/README.md

@@ -45,6 +45,7 @@ All settings are under the `codeql-mcp` namespace in VS Code settings:
 | `codeql-mcp.serverCommand`                 | `"node"`   | Command to launch the server. Override to `"npx"` or a custom path. |
 | `codeql-mcp.serverArgs`                    | `[]`       | Custom args. When empty, the bundled entry point is used.           |
 | `codeql-mcp.watchCodeqlExtension`          | `true`     | Watch for databases and results from the CodeQL extension.          |
+| `codeql-mcp.enableAnnotationTools`         | `true`     | Enable annotation, audit, and cache tools.                          |
 | `codeql-mcp.additionalEnv`                 | `{}`       | Extra environment variables passed to the server process.           |
 | `codeql-mcp.additionalDatabaseDirs`        | `[]`       | Additional directories to search for CodeQL databases.              |
 | `codeql-mcp.additionalMrvaRunResultsDirs`  | `[]`       | Additional directories containing MRVA run results.                 |

server/dist/codeql-development-mcp-server.js

@@ -184584,6 +184584,54 @@ Warning: Query processing error - ${error2}`
     };
   }
 }
+function cacheDatabaseAnalyzeResults(params, logger2) {
+  try {
+    const config2 = sessionDataManager.getConfig();
+    if (!config2.enableAnnotationTools) return;
+    const outputPath = params.output;
+    const format = params.format;
+    const dbPath = params.database;
+    const queries = params.queries;
+    if (!outputPath || !format || !dbPath) return;
+    if (!format.includes("sarif")) return;
+    let resultContent;
+    try {
+      resultContent = readFileSync6(outputPath, "utf8");
+    } catch {
+      return;
+    }
+    const codeqlVersion = getActualCodeqlVersion();
+    const queryName = queries ? basename4(queries, ".qls") : "database-analyze";
+    let resultCount = null;
+    try {
+      const sarif = JSON.parse(resultContent);
+      resultCount = sarif?.runs?.[0]?.results?.length ?? null;
+    } catch {
+    }
+    const cacheKey2 = computeQueryCacheKey({
+      codeqlVersion,
+      databasePath: dbPath,
+      outputFormat: format,
+      queryPath: queries || "database-analyze"
+    });
+    const store = sessionDataManager.getStore();
+    store.putCacheEntry({
+      cacheKey: cacheKey2,
+      codeqlVersion,
+      databasePath: dbPath,
+      interpretedPath: outputPath,
+      language: "unknown",
+      outputFormat: format,
+      queryName,
+      queryPath: queries || "database-analyze",
+      resultContent,
+      resultCount
+    });
+    logger2.info(`Cached database-analyze results with key: ${cacheKey2} (${resultCount ?? 0} results)`);
+  } catch (err) {
+    logger2.error("Failed to cache database-analyze results:", err);
+  }
+}
 
 // src/lib/cli-tool-registry.ts
 init_package_paths();
@@ -187572,6 +187620,9 @@ function registerCLITool(server, definition) {
             }
           }
         }
+        if (name === "codeql_database_analyze" && result.success && options.output) {
+          cacheDatabaseAnalyzeResults({ ...params, output: options.output, format: options.format }, logger);
+        }
         const processedResult = resultProcessor(result, params);
         return {
           content: [{