Improve cli-tool-registry code and testing

Author: data-douser

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

@@ -187355,16 +187355,21 @@ function registerCLITool(server, definition) {
           positionalArgs = [...positionalArgs, ...files];
         }
         if (file && name.startsWith("codeql_bqrs_")) {
-          let cleanFile = Array.isArray(file) ? String(file[0]) : String(file);
+          let cleanFile = Array.isArray(file) ? file.length > 0 ? String(file[0]) : "" : String(file);
           if (cleanFile.startsWith("[") && cleanFile.endsWith("]")) {
             try {
               const parsed = JSON.parse(cleanFile);
               if (Array.isArray(parsed) && parsed.length > 0) {
                 cleanFile = String(parsed[0]);
+              } else {
+                cleanFile = "";
               }
             } catch {
             }
           }
+          if (!cleanFile) {
+            throw new Error('The "file" parameter for BQRS tools must be a non-empty string path to a .bqrs file.');
+          }
           positionalArgs = [...positionalArgs, cleanFile];
         }
         if (qlref && name === "codeql_resolve_qlref") {
@@ -187498,26 +187503,30 @@ function registerCLITool(server, definition) {
           case "codeql_bqrs_interpret":
             if (options.database) {
               const dbPath = resolveDatabasePath(options.database);
-              const srcZipPath = join10(dbPath, "src.zip");
-              const srcDirPath = join10(dbPath, "src");
-              if (existsSync6(srcZipPath)) {
-                options["source-archive"] = srcZipPath;
-              } else if (existsSync6(srcDirPath)) {
-                options["source-archive"] = srcDirPath;
-              } else {
-                delete options.database;
-                throw new Error(
-                  `CodeQL database at "${dbPath}" does not contain a source archive (expected "src.zip" file or "src" directory).`
-                );
+              if (!options["source-archive"]) {
+                const srcZipPath = join10(dbPath, "src.zip");
+                const srcDirPath = join10(dbPath, "src");
+                if (existsSync6(srcZipPath)) {
+                  options["source-archive"] = srcZipPath;
+                } else if (existsSync6(srcDirPath)) {
+                  options["source-archive"] = srcDirPath;
+                } else {
+                  delete options.database;
+                  throw new Error(
+                    `CodeQL database at "${dbPath}" does not contain a source archive (expected "src.zip" file or "src" directory).`
+                  );
+                }
               }
-              const dbYmlPath = join10(dbPath, "codeql-database.yml");
-              try {
-                const dbYml = readFileSync7(dbYmlPath, "utf8");
-                const dbMeta = load(dbYml);
-                if (dbMeta?.sourceLocationPrefix && typeof dbMeta.sourceLocationPrefix === "string") {
-                  options["source-location-prefix"] = dbMeta.sourceLocationPrefix;
+              if (!options["source-location-prefix"]) {
+                const dbYmlPath = join10(dbPath, "codeql-database.yml");
+                try {
+                  const dbYml = readFileSync7(dbYmlPath, "utf8");
+                  const dbMeta = load(dbYml);
+                  if (dbMeta?.sourceLocationPrefix && typeof dbMeta.sourceLocationPrefix === "string") {
+                    options["source-location-prefix"] = dbMeta.sourceLocationPrefix;
+                  }
+                } catch {
                 }
-              } catch {
               }
               delete options.database;
             }