fix: extract additionalArgs as raw CLI arguments instead of --additionalArgs=value

Previously, `additionalArgs` (e.g., `["--sarif-include-query-help=always"]`)
stayed in the options object and was processed by `buildCodeQLArgs` into
`--additionalArgs=--sarif-include-query-help=always`, which is invalid.

Now `additionalArgs` is extracted from options before CLI arg building and
appended as raw arguments after positional args, so args like
`--sarif-include-query-help=always` and `--no-sarif-minify` are passed
through correctly to the `codeql` CLI.

Agent-Logs-Url: https://github.com/advanced-security/codeql-development-mcp-server/sessions/ff382e0c-2894-422a-a9c8-22c431c9a77a

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

Author: Copilot

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

@@ -57350,6 +57350,8 @@ function registerCLITool(server, definition) {
             mkdirSync5(outputDir, { recursive: true });
           }
         }
+        const userAdditionalArgs = Array.isArray(options.additionalArgs) ? options.additionalArgs : [];
+        delete options.additionalArgs;
         let result;
         if (command === "codeql") {
           let cwd;
@@ -57365,9 +57367,9 @@ function registerCLITool(server, definition) {
           if (name === "codeql_test_run") {
             options["keep-databases"] = true;
           }
-          result = await executeCodeQLCommand(subcommand, options, positionalArgs, cwd);
+          result = await executeCodeQLCommand(subcommand, options, [...positionalArgs, ...userAdditionalArgs], cwd);
         } else if (command === "qlt") {
-          result = await executeQLTCommand(subcommand, options, positionalArgs);
+          result = await executeQLTCommand(subcommand, options, [...positionalArgs, ...userAdditionalArgs]);
         } else {
           throw new Error(`Unsupported command: ${command}`);
         }