fix: handle space-separated managed flags in additionalArgs filtering

Replace .filter() with a for-loop that also skips the following value
token when a managed flag is supplied in space-separated form
(e.g. ['--output', '/override.sarif']) instead of inline form
(e.g. ['--output=/override.sarif']).  This prevents stray positional
arguments from leaking into the CLI invocation.

Add test coverage for the space-separated form.

Agent-Logs-Url: https://github.com/advanced-security/codeql-development-mcp-server/sessions/fb3b1eea-290e-4eaa-bf2b-26b1521e5a58

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

Author: Copilot

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

@@ -57359,16 +57359,25 @@ function registerCLITool(server, definition) {
           "tuple-counting",
           "verbosity"
         ]);
-        const userAdditionalArgs = queryLogDir ? rawAdditionalArgs.filter((arg) => {
-          const m = arg.match(/^--(?:no-)?([^=]+)/);
-          if (m && managedFlagNames.has(m[1])) {
-            logger.warn(
-              `Ignoring "${arg}" from additionalArgs for ${name}: this flag is managed internally. Use the corresponding named parameter instead.`
-            );
-            return false;
+        const userAdditionalArgs = queryLogDir ? (() => {
+          const filteredAdditionalArgs = [];
+          for (let i = 0; i < rawAdditionalArgs.length; i += 1) {
+            const arg = rawAdditionalArgs[i];
+            const m = arg.match(/^--(?:no-)?([^=]+)(?:=.*)?$/);
+            if (m && managedFlagNames.has(m[1])) {
+              logger.warn(
+                `Ignoring "${arg}" from additionalArgs for ${name}: this flag is managed internally. Use the corresponding named parameter instead.`
+              );
+              const hasInlineValue = arg.includes("=");
+              if (!hasInlineValue && i + 1 < rawAdditionalArgs.length) {
+                i += 1;
+              }
+              continue;
+            }
+            filteredAdditionalArgs.push(arg);
           }
-          return true;
-        }) : rawAdditionalArgs;
+          return filteredAdditionalArgs;
+        })() : rawAdditionalArgs;
         let result;
         if (command === "codeql") {
           let cwd;