fix: filter managed CLI flags from additionalArgs to prevent conflicts with post-processing

For tools with post-execution processing (query run, test run, database
analyze), flags like --logdir, --evaluator-log, --output, --verbosity,
and --tuple-counting are set internally and read back after execution.
If these appear in additionalArgs, they would create conflicting
duplicates and break post-processing. Now they are filtered out with a
warning directing the user to use the corresponding named parameter.

Agent-Logs-Url: https://github.com/advanced-security/codeql-development-mcp-server/sessions/dd017a82-a805-40c8-bb2f-4eae0678766d

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

Author: Copilot

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

@@ -57338,8 +57338,25 @@ function registerCLITool(server, definition) {
             mkdirSync5(outputDir, { recursive: true });
           }
         }
-        const userAdditionalArgs = Array.isArray(options.additionalArgs) ? options.additionalArgs : [];
+        const rawAdditionalArgs = Array.isArray(options.additionalArgs) ? options.additionalArgs : [];
         delete options.additionalArgs;
+        const managedFlagNames = /* @__PURE__ */ new Set([
+          "evaluator-log",
+          "logdir",
+          "output",
+          "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;
+          }
+          return true;
+        }) : rawAdditionalArgs;
         let result;
         if (command === "codeql") {
           let cwd;