Apply suggestions from code review

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Signed-off-by: Nathan Randall <70299490+data-douser@users.noreply.github.com>

Author: data-douser

client/README.md

@@ -33,11 +33,12 @@ gh ql-mcp-client <command> [flags]
 
 | Flag       | Default     | Description                           |
 | ---------- | ----------- | ------------------------------------- |
-| `--mode`   | `http`      | MCP server transport (`stdio`/`http`) |
+| `--mode`   | `stdio`     | MCP server transport (`stdio`/`http`) |
 | `--host`   | `localhost` | MCP server host (http mode)           |
 | `--port`   | `3000`      | MCP server port (http mode)           |
 | `--format` | `text`      | Output format (`text`/`json`)         |
 
+Transport is configured via CLI flags. The CLI does not currently read `MCP_MODE`.
 ### Commands
 
 #### `code-scanning` (alias: `cs`)

client/integration-tests/primitives/tools/codeql_query_run/custom_log_directory/test-config.json

@@ -3,7 +3,7 @@
   "arguments": {
     "query": "server/ql/javascript/examples/src/ExampleQuery1/ExampleQuery1.ql",
     "database": "server/ql/javascript/examples/test/ExampleQuery1/ExampleQuery1.testproj",
-    "logDir": "server/.tmp/query-logs/custom-test-dir",
+    "logDir": "{{tmpdir}}/query-logs/custom-log-directory",
     "tuple-counting": true
   }
 }

client/integration-tests/primitives/tools/codeql_test_run/custom_log_directory/test-config.json

@@ -2,6 +2,6 @@
   "toolName": "codeql_test_run",
   "arguments": {
     "tests": ["server/ql/javascript/examples/test/ExampleQuery1"],
-    "logDir": "server/.tmp/query-logs/custom-test-dir"
+    "logDir": "{{tmpdir}}/query-logs/codeql_test_run/custom_log_directory"
   }
 }