Use `UpdateAllowUnknown' for non-model related parameter. (#4961)

* Use `UpdateAllowUnknown' for non-model related parameter.

Model parameter can not pack an additional boolean value due to binary IO
format.  This commit deals only with non-model related parameter configuration.

* Add tidy command line arg for use-dmlc-gtest.

src/logging.cc

@@ -5,12 +5,13 @@
  * \author Tianqi Chen
  */
 #include <rabit/rabit.h>
-#include <dmlc/parameter.h>
-#include <xgboost/logging.h>
 
 #include <iostream>
 #include <map>
 
+#include "xgboost/parameter.h"
+#include "xgboost/logging.h"
+
 #if !defined(XGBOOST_STRICT_R_MODE) || XGBOOST_STRICT_R_MODE == 0
 // Override logging mechanism for non-R interfaces
 void dmlc::CustomLogMessage::Log(const std::string& msg) {
@@ -51,7 +52,7 @@ bool ConsoleLogger::ShouldLog(LogVerbosity verbosity) {
 }
 
 void ConsoleLogger::Configure(Args const& args) {
-  param_.InitAllowUnknown(args);
+  param_.UpdateAllowUnknown(args);
   // Deprecated, but when trying to display deprecation message some R
   // tests trying to catch stdout will fail.
   if (param_.silent) {