Move "using namespace std" after #includes

...so that namespace "std" already exists when we try to use it,
as it will have been declared by the standard headers #included.
Doing otherwise elicits a warning from Clang.

src/closestFile/closestMain.cpp

@@ -5,11 +5,11 @@
  *      Author: nek3d
  */
 
-using namespace std;
-
 #include "closestFile.h"
 #include "ContextClosest.h"
 
+using namespace std;
+
 // define our program name
 #define PROGRAM_NAME "bedtools closest"
 

src/utils/NewChromsweep/NewChromsweep.h

@@ -12,8 +12,6 @@
 #ifndef NEW_CHROMSWEEP_H
 #define NEW_CHROMSWEEP_H
 
-using namespace std;
-
 #include <string>
 #include "BTlist.h"
 #include "RecordKeyList.h"
@@ -24,6 +22,8 @@ using namespace std;
 #include <stdlib.h>
 #include "QuickString.h"
 
+using namespace std;
+
 class Record;
 class FileRecordMgr;
 class ContextIntersect;

src/utils/RecordOutputMgr/RecordOutputMgr.h

@@ -8,12 +8,12 @@
 #ifndef RECORDOUTPUTMGR_H_
 #define RECORDOUTPUTMGR_H_
 
-using namespace std;
-
 #include "ContextBase.h"
 #include "RecordKeyVector.h"
 #include "api/BamWriter.h"
 
+using namespace std;
+
 class BlockMgr;
 
 class RecordOutputMgr {

src/utils/general/CommonHelp.cpp

@@ -6,6 +6,8 @@
  */
 #include "CommonHelp.h"
 
+using namespace std;
+
 void CommonHelp() {
     cerr << "\t-iobuf\t"            << "Follow with desired integer size of read buffer." << endl;
     cerr << "\t\t" <<					"Optional suffixes K/M/G supported." << endl;

src/utils/general/CommonHelp.h

@@ -8,8 +8,6 @@
 #ifndef COMMONHELPFILE_H_
 #define COMMONHELPFILE_H_
 
-using namespace std;
-
 #include <iostream>
 
 extern void CommonHelp();