Added interface to Gromacs-like Replica EXchange

I am starting to merge my GREX branch, which should be
general enough to be used in any REX framework where
coordinates are swapped (a-la-gromacs). Since GREX
significantly modifies the MD-PLUMED interface through
the addition of several new cmd(), I tried to encapsulate
it as a separate objects with a cmd()-like interface.
Commands from MD starting with GREX are automatically
forwarded to that object. E.g.
plumed_cmd(plumed,"GREX init",NULL);
or so should initialize the GREX object, etc.

Up to this point I just upload the interface, later
on I will add the real GREX object, for which I still
have to do some cleaning.

src/PlumedMain.cpp

@@ -73,13 +73,17 @@ static class PlumedMainInitializer{
 
 PlumedMain::PlumedMain():
   initialized(false),
+  grex(NULL),
   log(comm),
   step(0),
   active(false),
   atoms(*this),
   actionSet((*this)),
   novirial(false)
-{
+{}
+
+PlumedMain::~PlumedMain(){
+  if(grex) delete grex;
 }
 
 /////////////////////////////////////////////////////////////
@@ -259,6 +263,9 @@ void PlumedMain::cmd(const std::string & word,void*val){
        int check=0;
        if(actionRegister().check(words[1])) check=1;
        *(static_cast<int*>(val))=check;
+     } else if(nw==2 && words[0]=="GREX"){
+       assert(grex);
+       grex->cmd(words[1],val);
      } else{
    // error
        fprintf(stderr,"+++ PLUMED ERROR\n");

src/PlumedMain.h

@@ -47,6 +47,7 @@ public:
   PlumedCommunicator comm;
 
 private:
+  WithCmd* grex;
 /// Flag to avoid double initialization
   bool  initialized;
 /// Name of MD engine
@@ -91,7 +92,7 @@ public:
 /// and an MD engine, this is the right place
 /// Notice that this interface should always keep retro-compatibility
   void cmd(const std::string&key,void*val=NULL);
-  ~PlumedMain(){};
+  ~PlumedMain();
 /// Read an input file.
 /// \param str name of the file
   void readInputFile(std::string str);