CLTools: added the possibility of setting PLUMED_ROOT

as an enviroment variable. This should allow to move
more easily a static executable of plumed.

I have implemented solutions 2 and 4 of #129

this close #129

src/config/Config.cpp.in

@@ -22,6 +22,7 @@
 
 #include "Config.h"
 #include "version.h"
+#include <cstdlib>
 #include <cstring>
 
 namespace PLMD{
@@ -36,7 +37,14 @@ bool isInstalled(){
 }
 
 std::string getPlumedRoot(){
-  return "@PLUMED_ROOT@";
+  char *env = std::getenv("PLUMED_ROOT");
+  std::string ss;
+  if( env == NULL) {
+    ss="@PLUMED_ROOT@";
+  } else {
+    ss=std::string( env );
+  }
+  return ss;
 }
 
 std::string getVersion(){

src/core/CLToolMain.cpp

@@ -167,9 +167,8 @@ int CLToolMain::run(int argc, char **argv,FILE*in,FILE*out,Communicator& pc){
     vector<string> files=Tools::ls(root);
     if(find(files.begin(),files.end(),"patches")==files.end()) {
       string msg=
-         "ERROR: I cannot find "+root+"/patches/ directory\n";
+         "WARNING: I cannot find "+root+"/patches/ directory. Set PLUMED_ROOT or reinstall PLUMED\n\n";
       fprintf(stderr,"%s",msg.c_str());
-      return 1;
     }
   }