Use process group signal handling to reach past the shell

Spawn processes is their own process group and then signal the
process group intstead of just the process we spawned to ensure
the signals also reach any subprocesses started by the process we
spawned (which is always the case as we are wrapping all our
processes spawning with "/bin/sh -c ...").

This make sending SIGINT work again, so revert back to that instead
of SIGKILL. The reason SIGINT wasn't working was the shell logic
is that this is expected to be sent to the process group, so it
doesn't need to pass it along or anything. See the bash signals
documentation page for more details

https://www.gnu.org/software/bash/manual/html_node/Signals.html

src/tools/Subprocess.cpp

@@ -51,19 +51,19 @@ class SubprocessPid {
   void stop() noexcept {
     // Signals give problems with MPI on Travis.
     // I disable them for now.
-    if(SubprocessPidGetenvSignals()) kill(pid,SIGSTOP);
+    if(SubprocessPidGetenvSignals()) kill(-pid,SIGSTOP);
   }
   void cont() noexcept {
     // Signals give problems with MPI on Travis.
     // I disable them for now.
-    if(SubprocessPidGetenvSignals()) kill(pid,SIGCONT);
+    if(SubprocessPidGetenvSignals()) kill(-pid,SIGCONT);
   }
   ~SubprocessPid() {
     // the destructor implies we do not need the subprocess anymore, so SIGKILL
     // is the fastest exit.
     // if we want to gracefully kill the process with a delay, it would be cleaner
     // to have another member function
-    kill(pid,SIGKILL);
+    kill(-pid,SIGINT);
     // Wait for the child process to terminate
     // This is anyway required to avoid leaks
     int status;
@@ -99,6 +99,7 @@ Subprocess::Subprocess(const std::string & cmd) {
     if(dup(pc[0])<0) plumed_error()<<"error duplicating file";
     if(close(pc[1])<0) plumed_error()<<"error closing file";
     if(close(cp[0])<0) plumed_error()<<"error closing file";
+    if(setpgid(0,0)<0) plumed_error()<<"error setting process group";;
     auto err=execv(arr[0],arr);
     plumed_error()<<"error in script file " << cmd << ", execv returned "<<err;
   }