Fixed a small bug in manual generation and corrected English in code instruction pages

patches/gromacs-4.5.5.config

@@ -21,7 +21,7 @@ function plumed_after_revert(){
 function plumed_patch_info(){
   echo ""
   echo "PLUMED can be incorporated into gromacs using a simple patching procedure."
-  echo "Patching must be done _after_ gromacs has been configured, _before_ gromacs is compiled"
+  echo "Patching must be done _after_ gromacs has been configured but  _before_ gromacs is compiled"
   echo 
   echo "For more information on gromacs you should visit http://www.gromacs.org"
 }

patches/gromacs-4.6.3.config

@@ -8,7 +8,7 @@ function plumed_preliminary_test(){
 function plumed_patch_info(){
   echo ""
   echo "PLUMED can be incorporated into gromacs using a simple patching procedure."
-  echo "Patching must be done _before_ cmake command is invoked"
+  echo "Patching must be done _before_ the cmake command is invoked"
   echo
   echo "For more information on gromacs you should visit http://www.gromacs.org"
 }

patches/lammps-6Apr13.config

@@ -18,9 +18,9 @@ function plumed_patch_info(){
   echo ""
   echo "PLUMED can be incorporated into LAMMPS using a simple patching procedure."
   echo "Patching must be done _before_ LAMMPS is configured."
-  echo "After patching, one should also enable PLUMED with"
+  echo "After patching, one should enable PLUMED using the command"
   echo "make yes-user-plumed"
-  echo "In the same way, before reverting one should disable PLUMED with"
+  echo "In the same way, before reverting one should disable PLUMED using the command"
   echo "make no-user-plumed"
   echo 
   echo "For more information on LAMMPS you should visit http://lammps.sandia.gov/"

user-doc/extract

@@ -142,8 +142,8 @@ do
         
         # Find src files in module and add a link to the module description
         for srcfile in `ls ../src/"$file"/*cpp` ; do
-            ndocs=`grep PLUMEDOC "$srcfile" | wc -l | awk '{print $1}'`
-            for ((line=1;line<$ndocs;++line)) ; do
+            ndocs=`grep PLUMEDOC "$srcfile" | grep -v END | wc -l | awk '{print $1}'`
+            for ((line=1;line<=$ndocs;++line)) ; do
                docfile=`grep PLUMEDOC "$srcfile" | grep -v END | head -n $line | tail -n 1 | awk '{print $3}'`
                cat automatic/"$docfile".tmp |
                {