Synchronize patch for GROMACS CMakeLists with upstream version

Also ignore errors when patchiing CMake recipes

gromacs/CMakeLists.txt.diff

@@ -1,13 +1,13 @@
 diff --git a/CMakeLists.txt b/CMakeLists.txt
-index 70b0369bed..cccfe2aa1b 100644
+index 3681e50c8c..108c35e8f5 100644
 --- a/CMakeLists.txt
 +++ b/CMakeLists.txt
-@@ -678,6 +678,8 @@ include(gmxManageLmfit)
+@@ -684,6 +684,8 @@ include(gmxManageLmfit)
 
  include(gmxManageMuparser)
 
 +include(gmxManageLepton)
 +
  include(gmxManageColvars)
 
- ##################################################
+ include(gmxManagePlumed)

update-colvars-code.sh

@@ -619,14 +619,7 @@ then
   target_folder=${target}/src/external/colvars
   patch_opts="-p1 --forward -s"
 
-  echo ""
-  if [ -d ${target_folder} ]
-  then
-    echo "${target} source tree seems to have already been patched."
-    echo "Updating to the current Colvars sources."
-  else
-    mkdir ${target_folder}
-  fi
+  mkdir -p ${target_folder}
 
   # Copy library files and proxy files to the "src/external/colvars" folder
   for src in ${source}/src/*.h ${source}/src/*.cpp
@@ -638,14 +631,19 @@ then
 
   # Patch CMake build recipe when applicable
   if [ -s ${source}/gromacs/gromacs-mdmodules/gmxManageColvars.cmake.diff ] ; then
-    patch -p1 -N -d ${target} < ${source}/gromacs/gromacs-mdmodules/gmxManageColvars.cmake.diff
+    patch ${patch_opts} -d ${target} < ${source}/gromacs/gromacs-mdmodules/gmxManageColvars.cmake.diff || true
   fi
-  if [ -s ${source}/gromacs/gromacs-mdmodules/CMakeLists1.txt.diff ] ; then
-    patch -p1 -N -d ${target} < ${source}/gromacs/gromacs-mdmodules/CMakeLists1.txt.diff
+  if [ -s ${source}/gromacs/gromacs-mdmodules/CMakeLists.txt.diff ] ; then
+    patch ${patch_opts} -d ${target} < ${source}/gromacs/gromacs-mdmodules/CMakeLists.txt.diff || true
   fi
-  if [ -s ${source}/gromacs/gromacs-mdmodules/CMakeLists2.txt.diff ] ; then
-    patch -p1 -N -d ${target} < ${source}/gromacs/gromacs-mdmodules/CMakeLists2.txt.diff
+  if [ -s ${source}/gromacs/CMakeLists.txt.diff ] ; then
+    patch ${patch_opts} -d ${target} < ${source}/gromacs/CMakeLists.txt.diff || true
   fi
+
+  if [ -s ${source}/gromacs/cmake/gmxManageColvars.cmake ] ; then
+    condcopy ${source}/gromacs/cmake/gmxManageColvars.cmake "${target}/cmake/gmxManageColvars.cmake"
+  fi
+
   if [ -s ${source}/gromacs/cmake/gmxManageLepton.cmake ] ; then
     condcopy ${source}/gromacs/cmake/gmxManageLepton.cmake "${target}/cmake/gmxManageLepton.cmake"
   fi
@@ -678,8 +676,8 @@ then
   echo ""
 
   # Apply patch for Gromacs files
-  if [ -f ${source}/gromacs/gromacs-mdmodules.patch ] ; then
-    patch ${patch_opts} -d ${target} < ${source}/gromacs/gromacs-mdmodules.patch
+  if [ -s ${source}/gromacs/gromacs-mdmodules.patch ] ; then
+    patch ${patch_opts} -d ${target} < ${source}/gromacs/gromacs-mdmodules.patch || true
   fi
   ret_val=$?
   if [ $ret_val -ne 0 ]