Merge branch release-5-1

Conflicts:
	src/gromacs/commandline/shellcompletions.cpp
Removed line no longer appropriate, now that zsh completion
is supported. Master had changed the previous line, which
git flags as a merge conflict.

Change-Id: Id9d37615b2bd121b1206ca0e6e8eac62fcf38f01

diff --cc src/gromacs/commandline/shellcompletions.cpp
index a0ef63e4c607e8917d6adb61ca97bb34d0ec1164,ce9f08a71779219b18ce4cb5a4786e91d9b17339..520ff469092dfc79a25b7095c878ff35b6aaed9f
--- 1/src/gromacs/commandline/shellcompletions.cpp
--- 2/src/gromacs/commandline/shellcompletions.cpp
+++ b/src/gromacs/commandline/shellcompletions.cpp
@@@ -217,8 -217,7 +217,7 @@@ TextOutputStream &ShellCompletionWriter
  
  void ShellCompletionWriter::startCompletions()
  {
 -    impl_->file_.reset(new File(impl_->binaryName_ + "-completion.bash", "w"));
 +    impl_->file_.reset(new TextWriter(impl_->binaryName_ + "-completion.bash"));
-     impl_->file_->writeLine("shopt -s extglob");
  }
  
  void ShellCompletionWriter::writeModuleCompletions(

diff --cc src/gromacs/gmxpreprocess/grompp.cpp
Simple merge

diff --cc src/gromacs/options/filenameoptionmanager.cpp
Simple merge

diff --cc src/gromacs/trajectoryanalysis/modules/sasa.cpp
Simple merge