Update the build script to do a submodule update

if necessary before building.

Update build instructions in README.md.

Fixes ufs-community#818.

README.md

@@ -59,20 +59,21 @@ It also uses the following repositories:
 
 ## Installing
 
-On Orion, Jet, Hera and WCOSS2, invoke the build script:
+On Orion, Jet, Hera and WCOSS2, set the 'fixed' directories
+using the 'link_fixdirs.sh' script in ./fix. See the script's 
+prolog for details.
+
+This repository uses submodules, so do:
 
 ```
-./build_all.sh
+git submodule init
+git submodule update
 ```
 
-Otherwise, do:
+Then, invoke the build script:
 
 ```
-mkdir build
-cd build
-cmake -DCMAKE_INSTALL_PREFIX=/path/to/install ..
-make -j2
-make install
+./build_all.sh
 ```
 
 ## Contents

build_all.sh

@@ -26,6 +26,13 @@ else
  set -x
 fi
 
+# Ensure the submodules have been initialized.
+
+if [[ ! -d ./ccpp-physics/physics ]];then
+  git submodule init
+  git submodule update
+fi
+
 # The unit test data download is part of the build system. Not all machines can
 # access the EMC ftp site, so turn off the build (-DBUILD_TESTING=OFF) of the units tests accordingly.
 # Those with access to the EMC ftp site are: Orion and Hera.