Improve documentation per Kate's recommendation.

Fixes ufs-community#818.

README.md

@@ -61,8 +61,12 @@ It also uses the following repositories:
 
 On Orion, Jet, Hera and WCOSS2 do the following:
 
-1) Set the 'fixed' directories using the 'link_fixdirs.sh'
-script in ./fix. See the script's prolog for details.
+1) Set the 'fixed' directories using the `link_fixdirs.sh`
+script in `./fix`. Usage: `./link_fixdirs.sh $RUN_ENVIR $machine`,
+where `$RUN_ENVIR` is "emc" or "nco" (most developers
+should choose "emc") and `$machine` is the platform.
+
+Example: `./link_fixdirs.sh emc hera`
 
 2) This repository uses submodules, so do:
 

fix/link_fixdirs.sh

@@ -1,7 +1,15 @@
 #!/bin/bash
 set -ex
 
-#--Make symbolic links to 'fixed' directories.
+# Set up the 'fixed' directories. 
+# 
+# This script takes two arguments:
+#
+#  $RUN_ENVIR - Either 'emc' (creates links) or
+#               'nco' (copies data).
+#
+#  $machine - is the machine. Choices are:
+#             'wcoss2', 'hera', 'jet', 'orion', 's4'
 
 RUN_ENVIR=${1}
 machine=${2}