update documentation

doc/source/user_guide/ug_running.rst

@@ -144,16 +144,11 @@ Some hints:
 
 - To change namelist, manually edit the **ice_in** file
 - To change batch settings, manually edit the top of the **cice.run** or **cice.test** (if running a test) file
-- When the run scripts are submitted, the current **ice_in**, **cice.settings**, and 
-**env.[machine]** files are copied from the case directory into the run directory.  Users 
-should generally not edit files in the run directory as these are overwritten when following
-the standard workflow.  An alias like the 
-following can be established to quickly switch between case and run directories::
+- When the run scripts are submitted, the current **ice_in**, **cice.settings**, and **env.[machine]** files are copied from the case directory into the run directory.  Users should generally not edit files in the run directory as these are overwritten when following the standard workflow.  **cice.settings** can be sourced to establish the case values in the login shell.  An alias like the following can be established to quickly switch between case and run directories::
 
     alias  cdrun 'cd `\grep "setenv ICE_RUNDIR"  cice.settings | awk "{print "\$"NF}"`'
     alias cdcase 'cd `\grep "setenv ICE_CASEDIR" cice.settings | awk "{print "\$"NF}"`'
 
-Or the **cice.settings** can be sourced to establish the case values in the login shell.
 - To turn on the debug compiler flags, set ``ICE_BLDDEBUG`` in **cice.setttings** to true.  It is also possible to use the ``debug`` option  (``-s debug``) when creating the case with **cice.setup** to set this option automatically.
 - To change compiler options, manually edit the Macros file
 - To clean the build before each compile, set ``ICE_CLEANBUILD`` in **cice.settings** to true (this is the default value), or use the ``buildclean`` option (``-s buildclean``)  when creating the case with **cice.setup**.  To not clean before the build, set ``ICE_CLEANBUILD`` in **cice.settings** to false, or use the ``buildincremental`` option  (``-s buildincremental``) when creating the case with **cice.setup**.  It is recommended that the ``ICE_CLEANBUILD`` be set to true if there are any questions about whether the build is proceeding properly.