Merge pull request #1883 from bertinia/master

minor update to sphinx documentation
Sphinx documentation update.

Test suite: N/A
Test baseline: N/A
Test namelist changes: N/A
Test status: [bit for bit, roundoff, climate changing] N/A

Fixes [CIME Github issue #] none

User interface changes?: none

Update gh-pages html (Y/N)?: Y

Code review:jedwards

doc/Makefile

@@ -26,7 +26,7 @@ Tools_api:
 	@$(SPHINXAPI) --force -o $(SOURCEDIR)/$@ $(SCRIPTSDIR)/Tools
 
 Tools_user:
-	rm $(SOURCEDIR)/$@/*.rst
+	rm -f $(SOURCEDIR)/$@/*.rst
 	./tools_autodoc.py
 
 .PHONY: help Makefile CIME_api Tools_api Tools_user

doc/source/index.rst

@@ -21,7 +21,6 @@ Table of contents
    data_models/index.rst
    driver_cpl/index.rst
    misc_tools/index.rst
-   glossary.rst
 
 Addendum
 ---------
@@ -34,12 +33,11 @@ Addendum
    CIME_api/modules.rst
    Tools_api/modules.rst
 
-Indices, Glossary and Search
-----------------------------
+Python Module Indices and Search
+---------------------------------
 
 * :ref:`genindex`
 * :ref:`modindex`
-* :ref:`glossary`
 * :ref:`search`
 
 

doc/source/users_guide/index.rst

@@ -23,7 +23,6 @@ CIME User's Guide Part 1: Beginner - Basic Usage
    cloning-a-case.rst
    troubleshooting.rst
 
-
 .. _users-guide2:
 
 #######################################################################################
@@ -42,7 +41,6 @@ CIME User's Guide Part 2: Intermediate - CIME Internals, Porting, Testing and Us
    multi-instance.rst
    adding-cases.rst
    use_cases/use-cases.rst
-   adding-components.rst
 
 
 Indices and tables

doc/source/users_guide/multi-instance.rst

@@ -68,6 +68,7 @@ As a result, you will have two instances of CAM, CLM and CICE (prescribed), RTM,
 Now consider the multi driver model.
 To use this mode change
 ::
+
    > ./xmlchange MULTI_DRIVER=TRUE
 
 This configuration will run each component instance on the original 144 tasks but will generate two copies of the model (in the same executable) for a total of 288 tasks.

doc/source/xml_files/cesm.rst

@@ -57,13 +57,13 @@ the following XML files.
 
 CESM XML settings for all-active component set (compset) configurations.
 
-.. literalinclude:: ../../../cime_config/config_compsets.xml
+.. literalinclude:: ../../../../cime_config/config_compsets.xml
 
 CESM XML settings for all-active test configurations.
 
-.. literalinclude:: ../../../cime_config/testlist_allactive.xml
+.. literalinclude:: ../../../../cime_config/testlist_allactive.xml
 
 CESM XML settings for optimized processor elements (PEs) layout configurations.
 
-.. literalinclude:: ../../../cime_config/config_pes.xml
+.. literalinclude:: ../../../../cime_config/config_pes.xml