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 <li class="toctree-l1"><a class="reference internal" href="../build_cpl/index.html">Building a Coupled Model with CIME</a></li>
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diff --git a/versions/master/html/Tools_user/case.qstatus.html b/versions/master/html/Tools_user/case.qstatus.html
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 <li class="toctree-l1"><a class="reference internal" href="../build_cpl/index.html">Building a Coupled Model with CIME</a></li>
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diff --git a/versions/master/html/Tools_user/case.setup.html b/versions/master/html/Tools_user/case.setup.html
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 <li class="toctree-l1"><a class="reference internal" href="../build_cpl/index.html">Building a Coupled Model with CIME</a></li>
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diff --git a/versions/master/html/Tools_user/case.submit.html b/versions/master/html/Tools_user/case.submit.html
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 <li class="toctree-l1"><a class="reference internal" href="../build_cpl/index.html">Building a Coupled Model with CIME</a></li>
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 <li class="toctree-l1"><a class="reference internal" href="../build_cpl/index.html">Building a Coupled Model with CIME</a></li>
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diff --git a/versions/master/html/Tools_user/check_case.html b/versions/master/html/Tools_user/check_case.html
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 <li class="toctree-l1"><a class="reference internal" href="../build_cpl/index.html">Building a Coupled Model with CIME</a></li>
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+<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html#configuring-the-case-control-system">Configuring the Case Control System</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../build_cpl/index.html">Building a Coupled Model with CIME</a></li>
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diff --git a/versions/master/html/Tools_user/check_lockedfiles.html b/versions/master/html/Tools_user/check_lockedfiles.html
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+<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html">Using the Case Control System</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html#configuring-the-case-control-system">Configuring the Case Control System</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../build_cpl/index.html">Building a Coupled Model with CIME</a></li>
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+<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html">Using the Case Control System</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html#configuring-the-case-control-system">Configuring the Case Control System</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../build_cpl/index.html">Building a Coupled Model with CIME</a></li>
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diff --git a/versions/master/html/Tools_user/code_checker.html b/versions/master/html/Tools_user/code_checker.html
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diff --git a/versions/master/html/Tools_user/create_clone.html b/versions/master/html/Tools_user/create_clone.html
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diff --git a/versions/master/html/Tools_user/create_newcase.html b/versions/master/html/Tools_user/create_newcase.html
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diff --git a/versions/master/html/Tools_user/create_test.html b/versions/master/html/Tools_user/create_test.html
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diff --git a/versions/master/html/Tools_user/cs.status.html b/versions/master/html/Tools_user/cs.status.html
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diff --git a/versions/master/html/Tools_user/e3sm_check_env.html b/versions/master/html/Tools_user/e3sm_check_env.html
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 <li class="toctree-l1"><a class="reference internal" href="../build_cpl/index.html">Building a Coupled Model with CIME</a></li>
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diff --git a/versions/master/html/Tools_user/getTiming.html b/versions/master/html/Tools_user/getTiming.html
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diff --git a/versions/master/html/Tools_user/get_case_env.html b/versions/master/html/Tools_user/get_case_env.html
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+<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html#configuring-the-case-control-system">Configuring the Case Control System</a></li>
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 <li class="toctree-l1"><a class="reference internal" href="../build_cpl/index.html">Building a Coupled Model with CIME</a></li>
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diff --git a/versions/master/html/Tools_user/index.html b/versions/master/html/Tools_user/index.html
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 <li class="toctree-l1"><a class="reference internal" href="../build_cpl/index.html">Building a Coupled Model with CIME</a></li>
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 <li class="toctree-l1"><a class="reference internal" href="../build_cpl/index.html">Building a Coupled Model with CIME</a></li>
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diff --git a/versions/master/html/Tools_user/preview_run.html b/versions/master/html/Tools_user/preview_run.html
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 <li class="toctree-l1"><a class="reference internal" href="../build_cpl/index.html">Building a Coupled Model with CIME</a></li>
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diff --git a/versions/master/html/Tools_user/query_config.html b/versions/master/html/Tools_user/query_config.html
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diff --git a/versions/master/html/Tools_user/query_testlists.html b/versions/master/html/Tools_user/query_testlists.html
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 <li class="toctree-l1"><a class="reference internal" href="../build_cpl/index.html">Building a Coupled Model with CIME</a></li>
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-<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html#case-control-system-part-2-configuration-porting-testing-and-use-cases">Case Control System Part 2: Configuration, Porting, Testing and Use Cases</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html">Using the Case Control System</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html#configuring-the-case-control-system">Configuring the Case Control System</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../build_cpl/index.html">Building a Coupled Model with CIME</a></li>
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diff --git a/versions/master/html/Tools_user/simple-py-prof.html b/versions/master/html/Tools_user/simple-py-prof.html
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+<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html#configuring-the-case-control-system">Configuring the Case Control System</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../build_cpl/index.html">Building a Coupled Model with CIME</a></li>
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diff --git a/versions/master/html/Tools_user/simple_compare.html b/versions/master/html/Tools_user/simple_compare.html
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 <li class="toctree-l1"><a class="reference internal" href="../build_cpl/index.html">Building a Coupled Model with CIME</a></li>
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diff --git a/versions/master/html/Tools_user/testreporter.py.html b/versions/master/html/Tools_user/testreporter.py.html
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+<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html">Using the Case Control System</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html#configuring-the-case-control-system">Configuring the Case Control System</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../build_cpl/index.html">Building a Coupled Model with CIME</a></li>
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diff --git a/versions/master/html/Tools_user/wait_for_tests.html b/versions/master/html/Tools_user/wait_for_tests.html
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-<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html">Case Control System Part 1: Basic Usage</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html#case-control-system-part-2-configuration-porting-testing-and-use-cases">Case Control System Part 2: Configuration, Porting, Testing and Use Cases</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html">Using the Case Control System</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html#configuring-the-case-control-system">Configuring the Case Control System</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../build_cpl/index.html">Building a Coupled Model with CIME</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../misc_tools/index.html">Miscellaneous Tools</a></li>
 </ul>
diff --git a/versions/master/html/Tools_user/xmlchange.html b/versions/master/html/Tools_user/xmlchange.html
index acda36e3a15..dff51da036a 100644
--- a/versions/master/html/Tools_user/xmlchange.html
+++ b/versions/master/html/Tools_user/xmlchange.html
@@ -50,8 +50,8 @@
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
               <ul>
 <li class="toctree-l1"><a class="reference internal" href="../what_cime/index.html">What is CIME?</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html">Case Control System Part 1: Basic Usage</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html#case-control-system-part-2-configuration-porting-testing-and-use-cases">Case Control System Part 2: Configuration, Porting, Testing and Use Cases</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html">Using the Case Control System</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html#configuring-the-case-control-system">Configuring the Case Control System</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../build_cpl/index.html">Building a Coupled Model with CIME</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../misc_tools/index.html">Miscellaneous Tools</a></li>
 </ul>
diff --git a/versions/master/html/Tools_user/xmlquery.html b/versions/master/html/Tools_user/xmlquery.html
index 213e74301a1..f4b55bb39e6 100644
--- a/versions/master/html/Tools_user/xmlquery.html
+++ b/versions/master/html/Tools_user/xmlquery.html
@@ -50,8 +50,8 @@
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
               <ul>
 <li class="toctree-l1"><a class="reference internal" href="../what_cime/index.html">What is CIME?</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html">Case Control System Part 1: Basic Usage</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html#case-control-system-part-2-configuration-porting-testing-and-use-cases">Case Control System Part 2: Configuration, Porting, Testing and Use Cases</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html">Using the Case Control System</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html#configuring-the-case-control-system">Configuring the Case Control System</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../build_cpl/index.html">Building a Coupled Model with CIME</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../misc_tools/index.html">Miscellaneous Tools</a></li>
 </ul>
diff --git a/versions/master/html/Tools_user/xmltestentry.html b/versions/master/html/Tools_user/xmltestentry.html
index 5c34f5accfd..df7e6bb883a 100644
--- a/versions/master/html/Tools_user/xmltestentry.html
+++ b/versions/master/html/Tools_user/xmltestentry.html
@@ -50,8 +50,8 @@
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
               <ul>
 <li class="toctree-l1"><a class="reference internal" href="../what_cime/index.html">What is CIME?</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html">Case Control System Part 1: Basic Usage</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html#case-control-system-part-2-configuration-porting-testing-and-use-cases">Case Control System Part 2: Configuration, Porting, Testing and Use Cases</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html">Using the Case Control System</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html#configuring-the-case-control-system">Configuring the Case Control System</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../build_cpl/index.html">Building a Coupled Model with CIME</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../misc_tools/index.html">Miscellaneous Tools</a></li>
 </ul>
diff --git a/versions/master/html/_modules/CIME/SystemTests/test_utils/user_nl_utils.html b/versions/master/html/_modules/CIME/SystemTests/test_utils/user_nl_utils.html
index fe13d608b53..a2f480c575a 100644
--- a/versions/master/html/_modules/CIME/SystemTests/test_utils/user_nl_utils.html
+++ b/versions/master/html/_modules/CIME/SystemTests/test_utils/user_nl_utils.html
@@ -47,8 +47,8 @@
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
               <ul>
 <li class="toctree-l1"><a class="reference internal" href="../../../../what_cime/index.html">What is CIME?</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../../../../users_guide/index.html">Case Control System Part 1: Basic Usage</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../../../../users_guide/index.html#case-control-system-part-2-configuration-porting-testing-and-use-cases">Case Control System Part 2: Configuration, Porting, Testing and Use Cases</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../../../users_guide/index.html">Using the Case Control System</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../../../users_guide/index.html#configuring-the-case-control-system">Configuring the Case Control System</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../../build_cpl/index.html">Building a Coupled Model with CIME</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../../misc_tools/index.html">Miscellaneous Tools</a></li>
 </ul>
diff --git a/versions/master/html/_modules/CIME/tests/case_fake.html b/versions/master/html/_modules/CIME/tests/case_fake.html
index c91c4d15a5f..fe96d06abcd 100644
--- a/versions/master/html/_modules/CIME/tests/case_fake.html
+++ b/versions/master/html/_modules/CIME/tests/case_fake.html
@@ -47,8 +47,8 @@
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
               <ul>
 <li class="toctree-l1"><a class="reference internal" href="../../../what_cime/index.html">What is CIME?</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../../../users_guide/index.html">Case Control System Part 1: Basic Usage</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../../../users_guide/index.html#case-control-system-part-2-configuration-porting-testing-and-use-cases">Case Control System Part 2: Configuration, Porting, Testing and Use Cases</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../../users_guide/index.html">Using the Case Control System</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../../users_guide/index.html#configuring-the-case-control-system">Configuring the Case Control System</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../build_cpl/index.html">Building a Coupled Model with CIME</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../misc_tools/index.html">Miscellaneous Tools</a></li>
 </ul>
diff --git a/versions/master/html/_modules/CIME/tests/test_unit_case_fake.html b/versions/master/html/_modules/CIME/tests/test_unit_case_fake.html
index 4db6f1b81c3..38f6aea4e86 100644
--- a/versions/master/html/_modules/CIME/tests/test_unit_case_fake.html
+++ b/versions/master/html/_modules/CIME/tests/test_unit_case_fake.html
@@ -47,8 +47,8 @@
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
               <ul>
 <li class="toctree-l1"><a class="reference internal" href="../../../what_cime/index.html">What is CIME?</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../../../users_guide/index.html">Case Control System Part 1: Basic Usage</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../../../users_guide/index.html#case-control-system-part-2-configuration-porting-testing-and-use-cases">Case Control System Part 2: Configuration, Porting, Testing and Use Cases</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../../users_guide/index.html">Using the Case Control System</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../../users_guide/index.html#configuring-the-case-control-system">Configuring the Case Control System</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../build_cpl/index.html">Building a Coupled Model with CIME</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../misc_tools/index.html">Miscellaneous Tools</a></li>
 </ul>
diff --git a/versions/master/html/_modules/CIME/tests/test_unit_paramgen.html b/versions/master/html/_modules/CIME/tests/test_unit_paramgen.html
index ead9858eac7..0b671d0b65a 100644
--- a/versions/master/html/_modules/CIME/tests/test_unit_paramgen.html
+++ b/versions/master/html/_modules/CIME/tests/test_unit_paramgen.html
@@ -47,8 +47,8 @@
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
               <ul>
 <li class="toctree-l1"><a class="reference internal" href="../../../what_cime/index.html">What is CIME?</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../../../users_guide/index.html">Case Control System Part 1: Basic Usage</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../../../users_guide/index.html#case-control-system-part-2-configuration-porting-testing-and-use-cases">Case Control System Part 2: Configuration, Porting, Testing and Use Cases</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../../users_guide/index.html">Using the Case Control System</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../../users_guide/index.html#configuring-the-case-control-system">Configuring the Case Control System</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../build_cpl/index.html">Building a Coupled Model with CIME</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../misc_tools/index.html">Miscellaneous Tools</a></li>
 </ul>
diff --git a/versions/master/html/_modules/CIME/tests/test_unit_user_nl_utils.html b/versions/master/html/_modules/CIME/tests/test_unit_user_nl_utils.html
index 5fa6d0c46bb..e79b7818fdd 100644
--- a/versions/master/html/_modules/CIME/tests/test_unit_user_nl_utils.html
+++ b/versions/master/html/_modules/CIME/tests/test_unit_user_nl_utils.html
@@ -47,8 +47,8 @@
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
               <ul>
 <li class="toctree-l1"><a class="reference internal" href="../../../what_cime/index.html">What is CIME?</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../../../users_guide/index.html">Case Control System Part 1: Basic Usage</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../../../users_guide/index.html#case-control-system-part-2-configuration-porting-testing-and-use-cases">Case Control System Part 2: Configuration, Porting, Testing and Use Cases</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../../users_guide/index.html">Using the Case Control System</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../../users_guide/index.html#configuring-the-case-control-system">Configuring the Case Control System</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../build_cpl/index.html">Building a Coupled Model with CIME</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../misc_tools/index.html">Miscellaneous Tools</a></li>
 </ul>
diff --git a/versions/master/html/_modules/index.html b/versions/master/html/_modules/index.html
index 05d0c5c6f8a..20537a6b5da 100644
--- a/versions/master/html/_modules/index.html
+++ b/versions/master/html/_modules/index.html
@@ -47,8 +47,8 @@
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
               <ul>
 <li class="toctree-l1"><a class="reference internal" href="../what_cime/index.html">What is CIME?</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html">Case Control System Part 1: Basic Usage</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html#case-control-system-part-2-configuration-porting-testing-and-use-cases">Case Control System Part 2: Configuration, Porting, Testing and Use Cases</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html">Using the Case Control System</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html#configuring-the-case-control-system">Configuring the Case Control System</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../build_cpl/index.html">Building a Coupled Model with CIME</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../misc_tools/index.html">Miscellaneous Tools</a></li>
 </ul>
diff --git a/versions/master/html/_sources/users_guide/cime-dir.rst.txt b/versions/master/html/_sources/users_guide/cime-dir.rst.txt
index 15643de5f05..9bdb6540a63 100644
--- a/versions/master/html/_sources/users_guide/cime-dir.rst.txt
+++ b/versions/master/html/_sources/users_guide/cime-dir.rst.txt
@@ -25,25 +25,22 @@ CIME's content is split into several subdirectories. Users should start in the *
    ========================== ==================================================================
    Directory or Filename               Description
    ========================== ==================================================================
+   **CIME/**	              **The main CIME source**
+   CIME/ParamGen              Python tool for generating runtime params
+   CIME/Servers		      Scripts to interact with input data servers
+   CIME/SystemTests           Scripts for create_test tests.
+   CIME/Tools		      Auxillary tools, scripts and functions.
    CMakeLists.txt	      For building with CMake
+   CONTRIBUTING.md            Guide for contributing to CIME
    ChangeLog		      Developer-maintained record of changes to CIME
    ChangeLog_template	      Template for an entry in ChangeLog
    LICENSE.TXT		      The CIME license
-   README		      Brief intro to CIME
+   MANIFEST.in                
    README.md		      README in markdown language
-   README.unit_testing	      Instructions for running unit tests with CIME
-   **config/**		      **Shared and model-specific configuration files**
-   config/cesm/	              CESM-specific configuration options
-   config/e3sm/	              E3SM-specific configuration options
+   conftest.py
+   doc			      Documentation for CIME in rst format
+   docker		      Container for CIME testing
    **scripts/**		      **The CIME user interface**
-   scripts/lib/  	      Infrastructure source code for CIME scripts and functions
-   scripts/Tools/	      Auxiliary tools; scripts and functions
-   **src/**		      **Model source code provided by CIME**
-   src/components/	      CIME-provided components including data and stub models
-   src/drivers/  	      CIME-provided main driver for a climate model
-   src/externals/	      Software provided with CIME for building a climate model
-   src/share/    	      Model source code provided by CIME and used by multiple components
-   **tests/**		      **Tests**
    **tools/**		      **Standalone climate modeling tools**
    utils/		      Some Perl source code needed by some prognostic components
    ========================== ==================================================================
diff --git a/versions/master/html/_sources/users_guide/create-a-case.rst.txt b/versions/master/html/_sources/users_guide/create-a-case.rst.txt
index c9257da19a6..3a74a0c87c2 100644
--- a/versions/master/html/_sources/users_guide/create-a-case.rst.txt
+++ b/versions/master/html/_sources/users_guide/create-a-case.rst.txt
@@ -63,7 +63,7 @@ In the argument to ``--case``, the case name is taken from the string after the
 The output from create_newcase includes information such as.
 
 - The compset longname is ``2000_DATM%NYF_SLND_DICE%SSMI_DOCN%DOM_DROF%NYF_SGLC_SWAV``
-- The model resolution is ``a%0.9x1.25_l%0.9x1.25_oi%gx1v6_r%r05_m%gx1v6_g%null_w%null``
+- The grid set is ``a%0.9x1.25_l%0.9x1.25_oi%gx1v6_r%r05_m%gx1v6_g%null_w%null``
 
 `create_newcase  <../Tools_user/create_newcase.html>`_ installs files in ``$CASEROOT`` that will build and run the model and to optionally archive the case on the target platform.
 
@@ -74,23 +74,26 @@ Running `create_newcase  <../Tools_user/create_newcase.html>`_ creates the follo
 - `case.build  <../Tools_user/case.build.html>`_
      Script to build component and utility libraries and model executable.
 
+- `case.cmpgen_namelist <../Tools_user/case.submit.html>`_
+     Script to perform namelist baseline operations (compare, generate, or both)."
+
+-  case.qstatus
+    Script to query the queue on any queue system.
+
 - `case.setup  <../Tools_user/case.setup.html>`_
     Script used to set up the case (create the case.run script, Macros file and user_nl_xxx files).
 
-- `case.st_archive <../Tools_user/case.st_archive.html>`_
-     Script to perform short term archiving to disk for your case output. Note that this script is run automatically by the normal CIME workflow.
-
 - `case.submit <../Tools_user/case.submit.html>`_
      Script to submit the case to run using the machine's batch queueing system.
 
-- `case.cmpgen_namelist <../Tools_user/case.submit.html>`_
-     Script to perform namelist baseline operations (compare, generate, or both)."
+- `check_case <../Tools_user/check_case.html>`_
+     Script to verify case is set up correctly.
 
-- `xmlchange <../Tools_user/xmlchange.html>`_
-     Script to modify values in the xml files.
+- `check_input_data <../Tools_user/check_input_data.html>`_
+     Script for checking for various input data sets and moving them into place.
 
-- `xmlquery <../Tools_user/xmlquery.html>`_
-     Script to query values in the xml files.
+- `pelayout <../Tools_user/pelayout.html>`_
+     Script to query and modify the NTASKS, ROOTPE, and NTHRDS for each component model.
 
 - `preview_namelists <../Tools_user/preview_namelists.html>`_
      Script for users to see their component namelists in ``$CASEROOT/CaseDocs`` before running the model.
@@ -98,15 +101,12 @@ Running `create_newcase  <../Tools_user/create_newcase.html>`_ creates the follo
 - `preview_run <../Tools_user/preview_run.html>`_
      Script for users to see batch submit and mpirun command."
 
-- `check_input_data <../Tools_user/check_input_data.html>`_
-     Script for checking for various input data sets and moving them into place.
+- `xmlchange <../Tools_user/xmlchange.html>`_
+     Script to modify values in the xml files.
 
-- `check_case <../Tools_user/check_case.html>`_
-     Script to verify case is set up correctly.
+- `xmlquery <../Tools_user/xmlquery.html>`_
+     Script to query values in the xml files.
 
-- `pelayout <../Tools_user/pelayout.html>`_
-     Script to query and modify the NTASKS, ROOTPE, and NTHRDS for each component model.
-     This a convenience script that can be used in place of `xmlchange <../Tools_user/xmlchange.html>`_ and `xmlquery <../Tools_user/xmlquery.html>`_.
 
 **XML Files**
 
@@ -114,24 +114,30 @@ Running `create_newcase  <../Tools_user/create_newcase.html>`_ creates the follo
    Defines patterns of files to be sent to the short-term archive.
    You can edit this file at any time. You **CANNOT** use `xmlchange <../Tools_user/xmlchange.html>`_  to modify variables in this file."
 
-- env_mach_specific.xml
-   Sets a number of machine-specific environment variables for building and/or running.
-   You **CANNOT** use `xmlchange <../Tools_user/xmlchange.html>`_  to modify variables in this file.
+- env_batch.xml
+   Sets batch system settings such as wallclock time and queue name."
 
 - env_build.xml
    Sets model build settings. This includes component resolutions and component compile-time configuration options.
    You must run the case.build command after changing this file.
 
-- env_run.xml
-   Sets runtime settings such as length of run, frequency of restarts, output of coupler diagnostics, and short-term and long-term archiving.
-   This file can be edited at any time before a job starts.
+- env_case.xml
+   Parameters set by create_newcase
 
 - env_mach_pes.xml
    Sets component machine-specific processor layout (see changing pe layout ).
    The settings in this are critical to a well-load-balanced simulation (see :ref:`load balancing <optimizing-processor-layout>`).
 
-- env_batch.xml
-   Sets batch system settings such as wallclock time and queue name."
+- env_mach_specific.xml
+   Sets a number of machine-specific environment variables for building and/or running.
+   You **CANNOT** use `xmlchange <../Tools_user/xmlchange.html>`_  to modify variables in this file.
+
+- env_run.xml
+   Sets runtime settings such as length of run, frequency of restarts, output of coupler diagnostics, and short-term and long-term archiving.
+   This file can be edited at any time before a job starts.
+
+- env_workflow.xml
+   Sets paramateres for the runtime workflow.
 
 **User Source Mods Directory**
 
diff --git a/versions/master/html/_sources/users_guide/index.rst.txt b/versions/master/html/_sources/users_guide/index.rst.txt
index 9df9b084490..c16896cdb28 100644
--- a/versions/master/html/_sources/users_guide/index.rst.txt
+++ b/versions/master/html/_sources/users_guide/index.rst.txt
@@ -6,7 +6,7 @@
 .. _users-guide1:
 
 #######################################
-Case Control System Part 1: Basic Usage
+Using the Case Control System
 #######################################
 
 .. toctree::
@@ -22,12 +22,13 @@ Case Control System Part 1: Basic Usage
    cime-change-namelist.rst
    cime-config.rst
    cime-customize.rst
+   testing.rst
    troubleshooting.rst
 
 .. _users-guide2:
 
 #######################################################################################
-Case Control System Part 2: Configuration, Porting, Testing and Use Cases
+Configuring the Case Control System
 #######################################################################################
 
 .. toctree::
@@ -40,8 +41,6 @@ Case Control System Part 2: Configuration, Porting, Testing and Use Cases
    machine.rst
    pes-threads.rst
    porting-cime.rst
-   timers.rst
-   testing.rst
    unit_testing.rst
    multi-instance.rst
    workflows.rst
diff --git a/versions/master/html/_sources/users_guide/introduction-and-overview.rst.txt b/versions/master/html/_sources/users_guide/introduction-and-overview.rst.txt
index 2371ef0fddc..4dbf673f2bf 100644
--- a/versions/master/html/_sources/users_guide/introduction-and-overview.rst.txt
+++ b/versions/master/html/_sources/users_guide/introduction-and-overview.rst.txt
@@ -26,7 +26,7 @@ Other prerequisites:
 
 CIME's commands are Python scripts and require a correct version of
 the Python interpreter to be installed. The Python version must be
-greater than 2.7.  Determine which version you have
+greater than 2.11.  Determine which version you have
 like this:
 ::
 
@@ -37,7 +37,7 @@ Consult your local documentation if you need to update your python version.
 Key Terms and concepts
 ======================
 
-The following key terms and concepts are ingrained in CIME and used frequently in this documentation.
+The following key terms and concepts are ingrained in the CCS and used frequently in this documentation.
 See the :ref:`glossary` for a more complete list of terms.
 
 **components**
@@ -63,26 +63,61 @@ See the :ref:`glossary` for a more complete list of terms.
    *data*: For some climate problems, it is necessary to reduce feedbacks within the system by replacing an active model with a
    version that sends and receives the same variables to and from other models, but with the values read from files rather
    than computed from the equations. The values received are ignored. These active-model substitutes are called *data models*.
-   CIME provides data models for each of the possible components.  You could add your own data model implementation of a component
-   but as for active models only one at a time can be used.
 
-   *stub*: For some configurations, no data model is needed, so CIME provides *stub* versions that simply occupy the
-   required place in the driver and do not send or receive any data.
+   *stub*: For some configurations, no data model is needed and one instead uses a *stub* version that simply occupies the
+   required place in the driver and does not send or receive any data.  For example, if you are setting up an aqua-planet case
+   you would only need a stub for the land model.
 
-**component set** or **compset**:   The particular combination of active, data and stub versions of the 7 components is referred to
+**component set** or **compset**:
+
+   The particular combination of active, data and stub versions of the 7 components is referred to
    as a *component set* or  *compset*.  The Case Control System allows one to define
-   several possible compsets and configure and run them on supported platforms. See :ref:`Component Sets<compsets>` for more information.
+   several possible compsets and configure and run them on supported platforms.
+   Here is an example of a component set *longname* from E3SM for a fully coupled active case:
+::
+
+   1850SOI_EAM%CMIP6_ELM%CNPRDCTCBCTOP_MPASSI_MPASO_MOSART_SGLC_SWAV
+
+See :ref:`Component Sets<compsets>` for more information. "GLC" originally meant "glacier model" and is now an ice-sheet model but the GLC letters have stuck.
+
+**compset alias**:
+
+   Typing a compset longname like the above can be exhausting so the CCS allows defining a shorter *compset alias*
+   which is a short string that substitutes for the longname. In E3SM, the above longname can be reffered to as "WCYCL1850".
+
+.. note:: 
+
+     Long ago, CESM established a convention for the first letter in a compset alias based
+     on the combination of active, data and stub components.
+     If you see mention of "B-case" or "F-case", it comes from these conventions.
+     They pre-date the introduction of a wave model as an option.
+
+    ===  ========================================================================================
+    A    All data models
+    B    All models fully active with stub glc
+    C    Active ocean with data atm, river and sea ice. stub lnd, glc
+    D    Active sea ice with data atm, ocean (slab) and river. stub lnd, glc
+    E    Active atm, lnd, sea-ice, river, data ocean (slab), stub glc
+    F    Active atm, lnd, river, sea-ice (thermodynamics only), data ocean (fixed SST), stub glc
+    G    Active ocean and sea ice, data atmosphere and river, stub lnd and glc 
+    H    Active ocean and sea ice, data atmosphere, stub lnd, river and glc 
+    I    Active land and river model, data atmosphere, stub ocn, sea-ice, glc
+    IG   Active land, river and ice-sheet, data atmosphere, stub ocn, sea-ice
+    S    All stub models (for testing only)
+    X    All x-compsets (2D sine waves for each component except stub glc; for testing only)
+    ===  ========================================================================================
+..
+**grid set**:
 
-**grid** or **model grid**:
    Each active model must solve its equations on a numerical grid. CIME allows models within the system to have
-   different grids. The resulting set of all numerical grids is called the *model grid* or sometimes just the *grid*, where
-   *grid* is a unique name that denotes a set of numerical grids. Sometimes the *resolution* also refers to a specific set
-   of grids.
+   different grids. The resulting set of all numerical grids is called the *grid set* or usually just the *grid*. Like
+   the compset longnamme, the CCS allows one to define an alias to represent a grid set.  This alias is also referred to
+   as the *grid* or sometimes the *resolution*.
 
 **machine and compilers**:
    The *machine* is the computer you are using to run CIME and build and run the climate model. It could be a workstation
    or a national supercomputer. The exact name of  *machine* is typically the UNIX hostname but it could be any string.  A machine
-   may have one more more versions of Fortran, C and C++ *compilers* that are needed to compile the model's source code and CIME
+   may have one more more versions of Fortran, C and C++ *compilers* that are needed to compile the model's source code and CIME.
 
 **case**:
     To build and execute a CIME-enabled climate model, you have to make choices of compset, model grid,
@@ -95,10 +130,10 @@ See the :ref:`glossary` for a more complete list of terms.
    the model source code and version-controlled together, its possible to match supported out-of-the-box cases with specific
    versions of the model source code, promoting reproducibility and provenance.  An out-of-the-box case is also called a *base case*
 
-CIME and your environment
+CCS and your environment
 =========================
 
-Before using any CIME commands, set the ``CIME_MODEL`` environment variable. In bash, use **export** as shown and replace
+Before using any CCS commands, set the ``CIME_MODEL`` environment variable. In bash, use **export** as shown and replace
 **<model>** with the appropriate text. Current possibilities are "e3sm" or "cesm."
 ::
 
@@ -139,17 +174,14 @@ After you submit the case, you can follow the progress of your run by monitoring
 Repeat the command until you see the message ``case.run success``.
 
 
-Discovering available cases with **query_config**
+Discovering available pre-defined compsets with **query_config**
 =================================================
 
-Your CIME-driven model has many more possible cases besides the simple one in the above Quick Start.
+Your CIME-driven model likely has many compset and gridset aliases defined for cases that are widely used by the
+model developers.
 
 Use the utility `query_config <../Tools_user/query_config.html>`_  to see which out-of-the-box compsets, components, grids and machines are available for your model.
 
-If CIME is downloaded in standalone mode, only standalone CIME compsets can be queried.
-
-If CIME is part of a CIME-driven model, `query_config <../Tools_user/query_config.html>`_ will allow you to query all prognostic component compsets.
-
 To see lists of available compsets, components, grids and machines, look at the **help** text::
 
   > query_config --help
diff --git a/versions/master/html/_sources/users_guide/setting-up-a-case.rst.txt b/versions/master/html/_sources/users_guide/setting-up-a-case.rst.txt
index feff58aaf49..2ffc473fafd 100644
--- a/versions/master/html/_sources/users_guide/setting-up-a-case.rst.txt
+++ b/versions/master/html/_sources/users_guide/setting-up-a-case.rst.txt
@@ -16,22 +16,39 @@ After creating a case or changing aspects of a case, such as the pe-layout, call
 This creates the following additional files and directories in ``$CASEROOT``:
 
    =============================   ===============================================================================================================================
-   .case.run                       A (hidden) file with the commands that will be used to run the model (such as “mpirun”) and any batch directives needed.
-                                   The directive values are generated using the contents
-                                   of **env_mach_pes.xml**. Running `case.setup --clean <../Tools_user/case.setup.html>`_  will remove this file.
-				   This file should not be edited directly and instead controlled through XML variables in **env_batch.xml**. It should also
-				   *never* be run directly.
+   .case.run                       A (hidden) file with the commands that will be used to run the model (such as “mpirun”)
+
+                                   and any batch directives needed.  The directive values are generated using the contents
+
+                                   of **env_mach_pes.xml**. Running `case.setup --clean <../Tools_user/case.setup.html>`_
+
+				   will remove this file.  This file should not be edited directly and instead controlled
+
+				   through XML variables in **env_batch.xml**. It should also *never* be run directly.
+
+   CaseStatus                      File containing a list of operations done in the current case.
+
+   case.st_archive                 Script to perform short term archiving to disk for your case
+
+                                   output. Note that this script is run automatically by the normal CIME workflow.
+
+   Depends.*                       Lists of source code files that needs special build options.
+
+   Macros.cmake                    File containing machine-specific makefile directives for your target platform/compiler.
 
-   Macros.make                     File containing machine-specific makefile directives for your target platform/compiler.
                                    This file is created if it does not already exist.
 
                                    The user can modify the file to change certain aspects of the build, such as compiler flags.
+
                                    Running `case.setup --clean <../Tools_user/case.setup.html>`_  will not remove the file once it has been created.
-                                   However. if you remove or rename the Macros.make file, running `case.setup <../Tools_user/case.setup.html>`_ recreates it.
+                                   However. if you remove or rename the Macros.make file, running
+
+				   `case.setup <../Tools_user/case.setup.html>`_ recreates it.
 
    user_nl_xxx[_NNNN]              Files where all user modifications to component namelists are made.
 
                                    **xxx** is any one of the set of components targeted for the case.
+
                                    For example, for a full active CESM compset, **xxx** is cam, clm or rtm, and so on.
 
                                    NNNN goes from 0001 to the number of instances of that component.
@@ -45,17 +62,22 @@ This creates the following additional files and directories in ``$CASEROOT``:
                                    Calling `case.setup --clean <../Tools_user/case.setup.html>`_ will *not remove* any user_nl files.
 
                                    Changing the number of instances in the **env_mach_pes.xml** file will cause only
+
                                    new user_nl files to be added to ``$CASEROOT``.
 
    CaseDocs/                       Directory that contains all the component namelists for the run.
 
                                    This is for reference only and files in this directory SHOULD NOT BE EDITED since they will
+
                                    be overwritten at build time and runtime.
 
    .env_mach_specific.*            Files summarizing the **module load** commands and environment variables that are set when
+
                                    the scripts in ``$CASEROOT`` are called. These files are not used by the case but can be
+
                                    useful for debugging **module load** and environment settings.
 
    software_environment.txt        This file records some aspects of the computing system on which the case is built,
+
                                    such as the shell environment.
    =============================   ===============================================================================================================================
diff --git a/versions/master/html/_sources/what_cime/index.rst.txt b/versions/master/html/_sources/what_cime/index.rst.txt
index f87b3bd6704..e2e3eade94a 100644
--- a/versions/master/html/_sources/what_cime/index.rst.txt
+++ b/versions/master/html/_sources/what_cime/index.rst.txt
@@ -17,12 +17,15 @@
 Overview
 *********
 
-CIME, pronounced "SEAM", primarily consists of a Case Control System that supports the configuration, compilation, execution, system testing and unit testing of an Earth System Model. The two main components of the Case Control System are:
+CIME (Common Infrastructure for Modeling the Earth, pronounced "SEAM") primarily consists of a Case Control System that supports the configuration, compilation, execution, system testing and unit testing of an Earth System Model. The three main components of the Case Control System are:
 
-1. Scripts to enable simple generation of model executables and associated input files for different scientific cases, component resolutions and combinations of full, data and stub components with a handful of commands.
-2. Testing utilities to run defined system tests and report results for different configurations of the coupled system.
+1. XML files that  describe the available machines, models and model configurations.
+2. Python scripts that take user commands and parse the XML files to configure a set of models with their
+   build and runtime options for a specified machine and the provide additional commands to build executables and
+   submit jobs.
+3. Testing utilities to run defined system tests and report results for different configurations of the coupled system.
 
-CIME also contains additional stand-alone tools, including:
+CIME also contains additional stand-alone tools useful for Earth system modeling including:
 
 1. Parallel regridding weight generation program
 2. Scripts to automate off-line load-balancing.
diff --git a/versions/master/html/build_cpl/adding-components.html b/versions/master/html/build_cpl/adding-components.html
index 625271e8d6a..5309e73c4fd 100644
--- a/versions/master/html/build_cpl/adding-components.html
+++ b/versions/master/html/build_cpl/adding-components.html
@@ -50,8 +50,8 @@
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
               <ul class="current">
 <li class="toctree-l1"><a class="reference internal" href="../what_cime/index.html">What is CIME?</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html">Case Control System Part 1: Basic Usage</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html#case-control-system-part-2-configuration-porting-testing-and-use-cases">Case Control System Part 2: Configuration, Porting, Testing and Use Cases</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html">Using the Case Control System</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html#configuring-the-case-control-system">Configuring the Case Control System</a></li>
 <li class="toctree-l1 current"><a class="reference internal" href="index.html">Building a Coupled Model with CIME</a><ul class="current">
 <li class="toctree-l2"><a class="reference internal" href="introduction.html">1. Introduction</a></li>
 <li class="toctree-l2 current"><a class="current reference internal" href="#">2. Adding components</a></li>
diff --git a/versions/master/html/build_cpl/index.html b/versions/master/html/build_cpl/index.html
index 78797f7f0f3..f9076689c66 100644
--- a/versions/master/html/build_cpl/index.html
+++ b/versions/master/html/build_cpl/index.html
@@ -23,7 +23,7 @@
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="1. Introduction" href="introduction.html" />
-    <link rel="prev" title="12. Directory content" href="../users_guide/cime-dir.html" /> 
+    <link rel="prev" title="10. Directory content" href="../users_guide/cime-dir.html" /> 
 </head>
 
 <body class="wy-body-for-nav"> 
@@ -50,8 +50,8 @@
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
               <ul class="current">
 <li class="toctree-l1"><a class="reference internal" href="../what_cime/index.html">What is CIME?</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html">Case Control System Part 1: Basic Usage</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html#case-control-system-part-2-configuration-porting-testing-and-use-cases">Case Control System Part 2: Configuration, Porting, Testing and Use Cases</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html">Using the Case Control System</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html#configuring-the-case-control-system">Configuring the Case Control System</a></li>
 <li class="toctree-l1 current"><a class="current reference internal" href="#">Building a Coupled Model with CIME</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="introduction.html">1. Introduction</a></li>
 <li class="toctree-l2"><a class="reference internal" href="adding-components.html">2. Adding components</a></li>
@@ -114,7 +114,7 @@ <h2>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Li
            </div>
           </div>
           <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
-        <a href="../users_guide/cime-dir.html" class="btn btn-neutral float-left" title="12. Directory content" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
+        <a href="../users_guide/cime-dir.html" class="btn btn-neutral float-left" title="10. Directory content" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
         <a href="introduction.html" class="btn btn-neutral float-right" title="1. Introduction" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
     </div>
 
diff --git a/versions/master/html/build_cpl/introduction.html b/versions/master/html/build_cpl/introduction.html
index 26d9ee5d28e..4c35c656986 100644
--- a/versions/master/html/build_cpl/introduction.html
+++ b/versions/master/html/build_cpl/introduction.html
@@ -50,8 +50,8 @@
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
               <ul class="current">
 <li class="toctree-l1"><a class="reference internal" href="../what_cime/index.html">What is CIME?</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html">Case Control System Part 1: Basic Usage</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html#case-control-system-part-2-configuration-porting-testing-and-use-cases">Case Control System Part 2: Configuration, Porting, Testing and Use Cases</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html">Using the Case Control System</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html#configuring-the-case-control-system">Configuring the Case Control System</a></li>
 <li class="toctree-l1 current"><a class="reference internal" href="index.html">Building a Coupled Model with CIME</a><ul class="current">
 <li class="toctree-l2 current"><a class="current reference internal" href="#">1. Introduction</a></li>
 <li class="toctree-l2"><a class="reference internal" href="adding-components.html">2. Adding components</a></li>
diff --git a/versions/master/html/change.html b/versions/master/html/change.html
index b54b4233abe..0705c4b7662 100644
--- a/versions/master/html/change.html
+++ b/versions/master/html/change.html
@@ -48,8 +48,8 @@
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
               <ul>
 <li class="toctree-l1"><a class="reference internal" href="what_cime/index.html">What is CIME?</a></li>
-<li class="toctree-l1"><a class="reference internal" href="users_guide/index.html">Case Control System Part 1: Basic Usage</a></li>
-<li class="toctree-l1"><a class="reference internal" href="users_guide/index.html#case-control-system-part-2-configuration-porting-testing-and-use-cases">Case Control System Part 2: Configuration, Porting, Testing and Use Cases</a></li>
+<li class="toctree-l1"><a class="reference internal" href="users_guide/index.html">Using the Case Control System</a></li>
+<li class="toctree-l1"><a class="reference internal" href="users_guide/index.html#configuring-the-case-control-system">Configuring the Case Control System</a></li>
 <li class="toctree-l1"><a class="reference internal" href="build_cpl/index.html">Building a Coupled Model with CIME</a></li>
 <li class="toctree-l1"><a class="reference internal" href="misc_tools/index.html">Miscellaneous Tools</a></li>
 </ul>
diff --git a/versions/master/html/genindex.html b/versions/master/html/genindex.html
index bf7bc379146..49c35d86444 100644
--- a/versions/master/html/genindex.html
+++ b/versions/master/html/genindex.html
@@ -47,8 +47,8 @@
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
               <ul>
 <li class="toctree-l1"><a class="reference internal" href="what_cime/index.html">What is CIME?</a></li>
-<li class="toctree-l1"><a class="reference internal" href="users_guide/index.html">Case Control System Part 1: Basic Usage</a></li>
-<li class="toctree-l1"><a class="reference internal" href="users_guide/index.html#case-control-system-part-2-configuration-porting-testing-and-use-cases">Case Control System Part 2: Configuration, Porting, Testing and Use Cases</a></li>
+<li class="toctree-l1"><a class="reference internal" href="users_guide/index.html">Using the Case Control System</a></li>
+<li class="toctree-l1"><a class="reference internal" href="users_guide/index.html#configuring-the-case-control-system">Configuring the Case Control System</a></li>
 <li class="toctree-l1"><a class="reference internal" href="build_cpl/index.html">Building a Coupled Model with CIME</a></li>
 <li class="toctree-l1"><a class="reference internal" href="misc_tools/index.html">Miscellaneous Tools</a></li>
 </ul>
diff --git a/versions/master/html/glossary/index.html b/versions/master/html/glossary/index.html
index 03bfee037d3..8a6ad58c0e1 100644
--- a/versions/master/html/glossary/index.html
+++ b/versions/master/html/glossary/index.html
@@ -50,8 +50,8 @@
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
               <ul>
 <li class="toctree-l1"><a class="reference internal" href="../what_cime/index.html">What is CIME?</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html">Case Control System Part 1: Basic Usage</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html#case-control-system-part-2-configuration-porting-testing-and-use-cases">Case Control System Part 2: Configuration, Porting, Testing and Use Cases</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html">Using the Case Control System</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html#configuring-the-case-control-system">Configuring the Case Control System</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../build_cpl/index.html">Building a Coupled Model with CIME</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../misc_tools/index.html">Miscellaneous Tools</a></li>
 </ul>
diff --git a/versions/master/html/index.html b/versions/master/html/index.html
index 9a3a245a8f5..62c27385a8f 100644
--- a/versions/master/html/index.html
+++ b/versions/master/html/index.html
@@ -49,8 +49,8 @@
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
               <ul>
 <li class="toctree-l1"><a class="reference internal" href="what_cime/index.html">What is CIME?</a></li>
-<li class="toctree-l1"><a class="reference internal" href="users_guide/index.html">Case Control System Part 1: Basic Usage</a></li>
-<li class="toctree-l1"><a class="reference internal" href="users_guide/index.html#case-control-system-part-2-configuration-porting-testing-and-use-cases">Case Control System Part 2: Configuration, Porting, Testing and Use Cases</a></li>
+<li class="toctree-l1"><a class="reference internal" href="users_guide/index.html">Using the Case Control System</a></li>
+<li class="toctree-l1"><a class="reference internal" href="users_guide/index.html#configuring-the-case-control-system">Configuring the Case Control System</a></li>
 <li class="toctree-l1"><a class="reference internal" href="build_cpl/index.html">Building a Coupled Model with CIME</a></li>
 <li class="toctree-l1"><a class="reference internal" href="misc_tools/index.html">Miscellaneous Tools</a></li>
 </ul>
@@ -101,7 +101,7 @@ <h2>Table of contents<a class="headerlink" href="#table-of-contents" title="Link
 <li class="toctree-l2"><a class="reference internal" href="what_cime/index.html#development">Development</a></li>
 </ul>
 </li>
-<li class="toctree-l1"><a class="reference internal" href="users_guide/index.html">Case Control System Part 1: Basic Usage</a><ul>
+<li class="toctree-l1"><a class="reference internal" href="users_guide/index.html">Using the Case Control System</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="users_guide/introduction-and-overview.html">1. Introduction</a></li>
 <li class="toctree-l2"><a class="reference internal" href="users_guide/create-a-case.html">2. Creating a Case</a></li>
 <li class="toctree-l2"><a class="reference internal" href="users_guide/setting-up-a-case.html">3. Setting up a Case</a></li>
@@ -111,22 +111,21 @@ <h2>Table of contents<a class="headerlink" href="#table-of-contents" title="Link
 <li class="toctree-l2"><a class="reference internal" href="users_guide/cime-change-namelist.html">7. Customizing your input variables</a></li>
 <li class="toctree-l2"><a class="reference internal" href="users_guide/cime-config.html">8. CIME user config directory</a></li>
 <li class="toctree-l2"><a class="reference internal" href="users_guide/cime-customize.html">9. CIME config and hooks</a></li>
-<li class="toctree-l2"><a class="reference internal" href="users_guide/troubleshooting.html">10. Troubleshooting</a></li>
+<li class="toctree-l2"><a class="reference internal" href="users_guide/testing.html">10. Testing</a></li>
+<li class="toctree-l2"><a class="reference internal" href="users_guide/troubleshooting.html">11. Troubleshooting</a></li>
 </ul>
 </li>
-<li class="toctree-l1"><a class="reference internal" href="users_guide/index.html#case-control-system-part-2-configuration-porting-testing-and-use-cases">Case Control System Part 2: Configuration, Porting, Testing and Use Cases</a><ul>
+<li class="toctree-l1"><a class="reference internal" href="users_guide/index.html#configuring-the-case-control-system">Configuring the Case Control System</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="users_guide/cime-internals.html">1. Main Configuration File</a></li>
 <li class="toctree-l2"><a class="reference internal" href="users_guide/compsets.html">2. Component sets</a></li>
 <li class="toctree-l2"><a class="reference internal" href="users_guide/grids.html">3. Model grids</a></li>
 <li class="toctree-l2"><a class="reference internal" href="users_guide/machine.html">4. Defining the machine</a></li>
 <li class="toctree-l2"><a class="reference internal" href="users_guide/pes-threads.html">5. Controlling processors and threads</a></li>
 <li class="toctree-l2"><a class="reference internal" href="users_guide/porting-cime.html">6. Porting and validating CIME on a new platform</a></li>
-<li class="toctree-l2"><a class="reference internal" href="users_guide/timers.html">7. Timers and timing</a></li>
-<li class="toctree-l2"><a class="reference internal" href="users_guide/testing.html">8. Testing</a></li>
-<li class="toctree-l2"><a class="reference internal" href="users_guide/unit_testing.html">9. Fortran Unit Testing</a></li>
-<li class="toctree-l2"><a class="reference internal" href="users_guide/multi-instance.html">10. Multi-instance component functionality</a></li>
-<li class="toctree-l2"><a class="reference internal" href="users_guide/workflows.html">11. Workflows</a></li>
-<li class="toctree-l2"><a class="reference internal" href="users_guide/cime-dir.html">12. Directory content</a></li>
+<li class="toctree-l2"><a class="reference internal" href="users_guide/unit_testing.html">7. Fortran Unit Testing</a></li>
+<li class="toctree-l2"><a class="reference internal" href="users_guide/multi-instance.html">8. Multi-instance component functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="users_guide/workflows.html">9. Workflows</a></li>
+<li class="toctree-l2"><a class="reference internal" href="users_guide/cime-dir.html">10. Directory content</a></li>
 <li class="toctree-l2"><a class="reference internal" href="users_guide/index.html#indices-and-tables">Indices and tables</a></li>
 </ul>
 </li>
diff --git a/versions/master/html/misc_tools/ect.html b/versions/master/html/misc_tools/ect.html
index 321e85730a7..502b1491e7f 100644
--- a/versions/master/html/misc_tools/ect.html
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 <li class="toctree-l1"><a class="reference internal" href="../what_cime/index.html">What is CIME?</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html">Case Control System Part 1: Basic Usage</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html#case-control-system-part-2-configuration-porting-testing-and-use-cases">Case Control System Part 2: Configuration, Porting, Testing and Use Cases</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html">Using the Case Control System</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html#configuring-the-case-control-system">Configuring the Case Control System</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../build_cpl/index.html">Building a Coupled Model with CIME</a></li>
 <li class="toctree-l1 current"><a class="reference internal" href="index.html">Miscellaneous Tools</a><ul class="current">
 <li class="toctree-l2 current"><a class="current reference internal" href="#">1. CESM-ECT (CESM Ensemble Consistency Test):</a><ul>
diff --git a/versions/master/html/misc_tools/index.html b/versions/master/html/misc_tools/index.html
index f961ac723fd..0f5c7853efc 100644
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-<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html">Case Control System Part 1: Basic Usage</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html#case-control-system-part-2-configuration-porting-testing-and-use-cases">Case Control System Part 2: Configuration, Porting, Testing and Use Cases</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html">Using the Case Control System</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html#configuring-the-case-control-system">Configuring the Case Control System</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../build_cpl/index.html">Building a Coupled Model with CIME</a></li>
 <li class="toctree-l1 current"><a class="current reference internal" href="#">Miscellaneous Tools</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="ect.html">1. CESM-ECT (CESM Ensemble Consistency Test):</a></li>
diff --git a/versions/master/html/misc_tools/load-balancing-tool.html b/versions/master/html/misc_tools/load-balancing-tool.html
index a260a2a1c8e..62f07e54769 100644
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@@ -50,8 +50,8 @@
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-<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html">Case Control System Part 1: Basic Usage</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html#case-control-system-part-2-configuration-porting-testing-and-use-cases">Case Control System Part 2: Configuration, Porting, Testing and Use Cases</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html">Using the Case Control System</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html#configuring-the-case-control-system">Configuring the Case Control System</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../build_cpl/index.html">Building a Coupled Model with CIME</a></li>
 <li class="toctree-l1 current"><a class="reference internal" href="index.html">Miscellaneous Tools</a><ul class="current">
 <li class="toctree-l2"><a class="reference internal" href="ect.html">1. CESM-ECT (CESM Ensemble Consistency Test):</a></li>
diff --git a/versions/master/html/objects.inv b/versions/master/html/objects.inv
index ce63a085a2a..6efaa684018 100644
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index c9901d9f13b..ec9f8a16504 100644
--- a/versions/master/html/py-modindex.html
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@@ -50,8 +50,8 @@
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
               <ul>
 <li class="toctree-l1"><a class="reference internal" href="what_cime/index.html">What is CIME?</a></li>
-<li class="toctree-l1"><a class="reference internal" href="users_guide/index.html">Case Control System Part 1: Basic Usage</a></li>
-<li class="toctree-l1"><a class="reference internal" href="users_guide/index.html#case-control-system-part-2-configuration-porting-testing-and-use-cases">Case Control System Part 2: Configuration, Porting, Testing and Use Cases</a></li>
+<li class="toctree-l1"><a class="reference internal" href="users_guide/index.html">Using the Case Control System</a></li>
+<li class="toctree-l1"><a class="reference internal" href="users_guide/index.html#configuring-the-case-control-system">Configuring the Case Control System</a></li>
 <li class="toctree-l1"><a class="reference internal" href="build_cpl/index.html">Building a Coupled Model with CIME</a></li>
 <li class="toctree-l1"><a class="reference internal" href="misc_tools/index.html">Miscellaneous Tools</a></li>
 </ul>
diff --git a/versions/master/html/search.html b/versions/master/html/search.html
index 48054c41b9f..a08eea558ad 100644
--- a/versions/master/html/search.html
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@@ -50,8 +50,8 @@
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
               <ul>
 <li class="toctree-l1"><a class="reference internal" href="what_cime/index.html">What is CIME?</a></li>
-<li class="toctree-l1"><a class="reference internal" href="users_guide/index.html">Case Control System Part 1: Basic Usage</a></li>
-<li class="toctree-l1"><a class="reference internal" href="users_guide/index.html#case-control-system-part-2-configuration-porting-testing-and-use-cases">Case Control System Part 2: Configuration, Porting, Testing and Use Cases</a></li>
+<li class="toctree-l1"><a class="reference internal" href="users_guide/index.html">Using the Case Control System</a></li>
+<li class="toctree-l1"><a class="reference internal" href="users_guide/index.html#configuring-the-case-control-system">Configuring the Case Control System</a></li>
 <li class="toctree-l1"><a class="reference internal" href="build_cpl/index.html">Building a Coupled Model with CIME</a></li>
 <li class="toctree-l1"><a class="reference internal" href="misc_tools/index.html">Miscellaneous Tools</a></li>
 </ul>
diff --git a/versions/master/html/searchindex.js b/versions/master/html/searchindex.js
index 9592eef3728..944001cf426 100644
--- a/versions/master/html/searchindex.js
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@@ -1 +1 @@
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module": [[14, "cime-tests-test-sys-grid-generation-module"]], "CIME.tests.test_sys_jenkins_generic_job module": [[14, "cime-tests-test-sys-jenkins-generic-job-module"]], "CIME.tests.test_sys_manage_and_query module": [[14, "cime-tests-test-sys-manage-and-query-module"]], "CIME.tests.test_sys_query_config module": [[14, "cime-tests-test-sys-query-config-module"]], "CIME.tests.test_sys_run_restart module": [[14, "cime-tests-test-sys-run-restart-module"]], "CIME.tests.test_sys_save_timings module": [[14, "cime-tests-test-sys-save-timings-module"]], "CIME.tests.test_sys_single_submit module": [[14, "cime-tests-test-sys-single-submit-module"]], "CIME.tests.test_sys_test_scheduler module": [[14, "cime-tests-test-sys-test-scheduler-module"]], "CIME.tests.test_sys_unittest module": [[14, "cime-tests-test-sys-unittest-module"]], "CIME.tests.test_sys_user_concurrent_mods module": [[14, "cime-tests-test-sys-user-concurrent-mods-module"]], "CIME.tests.test_sys_wait_for_tests module": [[14, "cime-tests-test-sys-wait-for-tests-module"]], "CIME.tests.test_unit_aprun module": [[14, "cime-tests-test-unit-aprun-module"]], "CIME.tests.test_unit_baselines_performance module": [[14, "cime-tests-test-unit-baselines-performance-module"]], "CIME.tests.test_unit_bless_test_results module": [[14, "cime-tests-test-unit-bless-test-results-module"]], "CIME.tests.test_unit_case module": [[14, "cime-tests-test-unit-case-module"]], "CIME.tests.test_unit_case_fake module": [[14, "module-CIME.tests.test_unit_case_fake"]], "CIME.tests.test_unit_case_run module": [[14, "cime-tests-test-unit-case-run-module"]], "CIME.tests.test_unit_case_setup module": [[14, "cime-tests-test-unit-case-setup-module"]], "CIME.tests.test_unit_compare_test_results module": [[14, "cime-tests-test-unit-compare-test-results-module"]], "CIME.tests.test_unit_compare_two module": [[14, "cime-tests-test-unit-compare-two-module"]], "CIME.tests.test_unit_config module": [[14, "cime-tests-test-unit-config-module"]], "CIME.tests.test_unit_cs_status module": [[14, "cime-tests-test-unit-cs-status-module"]], "CIME.tests.test_unit_custom_assertions_test_status module": [[14, "cime-tests-test-unit-custom-assertions-test-status-module"]], "CIME.tests.test_unit_doctest module": [[14, "cime-tests-test-unit-doctest-module"]], "CIME.tests.test_unit_expected_fails_file module": [[14, "cime-tests-test-unit-expected-fails-file-module"]], "CIME.tests.test_unit_grids module": [[14, "cime-tests-test-unit-grids-module"]], "CIME.tests.test_unit_hist_utils module": [[14, "cime-tests-test-unit-hist-utils-module"]], "CIME.tests.test_unit_nmlgen module": [[14, "cime-tests-test-unit-nmlgen-module"]], "CIME.tests.test_unit_paramgen module": [[14, "module-CIME.tests.test_unit_paramgen"]], "CIME.tests.test_unit_system_tests module": [[14, "cime-tests-test-unit-system-tests-module"]], "CIME.tests.test_unit_test_status module": [[14, "cime-tests-test-unit-test-status-module"]], "CIME.tests.test_unit_two_link_to_case2_output module": [[14, "cime-tests-test-unit-two-link-to-case2-output-module"]], "CIME.tests.test_unit_user_mod_support module": [[14, "cime-tests-test-unit-user-mod-support-module"]], "CIME.tests.test_unit_user_nl_utils module": [[14, "module-CIME.tests.test_unit_user_nl_utils"]], "CIME.tests.test_unit_utils module": [[14, "cime-tests-test-unit-utils-module"]], "CIME.tests.test_unit_xml_archive_base module": [[14, "cime-tests-test-unit-xml-archive-base-module"]], "CIME.tests.test_unit_xml_env_batch module": [[14, "cime-tests-test-unit-xml-env-batch-module"]], "CIME.tests.test_unit_xml_env_mach_specific module": [[14, "cime-tests-test-unit-xml-env-mach-specific-module"]], "CIME.tests.test_unit_xml_machines module": [[14, "cime-tests-test-unit-xml-machines-module"]], "CIME.tests.test_unit_xml_namelist_definition module": [[14, "cime-tests-test-unit-xml-namelist-definition-module"]], "CIME.tests.test_unit_xml_tests module": [[14, "cime-tests-test-unit-xml-tests-module"]], "CIME.tests.utils module": [[14, "cime-tests-utils-module"]], "CIME.user_mod_support module": [[0, "cime-user-mod-support-module"]], "CIME.utils module": [[0, "cime-utils-module"]], "CIME.wait_for_tests module": [[0, "cime-wait-for-tests-module"]], "CIMEROOT/config/cesm": [[103, "cimeroot-config-cesm"]], "CIMEROOT/config/config_headers.xml": [[104, "cimeroot-config-config-headers-xml"]], "CIMEROOT/config/config_tests.xml": [[104, "cimeroot-config-config-tests-xml"]], "CIMEROOT/config/e3sm": [[107, "cimeroot-config-e3sm"]], "CIMEROOT/src/components/data_comps/datm/cime_config": [[102, "cimeroot-src-components-data-comps-datm-cime-config"]], "CIMEROOT/src/components/data_comps/desp/cime_config": [[108, "cimeroot-src-components-data-comps-desp-cime-config"]], "CIMEROOT/src/components/data_comps/dice/cime_config": [[114, "cimeroot-src-components-data-comps-dice-cime-config"]], "CIMEROOT/src/components/data_comps/dlnd/cime_config": [[110, "cimeroot-src-components-data-comps-dlnd-cime-config"]], "CIMEROOT/src/components/data_comps/docn/cime_config": [[112, "cimeroot-src-components-data-comps-docn-cime-config"]], "CIMEROOT/src/components/data_comps/drof/cime_config": [[113, "cimeroot-src-components-data-comps-drof-cime-config"]], "CIMEROOT/src/components/data_comps/dwav/cime_config": [[115, "cimeroot-src-components-data-comps-dwav-cime-config"]], "CIMEROOT/src/components/stub_comps/satm/cime_config": [[102, "cimeroot-src-components-stub-comps-satm-cime-config"]], "CIMEROOT/src/components/stub_comps/sesp/cime_config": [[108, "cimeroot-src-components-stub-comps-sesp-cime-config"]], "CIMEROOT/src/components/stub_comps/sglc/cime_config": [[111, "cimeroot-src-components-stub-comps-sglc-cime-config"]], "CIMEROOT/src/components/stub_comps/sice/cime_config": [[114, "cimeroot-src-components-stub-comps-sice-cime-config"]], "CIMEROOT/src/components/stub_comps/slnd/cime_config": [[110, "cimeroot-src-components-stub-comps-slnd-cime-config"]], "CIMEROOT/src/components/stub_comps/socn/cime_config": [[112, "cimeroot-src-components-stub-comps-socn-cime-config"]], "CIMEROOT/src/components/stub_comps/srof/cime_config": [[113, "cimeroot-src-components-stub-comps-srof-cime-config"]], "CIMEROOT/src/components/stub_comps/swav/cime_config": [[115, "cimeroot-src-components-stub-comps-swav-cime-config"]], "CIMEROOT/src/components/xcpl_comps/xatm/cime_config": [[102, "cimeroot-src-components-xcpl-comps-xatm-cime-config"]], "CIMEROOT/src/components/xcpl_comps/xglc/cime_config": [[111, "cimeroot-src-components-xcpl-comps-xglc-cime-config"]], "CIMEROOT/src/components/xcpl_comps/xice/cime_config": [[114, "cimeroot-src-components-xcpl-comps-xice-cime-config"]], "CIMEROOT/src/components/xcpl_comps/xlnd/cime_config": [[110, "cimeroot-src-components-xcpl-comps-xlnd-cime-config"]], "CIMEROOT/src/components/xcpl_comps/xocn/cime_config": [[112, "cimeroot-src-components-xcpl-comps-xocn-cime-config"]], "CIMEROOT/src/components/xcpl_comps/xrof/cime_config": [[113, "cimeroot-src-components-xcpl-comps-xrof-cime-config"]], "CIMEROOT/src/components/xcpl_comps/xwav/cime_config": [[115, "cimeroot-src-components-xcpl-comps-xwav-cime-config"]], "CIMEROOT/src/drivers/mct/cime_config": [[106, "cimeroot-src-drivers-mct-cime-config"]], "CIMEROOT/src/drivers/mct/cime_config/namelist_definition_*.xml": [[106, "cimeroot-src-drivers-mct-cime-config-namelist-definition-xml"]], "CISM": [[79, "cism"]], "CLM": [[79, "clm"]], "Calling case.build": [[78, "calling-case-build"]], "Calling case.setup": [[95, "calling-case-setup"]], "Calling case.submit": [[94, "calling-case-submit"]], "Calling create_newcase": [[86, "calling-create-newcase"]], "Case Control System Part 1: Basic Usage": [[88, "case-control-system-part-1-basic-usage"]], "Case Control System Part 2: Configuration, Porting, Testing and Use Cases": [[88, "case-control-system-part-2-configuration-porting-testing-and-use-cases"]], "Case Resource Allocation": [[92, "case-resource-allocation"]], "Cloning a Case": [[84, "cloning-a-case"]], "Common XML Files": [[104, "common-xml-files"]], "Comparing a baseline": [[96, "comparing-a-baseline"]], "Compiler settings": [[90, "compiler-settings"]], "Component sets": [[85, "component-sets"]], "Component specific settings in a compset": [[85, "component-specific-settings-in-a-compset"]], "Compset longname": [[85, "compset-longname"]], "Controlling output data": [[94, "controlling-output-data"]], "Controlling processors and threads": [[92, "controlling-processors-and-threads"]], "Controlling timers": [[97, "controlling-timers"]], "Coupling": [[73, "coupling"]], "Creating New Compsets": [[85, "creating-new-compsets"]], "Creating a Case": [[86, "creating-a-case"]], "Creating a baseline": [[96, "creating-a-baseline"]], "Creating or obtaining a summary file:": [[75, "creating-or-obtaining-a-summary-file"]], "Creating test runs:": [[75, "creating-test-runs"]], "Customizing CESM active component-specific namelist settings": [[79, "customizing-cesm-active-component-specific-namelist-settings"]], "Customizing data model input variable and stream files": [[79, "customizing-data-model-input-variable-and-stream-files"]], "Customizing driver input variables": [[79, "customizing-driver-input-variables"]], "Customizing your input variables": [[79, "customizing-your-input-variables"]], "Data Assimilation and other External Processing": [[94, "data-assimilation-and-other-external-processing"]], "Data Assimilation scripts": [[94, "data-assimilation-scripts"]], "Data Atmosphere (DATM)": [[79, "data-atmosphere-datm"]], "Data Land (DLND)": [[79, "data-land-dlnd"]], "Data Ocean (DOCN)": [[79, "data-ocean-docn"]], "Data River (DROF)": [[79, "data-river-drof"]], "Data Sea-ice (DICE)": [[79, "data-sea-ice-dice"]], "Data, Stub and Driver Component XML Files": [[105, "data-stub-and-driver-component-xml-files"]], "Defining a test class in order to define setUp and tearDown methods": [[99, "defining-a-test-class-in-order-to-define-setup-and-teardown-methods"]], "Defining the machine": [[90, "defining-the-machine"]], "Development": [[73, "development"], [101, "development"]], "Directory content": [[82, "directory-content"]], "Discovering available cases with query_config": [[89, "discovering-available-cases-with-query-config"]], "Distributed Input Data Repositories": [[94, "distributed-input-data-repositories"]], "Documentation of the unit test build system": [[99, "documentation-of-the-unit-test-build-system"]], "Driver XML Files": [[106, "driver-xml-files"]], "E3SM Coupled Model XML Files": [[107, "e3sm-coupled-model-xml-files"]], "Entries in env_mach_pes.xml": [[92, "id3"]], "Extending the Load Balancing Tool": [[77, "extending-the-load-balancing-tool"]], "Files and Directories": [[73, "files-and-directories"]], "Finding more documentation and examples": [[99, "finding-more-documentation-and-examples"]], "Fortran Unit Testing": [[99, "fortran-unit-testing"]], "General": [[73, "general"]], "General guidelines for writing unit tests": [[99, "general-guidelines-for-writing-unit-tests"]], "Glossary": [[73, "glossary"]], "Grid longname": [[87, "grid-longname"]], "How does CIME load customizations?": [[81, "how-does-cime-load-customizations"]], "How to add unit testing support on your machine": [[99, "how-to-add-unit-testing-support-on-your-machine"]], "How to write a new unit test": [[99, "how-to-write-a-new-unit-test"]], "Indices and tables": [[70, "indices-and-tables"], [76, "indices-and-tables"], [88, "indices-and-tables"]], "Input data": [[78, "input-data"], [94, "input-data"]], "Introduction": [[71, "introduction"], [89, "introduction"], [99, "introduction"]], "Key Terms and concepts": [[89, "key-terms-and-concepts"]], "Locked files in your case directory": [[86, "locked-files-in-your-case-directory"]], "Long-term archiving": [[94, "long-term-archiving"]], "MOSART": [[79, "mosart"]], "Main Configuration File": [[83, "main-configuration-file"]], "Managing baselines": [[96, "managing-baselines"]], "Miscellaneous": [[73, "miscellaneous"]], "Miscellaneous Tools": [[76, "miscellaneous-tools"]], "Model grids": [[87, "model-grids"]], "Model timing data": [[97, "model-timing-data"]], "Module contents": [[0, "module-CIME"], [1, "module-CIME.BuildTools"], [2, "module-contents"], [3, "module-CIME.SystemTests"], [4, "module-CIME.SystemTests.test_utils"], [5, "module-CIME.Tools"], [6, "module-CIME.XML"], [7, "module-CIME.baselines"], [8, "module-CIME.build_scripts"], [9, "module-contents"], [10, "module-CIME.data"], [11, "module-CIME.data.config"], [12, "module-CIME.data.templates"], [13, "module-CIME.scripts"], [14, "module-CIME.tests"], [16, "module-Tools"]], "Monitoring case job statuses": [[94, "monitoring-case-job-statuses"]], "More about the algorithm": [[77, "more-about-the-algorithm"]], "More detailed examples in CIME": [[99, "more-detailed-examples-in-cime"]], "More details on writing pFUnit-based unit tests": [[99, "more-details-on-writing-pfunit-based-unit-tests"]], "More on test teardown": [[99, "more-on-test-teardown"]], "Multi-instance component functionality": [[91, "multi-instance-component-functionality"]], "No archiving": [[94, "no-archiving"]], "Optimizing processor layout": [[92, "optimizing-processor-layout"]], "Optimizing the layout using load_balacing_solve.py": [[77, "optimizing-the-layout-using-load-balacing-solve-py"]], "Other pFUnit documentation sources": [[99, "other-pfunit-documentation-sources"]], "Overview": [[101, "overview"]], "Overview of unit test support in CIME": [[99, "overview-of-unit-test-support-in-cime"]], "POP2": [[79, "pop2"]], "Performance baselines": [[96, "performance-baselines"]], "Performance tuning of a CESM port": [[93, "performance-tuning-of-a-cesm-port"]], "Porting and validating CIME on a new platform": [[93, "porting-and-validating-cime-on-a-new-platform"]], "Pre and Post run scripts": [[94, "pre-and-post-run-scripts"]], "Prerequisites": [[89, "prerequisites"]], "Python Module Indices and Search": [[74, "python-module-indices-and-search"]], "Query_testlists": [[96, "query-testlists"]], "Quick start": [[89, "quick-start"]], "Rebuilding the model": [[78, "rebuilding-the-model"]], "Required libraries/packages": [[93, "required-libraries-packages"]], "Restarting a run": [[94, "restarting-a-run"]], "Result of running case.submit": [[94, "result-of-running-case-submit"]], "Results of calling create_newcase": [[86, "results-of-calling-create-newcase"]], "Run-type initialization": [[94, "run-type-initialization"]], "Running CIME\u2019s Fortran unit tests": [[99, "running-cime-s-fortran-unit-tests"]], "Running a Case": [[94, "running-a-case"]], "Running simulations using load_balancing_submit.py": [[77, "running-simulations-using-load-balancing-submit-py"]], "Setting the PE layout": [[92, "setting-the-pe-layout"]], "Setting up a Case": [[95, "setting-up-a-case"]], "Setting up a branch or hybrid run": [[79, "setting-up-a-branch-or-hybrid-run"]], "Setting up a multi-year run": [[79, "setting-up-a-multi-year-run"]], "Short-term archiving": [[94, "short-term-archiving"]], "Starting from a reference case (REFCASE)": [[94, "starting-from-a-reference-case-refcase"]], "Starting, Stopping and Restarting a Run": [[94, "starting-stopping-and-restarting-a-run"]], "Steps for porting": [[93, "steps-for-porting"]], "Submodules": [[0, "submodules"], [1, "submodules"], [2, "submodules"], [3, "submodules"], [4, "submodules"], [5, "submodules"], [6, "submodules"], [7, "submodules"], [9, "submodules"], [13, "submodules"], [14, "submodules"], [16, "submodules"]], "Subpackages": [[0, "subpackages"], [3, "subpackages"], [10, "subpackages"]], "Table of contents": [[74, "table-of-contents"]], "Testing": [[73, "testing"], [77, "testing"], [96, "testing"]], "Testname syntax": [[96, "testname-syntax"]], "Timers and timing": [[97, "timers-and-timing"]], "Todo": [[85, "id2"], [99, "id1"]], "Tools": [[17, "tools"]], "Tools package": [[16, "tools-package"]], "Tools.generate_cylc_workflow module": [[16, "tools-generate-cylc-workflow-module"]], "Tools.standard_script_setup module": [[16, "tools-standard-script-setup-module"]], "Tools.testreporter module": [[16, "tools-testreporter-module"]], "Troubleshooting": [[98, "troubleshooting"]], "Troubleshooting a job that fails": [[94, "troubleshooting-a-job-that-fails"]], "Troubleshooting case creation": [[98, "troubleshooting-case-creation"]], "Troubleshooting job submission": [[98, "troubleshooting-job-submission"]], "Troubleshooting problems in cime scripts": [[98, "troubleshooting-problems-in-cime-scripts"]], "Troubleshooting runtime problems": [[98, "troubleshooting-runtime-problems"]], "User Tools": [[49, "user-tools"]], "Using create_test (E3SM)": [[96, "using-create-test-e3sm"]], "Validating a CESM port with prognostic components": [[93, "validating-a-cesm-port-with-prognostic-components"]], "What is CIME?": [[101, "what-is-cime"]], "What is a unit test?": [[99, "what-is-a-unit-test"]], "Workflows": [[100, "workflows"]], "XML Files": [[109, "xml-files"]], "advanced-py-prof": [[18, "advanced-py-prof"]], "archive_metadata": [[19, "archive-metadata"]], "bld_diff": [[20, "bld-diff"]], "bless_test_results": [[21, "bless-test-results"]], "case.build": [[22, "case-build"]], "case.cmpgen_namelists": [[23, "case-cmpgen-namelists"]], "case.qstatus": [[24, "case-qstatus"]], "case.setup": [[25, "case-setup"]], "case.submit": [[26, "case-submit"]], "case_diff": [[27, "case-diff"]], "check_case": [[28, "check-case"]], "check_input_data": [[29, "check-input-data"]], "check_lockedfiles": [[30, "check-lockedfiles"]], "cime_bisect": [[31, "cime-bisect"]], "code_checker": [[32, "code-checker"]], "compare_namelists": [[33, "compare-namelists"]], "compare_test_results": [[34, "compare-test-results"]], "component_compare_baseline": [[35, "component-compare-baseline"]], "component_compare_copy": [[36, "component-compare-copy"]], 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"user_mod_support": 0, "user_nl_util": 4, "util": [0, 14], "valid": 93, "variabl": 79, "wait_for_test": [0, 65], "wallclock": 97, "wave": 115, "wget": 2, "what": [99, 101], "workflow": [6, 100], "write": 99, "xatm": 102, "xcpl_comp": [102, 110, 111, 112, 113, 114, 115], "xglc": 111, "xice": 114, "xlnd": 110, "xml": [6, 90, 92, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115], "xmlchang": 66, "xmlqueri": 67, "xmltestentri": 68, "xocn": 112, "xrof": 113, "xwav": 115, "year": 79, "your": [79, 86, 89, 97, 99]}})
\ No newline at end of file
+Search.setIndex({"alltitles": {"Adding a \u2013user-mods-dir argument to create_newcase": [[86, "adding-a-user-mods-dir-argument-to-create-newcase"]], "Adding components": [[69, "adding-components"]], "Adding grids": [[87, "adding-grids"]], "Adding tests": [[96, "adding-tests"]], "Adding to the appropriate cmake file": [[99, "adding-to-the-appropriate-cmake-file"]], "Advice on setting your wallclock time": [[97, "advice-on-setting-your-wallclock-time"]], "An MPI example": [[93, "an-mpi-example"]], "Appendices": [[74, "appendices"]], "Archiving model output data": [[94, "archiving-model-output-data"]], "Assertion methods": [[99, "assertion-methods"]], "Backing up to a previous restart": [[94, "backing-up-to-a-previous-restart"]], "Baselines": [[96, "baselines"]], "Batch system definition": [[90, "batch-system-definition"]], "Building a Case": [[78, "building-a-case"]], "Building a Coupled Model with CIME": [[70, "building-a-coupled-model-with-cime"]], "Building pFUnit": [[99, "building-pfunit"]], "CAM": [[79, "cam"]], "CCS and your environment": [[89, "ccs-and-your-environment"]], "CESM Coupled Model XML Files": [[103, "cesm-coupled-model-xml-files"]], "CESM Linux and Mac Support": [[93, "cesm-linux-and-mac-support"]], "CESM-ECT (CESM Ensemble Consistency Test):": [[75, "cesm-ect-cesm-ensemble-consistency-test"]], "CICE": [[79, "cice"]], "CIME": [[15, "cime"]], "CIME Atmosphere Data and Stub XML Files": [[102, "cime-atmosphere-data-and-stub-xml-files"]], "CIME Developer\u2019s guide": [[96, "cime-developer-s-guide"]], "CIME ESP Data and Stub XML Files": [[108, "cime-esp-data-and-stub-xml-files"]], "CIME Land Data and Stub XML Files": [[110, "cime-land-data-and-stub-xml-files"]], "CIME Land Ice Data and Stub XML Files": [[111, "cime-land-ice-data-and-stub-xml-files"]], "CIME Load Balancing Tool": [[77, "cime-load-balancing-tool"]], "CIME Ocean Data and Stub XML Files": [[112, "cime-ocean-data-and-stub-xml-files"]], "CIME River Runoff Data and Stub XML Files": [[113, "cime-river-runoff-data-and-stub-xml-files"]], "CIME Sea Ice Data and Stub XML Files": [[114, "cime-sea-ice-data-and-stub-xml-files"]], "CIME Wave Data and Stub XML Files": [[115, "cime-wave-data-and-stub-xml-files"]], "CIME config": [[81, "cime-config"]], "CIME config and hooks": [[81, "cime-config-and-hooks"]], "CIME directory content": [[82, "id2"]], "CIME directory in a climate model": [[82, "id1"]], "CIME documentation": [[74, "cime-documentation"]], "CIME hooks": [[81, "cime-hooks"]], "CIME package": [[0, "cime-package"]], "CIME user config directory": [[80, "cime-user-config-directory"]], "CIME.BuildTools package": [[1, "cime-buildtools-package"]], "CIME.BuildTools.configure module": [[1, "cime-buildtools-configure-module"]], "CIME.Servers package": [[2, "cime-servers-package"]], "CIME.Servers.ftp module": [[2, "cime-servers-ftp-module"]], "CIME.Servers.generic_server module": [[2, "cime-servers-generic-server-module"]], "CIME.Servers.gftp module": [[2, "cime-servers-gftp-module"]], "CIME.Servers.svn module": [[2, "cime-servers-svn-module"]], "CIME.Servers.wget module": [[2, "cime-servers-wget-module"]], "CIME.SystemTests package": [[3, "cime-systemtests-package"]], "CIME.SystemTests.dae module": [[3, "cime-systemtests-dae-module"]], "CIME.SystemTests.eri module": [[3, "cime-systemtests-eri-module"]], "CIME.SystemTests.erio module": [[3, "cime-systemtests-erio-module"]], "CIME.SystemTests.erp module": [[3, "cime-systemtests-erp-module"]], "CIME.SystemTests.err module": [[3, "cime-systemtests-err-module"]], "CIME.SystemTests.erri module": [[3, "cime-systemtests-erri-module"]], "CIME.SystemTests.ers module": [[3, "cime-systemtests-ers-module"]], "CIME.SystemTests.ers2 module": [[3, "cime-systemtests-ers2-module"]], "CIME.SystemTests.ert module": [[3, "cime-systemtests-ert-module"]], "CIME.SystemTests.funit module": [[3, "cime-systemtests-funit-module"]], "CIME.SystemTests.homme module": [[3, "cime-systemtests-homme-module"]], "CIME.SystemTests.hommebaseclass module": [[3, "cime-systemtests-hommebaseclass-module"]], "CIME.SystemTests.hommebfb module": [[3, "cime-systemtests-hommebfb-module"]], "CIME.SystemTests.icp module": [[3, "cime-systemtests-icp-module"]], "CIME.SystemTests.irt module": [[3, "cime-systemtests-irt-module"]], "CIME.SystemTests.ldsta module": [[3, "cime-systemtests-ldsta-module"]], "CIME.SystemTests.mcc module": [[3, "cime-systemtests-mcc-module"]], "CIME.SystemTests.mvk module": [[3, "cime-systemtests-mvk-module"]], "CIME.SystemTests.nck module": [[3, "cime-systemtests-nck-module"]], "CIME.SystemTests.ncr module": [[3, "cime-systemtests-ncr-module"]], "CIME.SystemTests.nodefail module": [[3, "cime-systemtests-nodefail-module"]], "CIME.SystemTests.pea module": [[3, "cime-systemtests-pea-module"]], "CIME.SystemTests.pem module": [[3, "cime-systemtests-pem-module"]], "CIME.SystemTests.pet module": [[3, "cime-systemtests-pet-module"]], "CIME.SystemTests.pfs module": [[3, "cime-systemtests-pfs-module"]], "CIME.SystemTests.pgn module": [[3, "cime-systemtests-pgn-module"]], "CIME.SystemTests.pre module": [[3, "cime-systemtests-pre-module"]], "CIME.SystemTests.rep module": [[3, "cime-systemtests-rep-module"]], "CIME.SystemTests.restart_tests module": [[3, "cime-systemtests-restart-tests-module"]], "CIME.SystemTests.reuseinitfiles module": [[3, "cime-systemtests-reuseinitfiles-module"]], "CIME.SystemTests.seq module": [[3, "cime-systemtests-seq-module"]], "CIME.SystemTests.sms module": [[3, "cime-systemtests-sms-module"]], "CIME.SystemTests.system_tests_common module": [[3, "cime-systemtests-system-tests-common-module"]], "CIME.SystemTests.system_tests_compare_n module": [[3, "cime-systemtests-system-tests-compare-n-module"]], "CIME.SystemTests.system_tests_compare_two module": [[3, "cime-systemtests-system-tests-compare-two-module"]], "CIME.SystemTests.test_utils package": [[4, "cime-systemtests-test-utils-package"]], "CIME.SystemTests.test_utils.user_nl_utils module": [[4, "module-CIME.SystemTests.test_utils.user_nl_utils"]], "CIME.SystemTests.tsc module": [[3, "cime-systemtests-tsc-module"]], "CIME.Tools package": [[5, "cime-tools-package"]], "CIME.Tools.generate_cylc_workflow module": [[5, "cime-tools-generate-cylc-workflow-module"]], "CIME.Tools.standard_script_setup module": [[5, "cime-tools-standard-script-setup-module"]], "CIME.Tools.testreporter module": [[5, "cime-tools-testreporter-module"]], "CIME.XML package": [[6, "cime-xml-package"]], "CIME.XML.archive module": [[6, "cime-xml-archive-module"]], "CIME.XML.archive_base module": [[6, "cime-xml-archive-base-module"]], "CIME.XML.batch module": [[6, "cime-xml-batch-module"]], "CIME.XML.component module": [[6, "cime-xml-component-module"]], "CIME.XML.compsets module": [[6, "cime-xml-compsets-module"]], "CIME.XML.entry_id module": [[6, "cime-xml-entry-id-module"]], "CIME.XML.env_archive module": [[6, "cime-xml-env-archive-module"]], "CIME.XML.env_base module": [[6, "cime-xml-env-base-module"]], "CIME.XML.env_batch module": [[6, "cime-xml-env-batch-module"]], "CIME.XML.env_build module": [[6, "cime-xml-env-build-module"]], "CIME.XML.env_case module": [[6, "cime-xml-env-case-module"]], "CIME.XML.env_mach_pes module": [[6, "cime-xml-env-mach-pes-module"]], "CIME.XML.env_mach_specific module": [[6, "cime-xml-env-mach-specific-module"]], "CIME.XML.env_run module": [[6, "cime-xml-env-run-module"]], "CIME.XML.env_test module": [[6, "cime-xml-env-test-module"]], "CIME.XML.env_workflow module": [[6, "cime-xml-env-workflow-module"]], "CIME.XML.expected_fails_file module": [[6, "cime-xml-expected-fails-file-module"]], "CIME.XML.files module": [[6, "cime-xml-files-module"]], "CIME.XML.generic_xml module": [[6, "cime-xml-generic-xml-module"]], "CIME.XML.grids module": [[6, "cime-xml-grids-module"]], "CIME.XML.headers module": [[6, "cime-xml-headers-module"]], "CIME.XML.inputdata module": [[6, "cime-xml-inputdata-module"]], "CIME.XML.machines module": [[6, "cime-xml-machines-module"]], "CIME.XML.namelist_definition module": [[6, "cime-xml-namelist-definition-module"]], "CIME.XML.pes module": [[6, "cime-xml-pes-module"]], "CIME.XML.pio module": [[6, "cime-xml-pio-module"]], "CIME.XML.standard_module_setup module": [[6, "cime-xml-standard-module-setup-module"]], "CIME.XML.stream module": [[6, "cime-xml-stream-module"]], "CIME.XML.test_reporter module": [[6, "cime-xml-test-reporter-module"]], "CIME.XML.testlist module": [[6, "cime-xml-testlist-module"]], "CIME.XML.tests module": [[6, "cime-xml-tests-module"]], "CIME.XML.testspec module": [[6, "cime-xml-testspec-module"]], "CIME.XML.workflow module": [[6, "cime-xml-workflow-module"]], "CIME.aprun module": [[0, "cime-aprun-module"]], "CIME.baselines package": [[7, "cime-baselines-package"]], "CIME.baselines.performance module": [[7, "cime-baselines-performance-module"]], "CIME.bless_test_results module": [[0, "cime-bless-test-results-module"]], "CIME.build module": [[0, "cime-build-module"]], "CIME.build_scripts package": [[8, "cime-build-scripts-package"]], "CIME.buildlib module": [[0, "cime-buildlib-module"]], "CIME.buildnml module": [[0, "cime-buildnml-module"]], "CIME.case package": [[9, "cime-case-package"]], "CIME.case.case module": [[9, "cime-case-case-module"]], "CIME.case.case_clone module": [[9, "cime-case-case-clone-module"]], "CIME.case.case_cmpgen_namelists module": [[9, "cime-case-case-cmpgen-namelists-module"]], "CIME.case.case_run module": [[9, "cime-case-case-run-module"]], "CIME.case.case_setup module": [[9, "cime-case-case-setup-module"]], "CIME.case.case_st_archive module": [[9, "cime-case-case-st-archive-module"]], "CIME.case.case_submit module": [[9, "cime-case-case-submit-module"]], "CIME.case.case_test module": [[9, "cime-case-case-test-module"]], "CIME.case.check_input_data module": [[9, "cime-case-check-input-data-module"]], "CIME.case.check_lockedfiles module": [[9, "cime-case-check-lockedfiles-module"]], "CIME.case.preview_namelists module": [[9, "cime-case-preview-namelists-module"]], "CIME.code_checker module": [[0, "cime-code-checker-module"]], "CIME.compare_namelists module": [[0, "cime-compare-namelists-module"]], "CIME.compare_test_results module": [[0, "cime-compare-test-results-module"]], "CIME.config module": [[0, "cime-config-module"]], "CIME.cs_status module": [[0, "cime-cs-status-module"]], "CIME.cs_status_creator module": [[0, "cime-cs-status-creator-module"]], "CIME.data package": [[10, "cime-data-package"]], "CIME.data.config package": [[11, "cime-data-config-package"]], "CIME.data.templates package": [[12, "cime-data-templates-package"]], "CIME.date module": [[0, "cime-date-module"]], "CIME.expected_fails module": [[0, "cime-expected-fails-module"]], "CIME.get_tests module": [[0, "cime-get-tests-module"]], "CIME.get_timing module": [[0, "cime-get-timing-module"]], "CIME.hist_utils module": [[0, "cime-hist-utils-module"]], "CIME.jenkins_generic_job module": [[0, "cime-jenkins-generic-job-module"]], "CIME.locked_files module": [[0, "cime-locked-files-module"]], "CIME.namelist module": [[0, "cime-namelist-module"]], "CIME.nmlgen module": [[0, "cime-nmlgen-module"]], "CIME.provenance module": [[0, "cime-provenance-module"]], "CIME.scripts package": [[13, "cime-scripts-package"]], "CIME.scripts.create_clone module": [[13, "cime-scripts-create-clone-module"]], "CIME.scripts.create_newcase module": [[13, "cime-scripts-create-newcase-module"]], "CIME.scripts.create_test module": [[13, "cime-scripts-create-test-module"]], "CIME.scripts.query_config module": [[13, "cime-scripts-query-config-module"]], "CIME.scripts.query_testlists module": [[13, "cime-scripts-query-testlists-module"]], "CIME.simple_compare module": [[0, "cime-simple-compare-module"]], "CIME.test_scheduler module": [[0, "cime-test-scheduler-module"]], "CIME.test_status module": [[0, "cime-test-status-module"]], "CIME.test_utils module": [[0, "cime-test-utils-module"]], "CIME.tests package": [[14, "cime-tests-package"]], "CIME.tests.base module": [[14, "cime-tests-base-module"]], "CIME.tests.case_fake module": [[14, "module-CIME.tests.case_fake"]], "CIME.tests.custom_assertions_test_status module": [[14, "cime-tests-custom-assertions-test-status-module"]], "CIME.tests.scripts_regression_tests module": [[14, "cime-tests-scripts-regression-tests-module"]], "CIME.tests.test_sys_bless_tests_results module": [[14, "cime-tests-test-sys-bless-tests-results-module"]], "CIME.tests.test_sys_build_system module": [[14, "cime-tests-test-sys-build-system-module"]], "CIME.tests.test_sys_cime_case module": [[14, "cime-tests-test-sys-cime-case-module"]], "CIME.tests.test_sys_cime_performance module": [[14, "cime-tests-test-sys-cime-performance-module"]], "CIME.tests.test_sys_create_newcase module": [[14, "cime-tests-test-sys-create-newcase-module"]], "CIME.tests.test_sys_full_system module": [[14, "cime-tests-test-sys-full-system-module"]], "CIME.tests.test_sys_grid_generation module": [[14, "cime-tests-test-sys-grid-generation-module"]], "CIME.tests.test_sys_jenkins_generic_job module": [[14, "cime-tests-test-sys-jenkins-generic-job-module"]], "CIME.tests.test_sys_manage_and_query module": [[14, "cime-tests-test-sys-manage-and-query-module"]], "CIME.tests.test_sys_query_config module": [[14, "cime-tests-test-sys-query-config-module"]], "CIME.tests.test_sys_run_restart module": [[14, "cime-tests-test-sys-run-restart-module"]], "CIME.tests.test_sys_save_timings module": [[14, "cime-tests-test-sys-save-timings-module"]], "CIME.tests.test_sys_single_submit module": [[14, "cime-tests-test-sys-single-submit-module"]], "CIME.tests.test_sys_test_scheduler module": [[14, "cime-tests-test-sys-test-scheduler-module"]], "CIME.tests.test_sys_unittest module": [[14, "cime-tests-test-sys-unittest-module"]], "CIME.tests.test_sys_user_concurrent_mods module": [[14, "cime-tests-test-sys-user-concurrent-mods-module"]], "CIME.tests.test_sys_wait_for_tests module": [[14, "cime-tests-test-sys-wait-for-tests-module"]], "CIME.tests.test_unit_aprun module": [[14, "cime-tests-test-unit-aprun-module"]], "CIME.tests.test_unit_baselines_performance module": [[14, "cime-tests-test-unit-baselines-performance-module"]], "CIME.tests.test_unit_bless_test_results module": [[14, "cime-tests-test-unit-bless-test-results-module"]], "CIME.tests.test_unit_case module": [[14, "cime-tests-test-unit-case-module"]], "CIME.tests.test_unit_case_fake module": [[14, "module-CIME.tests.test_unit_case_fake"]], "CIME.tests.test_unit_case_run module": [[14, "cime-tests-test-unit-case-run-module"]], "CIME.tests.test_unit_case_setup module": [[14, "cime-tests-test-unit-case-setup-module"]], "CIME.tests.test_unit_compare_test_results module": [[14, "cime-tests-test-unit-compare-test-results-module"]], "CIME.tests.test_unit_compare_two module": [[14, "cime-tests-test-unit-compare-two-module"]], "CIME.tests.test_unit_config module": [[14, "cime-tests-test-unit-config-module"]], "CIME.tests.test_unit_cs_status module": [[14, "cime-tests-test-unit-cs-status-module"]], "CIME.tests.test_unit_custom_assertions_test_status module": [[14, "cime-tests-test-unit-custom-assertions-test-status-module"]], "CIME.tests.test_unit_doctest module": [[14, "cime-tests-test-unit-doctest-module"]], "CIME.tests.test_unit_expected_fails_file module": [[14, "cime-tests-test-unit-expected-fails-file-module"]], "CIME.tests.test_unit_grids module": [[14, "cime-tests-test-unit-grids-module"]], "CIME.tests.test_unit_hist_utils module": [[14, "cime-tests-test-unit-hist-utils-module"]], "CIME.tests.test_unit_nmlgen module": [[14, "cime-tests-test-unit-nmlgen-module"]], "CIME.tests.test_unit_paramgen module": [[14, "module-CIME.tests.test_unit_paramgen"]], "CIME.tests.test_unit_system_tests module": [[14, "cime-tests-test-unit-system-tests-module"]], "CIME.tests.test_unit_test_status module": [[14, "cime-tests-test-unit-test-status-module"]], "CIME.tests.test_unit_two_link_to_case2_output 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"Component sets": [[85, "component-sets"]], "Component specific settings in a compset": [[85, "component-specific-settings-in-a-compset"]], "Compset longname": [[85, "compset-longname"]], "Configuring the Case Control System": [[88, "configuring-the-case-control-system"]], "Controlling output data": [[94, "controlling-output-data"]], "Controlling processors and threads": [[92, "controlling-processors-and-threads"]], "Controlling timers": [[97, "controlling-timers"]], "Coupling": [[73, "coupling"]], "Creating New Compsets": [[85, "creating-new-compsets"]], "Creating a Case": [[86, "creating-a-case"]], "Creating a baseline": [[96, "creating-a-baseline"]], "Creating or obtaining a summary file:": [[75, "creating-or-obtaining-a-summary-file"]], "Creating test runs:": [[75, "creating-test-runs"]], "Customizing CESM active component-specific namelist settings": [[79, "customizing-cesm-active-component-specific-namelist-settings"]], "Customizing data model input variable and stream files": 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diff --git a/versions/master/html/users_guide/building-a-case.html b/versions/master/html/users_guide/building-a-case.html
index d397a1a67ee..496ba58268e 100644
--- a/versions/master/html/users_guide/building-a-case.html
+++ b/versions/master/html/users_guide/building-a-case.html
@@ -50,7 +50,7 @@
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               <ul class="current">
 <li class="toctree-l1"><a class="reference internal" href="../what_cime/index.html">What is CIME?</a></li>
-<li class="toctree-l1 current"><a class="reference internal" href="index.html">Case Control System Part 1: Basic Usage</a><ul class="current">
+<li class="toctree-l1 current"><a class="reference internal" href="index.html">Using the Case Control System</a><ul class="current">
 <li class="toctree-l2"><a class="reference internal" href="introduction-and-overview.html">1. Introduction</a></li>
 <li class="toctree-l2"><a class="reference internal" href="create-a-case.html">2. Creating a Case</a></li>
 <li class="toctree-l2"><a class="reference internal" href="setting-up-a-case.html">3. Setting up a Case</a></li>
@@ -65,10 +65,11 @@
 <li class="toctree-l2"><a class="reference internal" href="cime-change-namelist.html">7. Customizing your input variables</a></li>
 <li class="toctree-l2"><a class="reference internal" href="cime-config.html">8. CIME user config directory</a></li>
 <li class="toctree-l2"><a class="reference internal" href="cime-customize.html">9. CIME config and hooks</a></li>
-<li class="toctree-l2"><a class="reference internal" href="troubleshooting.html">10. Troubleshooting</a></li>
+<li class="toctree-l2"><a class="reference internal" href="testing.html">10. Testing</a></li>
+<li class="toctree-l2"><a class="reference internal" href="troubleshooting.html">11. Troubleshooting</a></li>
 </ul>
 </li>
-<li class="toctree-l1"><a class="reference internal" href="index.html#case-control-system-part-2-configuration-porting-testing-and-use-cases">Case Control System Part 2: Configuration, Porting, Testing and Use Cases</a></li>
+<li class="toctree-l1"><a class="reference internal" href="index.html#configuring-the-case-control-system">Configuring the Case Control System</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../build_cpl/index.html">Building a Coupled Model with CIME</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../misc_tools/index.html">Miscellaneous Tools</a></li>
 </ul>
@@ -94,7 +95,7 @@
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
       <li><a href="../index.html" class="icon icon-home" aria-label="Home"></a></li>
-          <li class="breadcrumb-item"><a href="index.html">Case Control System Part 1: Basic Usage</a></li>
+          <li class="breadcrumb-item"><a href="index.html">Using the Case Control System</a></li>
       <li class="breadcrumb-item active"><span class="section-number">4. </span>Building a Case</li>
       <li class="wy-breadcrumbs-aside">
             <a href="../_sources/users_guide/building-a-case.rst.txt" rel="nofollow"> View page source</a>
diff --git a/versions/master/html/users_guide/cime-change-namelist.html b/versions/master/html/users_guide/cime-change-namelist.html
index 8340b0f8a2b..8a004dba9bf 100644
--- a/versions/master/html/users_guide/cime-change-namelist.html
+++ b/versions/master/html/users_guide/cime-change-namelist.html
@@ -50,7 +50,7 @@
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
               <ul class="current">
 <li class="toctree-l1"><a class="reference internal" href="../what_cime/index.html">What is CIME?</a></li>
-<li class="toctree-l1 current"><a class="reference internal" href="index.html">Case Control System Part 1: Basic Usage</a><ul class="current">
+<li class="toctree-l1 current"><a class="reference internal" href="index.html">Using the Case Control System</a><ul class="current">
 <li class="toctree-l2"><a class="reference internal" href="introduction-and-overview.html">1. Introduction</a></li>
 <li class="toctree-l2"><a class="reference internal" href="create-a-case.html">2. Creating a Case</a></li>
 <li class="toctree-l2"><a class="reference internal" href="setting-up-a-case.html">3. Setting up a Case</a></li>
@@ -84,10 +84,11 @@
 </li>
 <li class="toctree-l2"><a class="reference internal" href="cime-config.html">8. CIME user config directory</a></li>
 <li class="toctree-l2"><a class="reference internal" href="cime-customize.html">9. CIME config and hooks</a></li>
-<li class="toctree-l2"><a class="reference internal" href="troubleshooting.html">10. Troubleshooting</a></li>
+<li class="toctree-l2"><a class="reference internal" href="testing.html">10. Testing</a></li>
+<li class="toctree-l2"><a class="reference internal" href="troubleshooting.html">11. Troubleshooting</a></li>
 </ul>
 </li>
-<li class="toctree-l1"><a class="reference internal" href="index.html#case-control-system-part-2-configuration-porting-testing-and-use-cases">Case Control System Part 2: Configuration, Porting, Testing and Use Cases</a></li>
+<li class="toctree-l1"><a class="reference internal" href="index.html#configuring-the-case-control-system">Configuring the Case Control System</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../build_cpl/index.html">Building a Coupled Model with CIME</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../misc_tools/index.html">Miscellaneous Tools</a></li>
 </ul>
@@ -113,7 +114,7 @@
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
       <li><a href="../index.html" class="icon icon-home" aria-label="Home"></a></li>
-          <li class="breadcrumb-item"><a href="index.html">Case Control System Part 1: Basic Usage</a></li>
+          <li class="breadcrumb-item"><a href="index.html">Using the Case Control System</a></li>
       <li class="breadcrumb-item active"><span class="section-number">7. </span>Customizing your input variables</li>
       <li class="wy-breadcrumbs-aside">
             <a href="../_sources/users_guide/cime-change-namelist.rst.txt" rel="nofollow"> View page source</a>
diff --git a/versions/master/html/users_guide/cime-config.html b/versions/master/html/users_guide/cime-config.html
index 006bb39ecd7..ab5294704d4 100644
--- a/versions/master/html/users_guide/cime-config.html
+++ b/versions/master/html/users_guide/cime-config.html
@@ -50,7 +50,7 @@
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
               <ul class="current">
 <li class="toctree-l1"><a class="reference internal" href="../what_cime/index.html">What is CIME?</a></li>
-<li class="toctree-l1 current"><a class="reference internal" href="index.html">Case Control System Part 1: Basic Usage</a><ul class="current">
+<li class="toctree-l1 current"><a class="reference internal" href="index.html">Using the Case Control System</a><ul class="current">
 <li class="toctree-l2"><a class="reference internal" href="introduction-and-overview.html">1. Introduction</a></li>
 <li class="toctree-l2"><a class="reference internal" href="create-a-case.html">2. Creating a Case</a></li>
 <li class="toctree-l2"><a class="reference internal" href="setting-up-a-case.html">3. Setting up a Case</a></li>
@@ -60,10 +60,11 @@
 <li class="toctree-l2"><a class="reference internal" href="cime-change-namelist.html">7. Customizing your input variables</a></li>
 <li class="toctree-l2 current"><a class="current reference internal" href="#">8. CIME user config directory</a></li>
 <li class="toctree-l2"><a class="reference internal" href="cime-customize.html">9. CIME config and hooks</a></li>
-<li class="toctree-l2"><a class="reference internal" href="troubleshooting.html">10. Troubleshooting</a></li>
+<li class="toctree-l2"><a class="reference internal" href="testing.html">10. Testing</a></li>
+<li class="toctree-l2"><a class="reference internal" href="troubleshooting.html">11. Troubleshooting</a></li>
 </ul>
 </li>
-<li class="toctree-l1"><a class="reference internal" href="index.html#case-control-system-part-2-configuration-porting-testing-and-use-cases">Case Control System Part 2: Configuration, Porting, Testing and Use Cases</a></li>
+<li class="toctree-l1"><a class="reference internal" href="index.html#configuring-the-case-control-system">Configuring the Case Control System</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../build_cpl/index.html">Building a Coupled Model with CIME</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../misc_tools/index.html">Miscellaneous Tools</a></li>
 </ul>
@@ -89,7 +90,7 @@
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
       <li><a href="../index.html" class="icon icon-home" aria-label="Home"></a></li>
-          <li class="breadcrumb-item"><a href="index.html">Case Control System Part 1: Basic Usage</a></li>
+          <li class="breadcrumb-item"><a href="index.html">Using the Case Control System</a></li>
       <li class="breadcrumb-item active"><span class="section-number">8. </span>CIME user config directory</li>
       <li class="wy-breadcrumbs-aside">
             <a href="../_sources/users_guide/cime-config.rst.txt" rel="nofollow"> View page source</a>
diff --git a/versions/master/html/users_guide/cime-customize.html b/versions/master/html/users_guide/cime-customize.html
index 31ac5fea88a..75e24ce421a 100644
--- a/versions/master/html/users_guide/cime-customize.html
+++ b/versions/master/html/users_guide/cime-customize.html
@@ -22,7 +22,7 @@
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
-    <link rel="next" title="10. Troubleshooting" href="troubleshooting.html" />
+    <link rel="next" title="10. Testing" href="testing.html" />
     <link rel="prev" title="8. CIME user config directory" href="cime-config.html" /> 
 </head>
 
@@ -50,7 +50,7 @@
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               <ul class="current">
 <li class="toctree-l1"><a class="reference internal" href="../what_cime/index.html">What is CIME?</a></li>
-<li class="toctree-l1 current"><a class="reference internal" href="index.html">Case Control System Part 1: Basic Usage</a><ul class="current">
+<li class="toctree-l1 current"><a class="reference internal" href="index.html">Using the Case Control System</a><ul class="current">
 <li class="toctree-l2"><a class="reference internal" href="introduction-and-overview.html">1. Introduction</a></li>
 <li class="toctree-l2"><a class="reference internal" href="create-a-case.html">2. Creating a Case</a></li>
 <li class="toctree-l2"><a class="reference internal" href="setting-up-a-case.html">3. Setting up a Case</a></li>
@@ -65,10 +65,11 @@
 <li class="toctree-l3"><a class="reference internal" href="#cime-hooks">9.3. CIME hooks</a></li>
 </ul>
 </li>
-<li class="toctree-l2"><a class="reference internal" href="troubleshooting.html">10. Troubleshooting</a></li>
+<li class="toctree-l2"><a class="reference internal" href="testing.html">10. Testing</a></li>
+<li class="toctree-l2"><a class="reference internal" href="troubleshooting.html">11. Troubleshooting</a></li>
 </ul>
 </li>
-<li class="toctree-l1"><a class="reference internal" href="index.html#case-control-system-part-2-configuration-porting-testing-and-use-cases">Case Control System Part 2: Configuration, Porting, Testing and Use Cases</a></li>
+<li class="toctree-l1"><a class="reference internal" href="index.html#configuring-the-case-control-system">Configuring the Case Control System</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../build_cpl/index.html">Building a Coupled Model with CIME</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../misc_tools/index.html">Miscellaneous Tools</a></li>
 </ul>
@@ -94,7 +95,7 @@
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
       <li><a href="../index.html" class="icon icon-home" aria-label="Home"></a></li>
-          <li class="breadcrumb-item"><a href="index.html">Case Control System Part 1: Basic Usage</a></li>
+          <li class="breadcrumb-item"><a href="index.html">Using the Case Control System</a></li>
       <li class="breadcrumb-item active"><span class="section-number">9. </span>CIME config and hooks</li>
       <li class="wy-breadcrumbs-aside">
             <a href="../_sources/users_guide/cime-customize.rst.txt" rel="nofollow"> View page source</a>
@@ -328,7 +329,7 @@ <h2><span class="section-number">9.3. </span>CIME hooks<a class="headerlink" hre
           </div>
           <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
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+        <a href="testing.html" class="btn btn-neutral float-right" title="10. Testing" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
     </div>
 
   <hr/>
diff --git a/versions/master/html/users_guide/cime-dir.html b/versions/master/html/users_guide/cime-dir.html
index 0ee914c2273..27781998cf6 100644
--- a/versions/master/html/users_guide/cime-dir.html
+++ b/versions/master/html/users_guide/cime-dir.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>12. Directory content &mdash; CIME master documentation</title>
+  <title>10. Directory content &mdash; CIME master documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../_static/custom.css" />
@@ -23,7 +23,7 @@
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="Building a Coupled Model with CIME" href="../build_cpl/index.html" />
-    <link rel="prev" title="11. Workflows" href="workflows.html" /> 
+    <link rel="prev" title="9. Workflows" href="workflows.html" /> 
 </head>
 
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@@ -50,20 +50,18 @@
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
               <ul class="current">
 <li class="toctree-l1"><a class="reference internal" href="../what_cime/index.html">What is CIME?</a></li>
-<li class="toctree-l1"><a class="reference internal" href="index.html">Case Control System Part 1: Basic Usage</a></li>
-<li class="toctree-l1 current"><a class="reference internal" href="index.html#case-control-system-part-2-configuration-porting-testing-and-use-cases">Case Control System Part 2: Configuration, Porting, Testing and Use Cases</a><ul class="current">
+<li class="toctree-l1"><a class="reference internal" href="index.html">Using the Case Control System</a></li>
+<li class="toctree-l1 current"><a class="reference internal" href="index.html#configuring-the-case-control-system">Configuring the Case Control System</a><ul class="current">
 <li class="toctree-l2"><a class="reference internal" href="cime-internals.html">1. Main Configuration File</a></li>
 <li class="toctree-l2"><a class="reference internal" href="compsets.html">2. Component sets</a></li>
 <li class="toctree-l2"><a class="reference internal" href="grids.html">3. Model grids</a></li>
 <li class="toctree-l2"><a class="reference internal" href="machine.html">4. Defining the machine</a></li>
 <li class="toctree-l2"><a class="reference internal" href="pes-threads.html">5. Controlling processors and threads</a></li>
 <li class="toctree-l2"><a class="reference internal" href="porting-cime.html">6. Porting and validating CIME on a new platform</a></li>
-<li class="toctree-l2"><a class="reference internal" href="timers.html">7. Timers and timing</a></li>
-<li class="toctree-l2"><a class="reference internal" href="testing.html">8. Testing</a></li>
-<li class="toctree-l2"><a class="reference internal" href="unit_testing.html">9. Fortran Unit Testing</a></li>
-<li class="toctree-l2"><a class="reference internal" href="multi-instance.html">10. Multi-instance component functionality</a></li>
-<li class="toctree-l2"><a class="reference internal" href="workflows.html">11. Workflows</a></li>
-<li class="toctree-l2 current"><a class="current reference internal" href="#">12. Directory content</a></li>
+<li class="toctree-l2"><a class="reference internal" href="unit_testing.html">7. Fortran Unit Testing</a></li>
+<li class="toctree-l2"><a class="reference internal" href="multi-instance.html">8. Multi-instance component functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="workflows.html">9. Workflows</a></li>
+<li class="toctree-l2 current"><a class="current reference internal" href="#">10. Directory content</a></li>
 <li class="toctree-l2"><a class="reference internal" href="index.html#indices-and-tables">Indices and tables</a></li>
 </ul>
 </li>
@@ -92,8 +90,8 @@
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
       <li><a href="../index.html" class="icon icon-home" aria-label="Home"></a></li>
-          <li class="breadcrumb-item"><a href="index.html">Case Control System Part 1: Basic Usage</a></li>
-      <li class="breadcrumb-item active"><span class="section-number">12. </span>Directory content</li>
+          <li class="breadcrumb-item"><a href="index.html">Using the Case Control System</a></li>
+      <li class="breadcrumb-item active"><span class="section-number">10. </span>Directory content</li>
       <li class="wy-breadcrumbs-aside">
             <a href="../_sources/users_guide/cime-dir.rst.txt" rel="nofollow"> View page source</a>
       </li>
@@ -104,7 +102,7 @@
            <div itemprop="articleBody">
              
   <section id="directory-content">
-<span id="cime-dir"></span><h1><span class="section-number">12. </span>Directory content<a class="headerlink" href="#directory-content" title="Link to this heading"></a></h1>
+<span id="cime-dir"></span><h1><span class="section-number">10. </span>Directory content<a class="headerlink" href="#directory-content" title="Link to this heading"></a></h1>
 <p>If you use CIME as part of a climate model or standalone, the content of the <strong>cime</strong> directory is the same.</p>
 <p>If you are using it as part of a climate model, <strong>cime</strong> is usually one of the first subdirectories under the main directory.</p>
 <table class="docutils align-default" id="id1">
@@ -135,9 +133,27 @@
 </tr>
 </thead>
 <tbody>
-<tr class="row-even"><td><p>CMakeLists.txt</p></td>
+<tr class="row-even"><td><p><strong>CIME/</strong></p></td>
+<td><p><strong>The main CIME source</strong></p></td>
+</tr>
+<tr class="row-odd"><td><p>CIME/ParamGen</p></td>
+<td><p>Python tool for generating runtime params</p></td>
+</tr>
+<tr class="row-even"><td><p>CIME/Servers</p></td>
+<td><p>Scripts to interact with input data servers</p></td>
+</tr>
+<tr class="row-odd"><td><p>CIME/SystemTests</p></td>
+<td><p>Scripts for create_test tests.</p></td>
+</tr>
+<tr class="row-even"><td><p>CIME/Tools</p></td>
+<td><p>Auxillary tools, scripts and functions.</p></td>
+</tr>
+<tr class="row-odd"><td><p>CMakeLists.txt</p></td>
 <td><p>For building with CMake</p></td>
 </tr>
+<tr class="row-even"><td><p>CONTRIBUTING.md</p></td>
+<td><p>Guide for contributing to CIME</p></td>
+</tr>
 <tr class="row-odd"><td><p>ChangeLog</p></td>
 <td><p>Developer-maintained record of changes to CIME</p></td>
 </tr>
@@ -147,55 +163,28 @@
 <tr class="row-odd"><td><p>LICENSE.TXT</p></td>
 <td><p>The CIME license</p></td>
 </tr>
-<tr class="row-even"><td><p>README</p></td>
-<td><p>Brief intro to CIME</p></td>
+<tr class="row-even"><td><p>MANIFEST.in</p></td>
+<td></td>
 </tr>
 <tr class="row-odd"><td><p>README.md</p></td>
 <td><p>README in markdown language</p></td>
 </tr>
-<tr class="row-even"><td><p>README.unit_testing</p></td>
-<td><p>Instructions for running unit tests with CIME</p></td>
+<tr class="row-even"><td><p>conftest.py</p></td>
+<td></td>
 </tr>
-<tr class="row-odd"><td><p><strong>config/</strong></p></td>
-<td><p><strong>Shared and model-specific configuration files</strong></p></td>
+<tr class="row-odd"><td><p>doc</p></td>
+<td><p>Documentation for CIME in rst format</p></td>
 </tr>
-<tr class="row-even"><td><p>config/cesm/</p></td>
-<td><p>CESM-specific configuration options</p></td>
+<tr class="row-even"><td><p>docker</p></td>
+<td><p>Container for CIME testing</p></td>
 </tr>
-<tr class="row-odd"><td><p>config/e3sm/</p></td>
-<td><p>E3SM-specific configuration options</p></td>
-</tr>
-<tr class="row-even"><td><p><strong>scripts/</strong></p></td>
+<tr class="row-odd"><td><p><strong>scripts/</strong></p></td>
 <td><p><strong>The CIME user interface</strong></p></td>
 </tr>
-<tr class="row-odd"><td><p>scripts/lib/</p></td>
-<td><p>Infrastructure source code for CIME scripts and functions</p></td>
-</tr>
-<tr class="row-even"><td><p>scripts/Tools/</p></td>
-<td><p>Auxiliary tools; scripts and functions</p></td>
-</tr>
-<tr class="row-odd"><td><p><strong>src/</strong></p></td>
-<td><p><strong>Model source code provided by CIME</strong></p></td>
-</tr>
-<tr class="row-even"><td><p>src/components/</p></td>
-<td><p>CIME-provided components including data and stub models</p></td>
-</tr>
-<tr class="row-odd"><td><p>src/drivers/</p></td>
-<td><p>CIME-provided main driver for a climate model</p></td>
-</tr>
-<tr class="row-even"><td><p>src/externals/</p></td>
-<td><p>Software provided with CIME for building a climate model</p></td>
-</tr>
-<tr class="row-odd"><td><p>src/share/</p></td>
-<td><p>Model source code provided by CIME and used by multiple components</p></td>
-</tr>
-<tr class="row-even"><td><p><strong>tests/</strong></p></td>
-<td><p><strong>Tests</strong></p></td>
-</tr>
-<tr class="row-odd"><td><p><strong>tools/</strong></p></td>
+<tr class="row-even"><td><p><strong>tools/</strong></p></td>
 <td><p><strong>Standalone climate modeling tools</strong></p></td>
 </tr>
-<tr class="row-even"><td><p>utils/</p></td>
+<tr class="row-odd"><td><p>utils/</p></td>
 <td><p>Some Perl source code needed by some prognostic components</p></td>
 </tr>
 </tbody>
@@ -206,7 +195,7 @@
            </div>
           </div>
           <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
-        <a href="workflows.html" class="btn btn-neutral float-left" title="11. Workflows" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
+        <a href="workflows.html" class="btn btn-neutral float-left" title="9. Workflows" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
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diff --git a/versions/master/html/users_guide/cime-internals.html b/versions/master/html/users_guide/cime-internals.html
index b0e7196d3c1..f557ecde435 100644
--- a/versions/master/html/users_guide/cime-internals.html
+++ b/versions/master/html/users_guide/cime-internals.html
@@ -23,7 +23,7 @@
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="2. Component sets" href="compsets.html" />
-    <link rel="prev" title="10. Troubleshooting" href="troubleshooting.html" /> 
+    <link rel="prev" title="11. Troubleshooting" href="troubleshooting.html" /> 
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@@ -50,20 +50,18 @@
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
               <ul class="current">
 <li class="toctree-l1"><a class="reference internal" href="../what_cime/index.html">What is CIME?</a></li>
-<li class="toctree-l1"><a class="reference internal" href="index.html">Case Control System Part 1: Basic Usage</a></li>
-<li class="toctree-l1 current"><a class="reference internal" href="index.html#case-control-system-part-2-configuration-porting-testing-and-use-cases">Case Control System Part 2: Configuration, Porting, Testing and Use Cases</a><ul class="current">
+<li class="toctree-l1"><a class="reference internal" href="index.html">Using the Case Control System</a></li>
+<li class="toctree-l1 current"><a class="reference internal" href="index.html#configuring-the-case-control-system">Configuring the Case Control System</a><ul class="current">
 <li class="toctree-l2 current"><a class="current reference internal" href="#">1. Main Configuration File</a></li>
 <li class="toctree-l2"><a class="reference internal" href="compsets.html">2. Component sets</a></li>
 <li class="toctree-l2"><a class="reference internal" href="grids.html">3. Model grids</a></li>
 <li class="toctree-l2"><a class="reference internal" href="machine.html">4. Defining the machine</a></li>
 <li class="toctree-l2"><a class="reference internal" href="pes-threads.html">5. Controlling processors and threads</a></li>
 <li class="toctree-l2"><a class="reference internal" href="porting-cime.html">6. Porting and validating CIME on a new platform</a></li>
-<li class="toctree-l2"><a class="reference internal" href="timers.html">7. Timers and timing</a></li>
-<li class="toctree-l2"><a class="reference internal" href="testing.html">8. Testing</a></li>
-<li class="toctree-l2"><a class="reference internal" href="unit_testing.html">9. Fortran Unit Testing</a></li>
-<li class="toctree-l2"><a class="reference internal" href="multi-instance.html">10. Multi-instance component functionality</a></li>
-<li class="toctree-l2"><a class="reference internal" href="workflows.html">11. Workflows</a></li>
-<li class="toctree-l2"><a class="reference internal" href="cime-dir.html">12. Directory content</a></li>
+<li class="toctree-l2"><a class="reference internal" href="unit_testing.html">7. Fortran Unit Testing</a></li>
+<li class="toctree-l2"><a class="reference internal" href="multi-instance.html">8. Multi-instance component functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="workflows.html">9. Workflows</a></li>
+<li class="toctree-l2"><a class="reference internal" href="cime-dir.html">10. Directory content</a></li>
 <li class="toctree-l2"><a class="reference internal" href="index.html#indices-and-tables">Indices and tables</a></li>
 </ul>
 </li>
@@ -92,7 +90,7 @@
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
       <li><a href="../index.html" class="icon icon-home" aria-label="Home"></a></li>
-          <li class="breadcrumb-item"><a href="index.html">Case Control System Part 1: Basic Usage</a></li>
+          <li class="breadcrumb-item"><a href="index.html">Using the Case Control System</a></li>
       <li class="breadcrumb-item active"><span class="section-number">1. </span>Main Configuration File</li>
       <li class="wy-breadcrumbs-aside">
             <a href="../_sources/users_guide/cime-internals.rst.txt" rel="nofollow"> View page source</a>
@@ -155,7 +153,7 @@
            </div>
           </div>
           <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
-        <a href="troubleshooting.html" class="btn btn-neutral float-left" title="10. Troubleshooting" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
+        <a href="troubleshooting.html" class="btn btn-neutral float-left" title="11. Troubleshooting" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
         <a href="compsets.html" class="btn btn-neutral float-right" title="2. Component sets" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
     </div>
 
diff --git a/versions/master/html/users_guide/cloning-a-case.html b/versions/master/html/users_guide/cloning-a-case.html
index d0ee17fcf61..a5e587e4bde 100644
--- a/versions/master/html/users_guide/cloning-a-case.html
+++ b/versions/master/html/users_guide/cloning-a-case.html
@@ -50,7 +50,7 @@
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
               <ul class="current">
 <li class="toctree-l1"><a class="reference internal" href="../what_cime/index.html">What is CIME?</a></li>
-<li class="toctree-l1 current"><a class="reference internal" href="index.html">Case Control System Part 1: Basic Usage</a><ul class="current">
+<li class="toctree-l1 current"><a class="reference internal" href="index.html">Using the Case Control System</a><ul class="current">
 <li class="toctree-l2"><a class="reference internal" href="introduction-and-overview.html">1. Introduction</a></li>
 <li class="toctree-l2"><a class="reference internal" href="create-a-case.html">2. Creating a Case</a></li>
 <li class="toctree-l2"><a class="reference internal" href="setting-up-a-case.html">3. Setting up a Case</a></li>
@@ -60,10 +60,11 @@
 <li class="toctree-l2"><a class="reference internal" href="cime-change-namelist.html">7. Customizing your input variables</a></li>
 <li class="toctree-l2"><a class="reference internal" href="cime-config.html">8. CIME user config directory</a></li>
 <li class="toctree-l2"><a class="reference internal" href="cime-customize.html">9. CIME config and hooks</a></li>
-<li class="toctree-l2"><a class="reference internal" href="troubleshooting.html">10. Troubleshooting</a></li>
+<li class="toctree-l2"><a class="reference internal" href="testing.html">10. Testing</a></li>
+<li class="toctree-l2"><a class="reference internal" href="troubleshooting.html">11. Troubleshooting</a></li>
 </ul>
 </li>
-<li class="toctree-l1"><a class="reference internal" href="index.html#case-control-system-part-2-configuration-porting-testing-and-use-cases">Case Control System Part 2: Configuration, Porting, Testing and Use Cases</a></li>
+<li class="toctree-l1"><a class="reference internal" href="index.html#configuring-the-case-control-system">Configuring the Case Control System</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../build_cpl/index.html">Building a Coupled Model with CIME</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../misc_tools/index.html">Miscellaneous Tools</a></li>
 </ul>
@@ -89,7 +90,7 @@
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
       <li><a href="../index.html" class="icon icon-home" aria-label="Home"></a></li>
-          <li class="breadcrumb-item"><a href="index.html">Case Control System Part 1: Basic Usage</a></li>
+          <li class="breadcrumb-item"><a href="index.html">Using the Case Control System</a></li>
       <li class="breadcrumb-item active"><span class="section-number">6. </span>Cloning a Case</li>
       <li class="wy-breadcrumbs-aside">
             <a href="../_sources/users_guide/cloning-a-case.rst.txt" rel="nofollow"> View page source</a>
diff --git a/versions/master/html/users_guide/compsets.html b/versions/master/html/users_guide/compsets.html
index e41f2d0d194..b01f969d39e 100644
--- a/versions/master/html/users_guide/compsets.html
+++ b/versions/master/html/users_guide/compsets.html
@@ -50,8 +50,8 @@
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
               <ul class="current">
 <li class="toctree-l1"><a class="reference internal" href="../what_cime/index.html">What is CIME?</a></li>
-<li class="toctree-l1"><a class="reference internal" href="index.html">Case Control System Part 1: Basic Usage</a></li>
-<li class="toctree-l1 current"><a class="reference internal" href="index.html#case-control-system-part-2-configuration-porting-testing-and-use-cases">Case Control System Part 2: Configuration, Porting, Testing and Use Cases</a><ul class="current">
+<li class="toctree-l1"><a class="reference internal" href="index.html">Using the Case Control System</a></li>
+<li class="toctree-l1 current"><a class="reference internal" href="index.html#configuring-the-case-control-system">Configuring the Case Control System</a><ul class="current">
 <li class="toctree-l2"><a class="reference internal" href="cime-internals.html">1. Main Configuration File</a></li>
 <li class="toctree-l2 current"><a class="current reference internal" href="#">2. Component sets</a><ul>
 <li class="toctree-l3"><a class="reference internal" href="#compset-longname">2.1. Compset longname</a></li>
@@ -63,12 +63,10 @@
 <li class="toctree-l2"><a class="reference internal" href="machine.html">4. Defining the machine</a></li>
 <li class="toctree-l2"><a class="reference internal" href="pes-threads.html">5. Controlling processors and threads</a></li>
 <li class="toctree-l2"><a class="reference internal" href="porting-cime.html">6. Porting and validating CIME on a new platform</a></li>
-<li class="toctree-l2"><a class="reference internal" href="timers.html">7. Timers and timing</a></li>
-<li class="toctree-l2"><a class="reference internal" href="testing.html">8. Testing</a></li>
-<li class="toctree-l2"><a class="reference internal" href="unit_testing.html">9. Fortran Unit Testing</a></li>
-<li class="toctree-l2"><a class="reference internal" href="multi-instance.html">10. Multi-instance component functionality</a></li>
-<li class="toctree-l2"><a class="reference internal" href="workflows.html">11. Workflows</a></li>
-<li class="toctree-l2"><a class="reference internal" href="cime-dir.html">12. Directory content</a></li>
+<li class="toctree-l2"><a class="reference internal" href="unit_testing.html">7. Fortran Unit Testing</a></li>
+<li class="toctree-l2"><a class="reference internal" href="multi-instance.html">8. Multi-instance component functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="workflows.html">9. Workflows</a></li>
+<li class="toctree-l2"><a class="reference internal" href="cime-dir.html">10. Directory content</a></li>
 <li class="toctree-l2"><a class="reference internal" href="index.html#indices-and-tables">Indices and tables</a></li>
 </ul>
 </li>
@@ -97,7 +95,7 @@
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
       <li><a href="../index.html" class="icon icon-home" aria-label="Home"></a></li>
-          <li class="breadcrumb-item"><a href="index.html">Case Control System Part 1: Basic Usage</a></li>
+          <li class="breadcrumb-item"><a href="index.html">Using the Case Control System</a></li>
       <li class="breadcrumb-item active"><span class="section-number">2. </span>Component sets</li>
       <li class="wy-breadcrumbs-aside">
             <a href="../_sources/users_guide/compsets.rst.txt" rel="nofollow"> View page source</a>
diff --git a/versions/master/html/users_guide/create-a-case.html b/versions/master/html/users_guide/create-a-case.html
index 52dfed3435f..26ad6bc548b 100644
--- a/versions/master/html/users_guide/create-a-case.html
+++ b/versions/master/html/users_guide/create-a-case.html
@@ -50,7 +50,7 @@
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
               <ul class="current">
 <li class="toctree-l1"><a class="reference internal" href="../what_cime/index.html">What is CIME?</a></li>
-<li class="toctree-l1 current"><a class="reference internal" href="index.html">Case Control System Part 1: Basic Usage</a><ul class="current">
+<li class="toctree-l1 current"><a class="reference internal" href="index.html">Using the Case Control System</a><ul class="current">
 <li class="toctree-l2"><a class="reference internal" href="introduction-and-overview.html">1. Introduction</a></li>
 <li class="toctree-l2 current"><a class="current reference internal" href="#">2. Creating a Case</a><ul>
 <li class="toctree-l3"><a class="reference internal" href="#calling-create-newcase">2.1. Calling <strong>create_newcase</strong></a></li>
@@ -66,10 +66,11 @@
 <li class="toctree-l2"><a class="reference internal" href="cime-change-namelist.html">7. Customizing your input variables</a></li>
 <li class="toctree-l2"><a class="reference internal" href="cime-config.html">8. CIME user config directory</a></li>
 <li class="toctree-l2"><a class="reference internal" href="cime-customize.html">9. CIME config and hooks</a></li>
-<li class="toctree-l2"><a class="reference internal" href="troubleshooting.html">10. Troubleshooting</a></li>
+<li class="toctree-l2"><a class="reference internal" href="testing.html">10. Testing</a></li>
+<li class="toctree-l2"><a class="reference internal" href="troubleshooting.html">11. Troubleshooting</a></li>
 </ul>
 </li>
-<li class="toctree-l1"><a class="reference internal" href="index.html#case-control-system-part-2-configuration-porting-testing-and-use-cases">Case Control System Part 2: Configuration, Porting, Testing and Use Cases</a></li>
+<li class="toctree-l1"><a class="reference internal" href="index.html#configuring-the-case-control-system">Configuring the Case Control System</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../build_cpl/index.html">Building a Coupled Model with CIME</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../misc_tools/index.html">Miscellaneous Tools</a></li>
 </ul>
@@ -95,7 +96,7 @@
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
       <li><a href="../index.html" class="icon icon-home" aria-label="Home"></a></li>
-          <li class="breadcrumb-item"><a href="index.html">Case Control System Part 1: Basic Usage</a></li>
+          <li class="breadcrumb-item"><a href="index.html">Using the Case Control System</a></li>
       <li class="breadcrumb-item active"><span class="section-number">2. </span>Creating a Case</li>
       <li class="wy-breadcrumbs-aside">
             <a href="../_sources/users_guide/create-a-case.rst.txt" rel="nofollow"> View page source</a>
@@ -159,7 +160,7 @@ <h2><span class="section-number">2.2. </span>Results of calling <strong>create_n
 <p>The output from create_newcase includes information such as.</p>
 <ul class="simple">
 <li><p>The compset longname is <code class="docutils literal notranslate"><span class="pre">2000_DATM%NYF_SLND_DICE%SSMI_DOCN%DOM_DROF%NYF_SGLC_SWAV</span></code></p></li>
-<li><p>The model resolution is <code class="docutils literal notranslate"><span class="pre">a%0.9x1.25_l%0.9x1.25_oi%gx1v6_r%r05_m%gx1v6_g%null_w%null</span></code></p></li>
+<li><p>The grid set is <code class="docutils literal notranslate"><span class="pre">a%0.9x1.25_l%0.9x1.25_oi%gx1v6_r%r05_m%gx1v6_g%null_w%null</span></code></p></li>
 </ul>
 <p><a class="reference external" href="../Tools_user/create_newcase.html">create_newcase</a> installs files in <code class="docutils literal notranslate"><span class="pre">$CASEROOT</span></code> that will build and run the model and to optionally archive the case on the target platform.</p>
 <p>Running <a class="reference external" href="../Tools_user/create_newcase.html">create_newcase</a> creates the following scripts, files and directories in <code class="docutils literal notranslate"><span class="pre">$CASEROOT</span></code>:</p>
@@ -171,58 +172,57 @@ <h2><span class="section-number">2.2. </span>Results of calling <strong>create_n
 </dl>
 </li>
 <li><dl class="simple">
-<dt><a class="reference external" href="../Tools_user/case.setup.html">case.setup</a></dt><dd><p>Script used to set up the case (create the case.run script, Macros file and user_nl_xxx files).</p>
+<dt><a class="reference external" href="../Tools_user/case.submit.html">case.cmpgen_namelist</a></dt><dd><p>Script to perform namelist baseline operations (compare, generate, or both).”</p>
 </dd>
 </dl>
 </li>
 <li><dl class="simple">
-<dt><a class="reference external" href="../Tools_user/case.st_archive.html">case.st_archive</a></dt><dd><p>Script to perform short term archiving to disk for your case output. Note that this script is run automatically by the normal CIME workflow.</p>
+<dt>case.qstatus</dt><dd><p>Script to query the queue on any queue system.</p>
 </dd>
 </dl>
 </li>
 <li><dl class="simple">
-<dt><a class="reference external" href="../Tools_user/case.submit.html">case.submit</a></dt><dd><p>Script to submit the case to run using the machine’s batch queueing system.</p>
+<dt><a class="reference external" href="../Tools_user/case.setup.html">case.setup</a></dt><dd><p>Script used to set up the case (create the case.run script, Macros file and user_nl_xxx files).</p>
 </dd>
 </dl>
 </li>
 <li><dl class="simple">
-<dt><a class="reference external" href="../Tools_user/case.submit.html">case.cmpgen_namelist</a></dt><dd><p>Script to perform namelist baseline operations (compare, generate, or both).”</p>
+<dt><a class="reference external" href="../Tools_user/case.submit.html">case.submit</a></dt><dd><p>Script to submit the case to run using the machine’s batch queueing system.</p>
 </dd>
 </dl>
 </li>
 <li><dl class="simple">
-<dt><a class="reference external" href="../Tools_user/xmlchange.html">xmlchange</a></dt><dd><p>Script to modify values in the xml files.</p>
+<dt><a class="reference external" href="../Tools_user/check_case.html">check_case</a></dt><dd><p>Script to verify case is set up correctly.</p>
 </dd>
 </dl>
 </li>
 <li><dl class="simple">
-<dt><a class="reference external" href="../Tools_user/xmlquery.html">xmlquery</a></dt><dd><p>Script to query values in the xml files.</p>
+<dt><a class="reference external" href="../Tools_user/check_input_data.html">check_input_data</a></dt><dd><p>Script for checking for various input data sets and moving them into place.</p>
 </dd>
 </dl>
 </li>
 <li><dl class="simple">
-<dt><a class="reference external" href="../Tools_user/preview_namelists.html">preview_namelists</a></dt><dd><p>Script for users to see their component namelists in <code class="docutils literal notranslate"><span class="pre">$CASEROOT/CaseDocs</span></code> before running the model.</p>
+<dt><a class="reference external" href="../Tools_user/pelayout.html">pelayout</a></dt><dd><p>Script to query and modify the NTASKS, ROOTPE, and NTHRDS for each component model.</p>
 </dd>
 </dl>
 </li>
 <li><dl class="simple">
-<dt><a class="reference external" href="../Tools_user/preview_run.html">preview_run</a></dt><dd><p>Script for users to see batch submit and mpirun command.”</p>
+<dt><a class="reference external" href="../Tools_user/preview_namelists.html">preview_namelists</a></dt><dd><p>Script for users to see their component namelists in <code class="docutils literal notranslate"><span class="pre">$CASEROOT/CaseDocs</span></code> before running the model.</p>
 </dd>
 </dl>
 </li>
 <li><dl class="simple">
-<dt><a class="reference external" href="../Tools_user/check_input_data.html">check_input_data</a></dt><dd><p>Script for checking for various input data sets and moving them into place.</p>
+<dt><a class="reference external" href="../Tools_user/preview_run.html">preview_run</a></dt><dd><p>Script for users to see batch submit and mpirun command.”</p>
 </dd>
 </dl>
 </li>
 <li><dl class="simple">
-<dt><a class="reference external" href="../Tools_user/check_case.html">check_case</a></dt><dd><p>Script to verify case is set up correctly.</p>
+<dt><a class="reference external" href="../Tools_user/xmlchange.html">xmlchange</a></dt><dd><p>Script to modify values in the xml files.</p>
 </dd>
 </dl>
 </li>
 <li><dl class="simple">
-<dt><a class="reference external" href="../Tools_user/pelayout.html">pelayout</a></dt><dd><p>Script to query and modify the NTASKS, ROOTPE, and NTHRDS for each component model.
-This a convenience script that can be used in place of <a class="reference external" href="../Tools_user/xmlchange.html">xmlchange</a> and <a class="reference external" href="../Tools_user/xmlquery.html">xmlquery</a>.</p>
+<dt><a class="reference external" href="../Tools_user/xmlquery.html">xmlquery</a></dt><dd><p>Script to query values in the xml files.</p>
 </dd>
 </dl>
 </li>
@@ -236,8 +236,7 @@ <h2><span class="section-number">2.2. </span>Results of calling <strong>create_n
 </dl>
 </li>
 <li><dl class="simple">
-<dt>env_mach_specific.xml</dt><dd><p>Sets a number of machine-specific environment variables for building and/or running.
-You <strong>CANNOT</strong> use <a class="reference external" href="../Tools_user/xmlchange.html">xmlchange</a>  to modify variables in this file.</p>
+<dt>env_batch.xml</dt><dd><p>Sets batch system settings such as wallclock time and queue name.”</p>
 </dd>
 </dl>
 </li>
@@ -248,8 +247,7 @@ <h2><span class="section-number">2.2. </span>Results of calling <strong>create_n
 </dl>
 </li>
 <li><dl class="simple">
-<dt>env_run.xml</dt><dd><p>Sets runtime settings such as length of run, frequency of restarts, output of coupler diagnostics, and short-term and long-term archiving.
-This file can be edited at any time before a job starts.</p>
+<dt>env_case.xml</dt><dd><p>Parameters set by create_newcase</p>
 </dd>
 </dl>
 </li>
@@ -260,7 +258,19 @@ <h2><span class="section-number">2.2. </span>Results of calling <strong>create_n
 </dl>
 </li>
 <li><dl class="simple">
-<dt>env_batch.xml</dt><dd><p>Sets batch system settings such as wallclock time and queue name.”</p>
+<dt>env_mach_specific.xml</dt><dd><p>Sets a number of machine-specific environment variables for building and/or running.
+You <strong>CANNOT</strong> use <a class="reference external" href="../Tools_user/xmlchange.html">xmlchange</a>  to modify variables in this file.</p>
+</dd>
+</dl>
+</li>
+<li><dl class="simple">
+<dt>env_run.xml</dt><dd><p>Sets runtime settings such as length of run, frequency of restarts, output of coupler diagnostics, and short-term and long-term archiving.
+This file can be edited at any time before a job starts.</p>
+</dd>
+</dl>
+</li>
+<li><dl class="simple">
+<dt>env_workflow.xml</dt><dd><p>Sets paramateres for the runtime workflow.</p>
 </dd>
 </dl>
 </li>
diff --git a/versions/master/html/users_guide/grids.html b/versions/master/html/users_guide/grids.html
index 1032fdc4aef..ab3400013ea 100644
--- a/versions/master/html/users_guide/grids.html
+++ b/versions/master/html/users_guide/grids.html
@@ -50,8 +50,8 @@
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
               <ul class="current">
 <li class="toctree-l1"><a class="reference internal" href="../what_cime/index.html">What is CIME?</a></li>
-<li class="toctree-l1"><a class="reference internal" href="index.html">Case Control System Part 1: Basic Usage</a></li>
-<li class="toctree-l1 current"><a class="reference internal" href="index.html#case-control-system-part-2-configuration-porting-testing-and-use-cases">Case Control System Part 2: Configuration, Porting, Testing and Use Cases</a><ul class="current">
+<li class="toctree-l1"><a class="reference internal" href="index.html">Using the Case Control System</a></li>
+<li class="toctree-l1 current"><a class="reference internal" href="index.html#configuring-the-case-control-system">Configuring the Case Control System</a><ul class="current">
 <li class="toctree-l2"><a class="reference internal" href="cime-internals.html">1. Main Configuration File</a></li>
 <li class="toctree-l2"><a class="reference internal" href="compsets.html">2. Component sets</a></li>
 <li class="toctree-l2 current"><a class="current reference internal" href="#">3. Model grids</a><ul>
@@ -62,12 +62,10 @@
 <li class="toctree-l2"><a class="reference internal" href="machine.html">4. Defining the machine</a></li>
 <li class="toctree-l2"><a class="reference internal" href="pes-threads.html">5. Controlling processors and threads</a></li>
 <li class="toctree-l2"><a class="reference internal" href="porting-cime.html">6. Porting and validating CIME on a new platform</a></li>
-<li class="toctree-l2"><a class="reference internal" href="timers.html">7. Timers and timing</a></li>
-<li class="toctree-l2"><a class="reference internal" href="testing.html">8. Testing</a></li>
-<li class="toctree-l2"><a class="reference internal" href="unit_testing.html">9. Fortran Unit Testing</a></li>
-<li class="toctree-l2"><a class="reference internal" href="multi-instance.html">10. Multi-instance component functionality</a></li>
-<li class="toctree-l2"><a class="reference internal" href="workflows.html">11. Workflows</a></li>
-<li class="toctree-l2"><a class="reference internal" href="cime-dir.html">12. Directory content</a></li>
+<li class="toctree-l2"><a class="reference internal" href="unit_testing.html">7. Fortran Unit Testing</a></li>
+<li class="toctree-l2"><a class="reference internal" href="multi-instance.html">8. Multi-instance component functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="workflows.html">9. Workflows</a></li>
+<li class="toctree-l2"><a class="reference internal" href="cime-dir.html">10. Directory content</a></li>
 <li class="toctree-l2"><a class="reference internal" href="index.html#indices-and-tables">Indices and tables</a></li>
 </ul>
 </li>
@@ -96,7 +94,7 @@
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
       <li><a href="../index.html" class="icon icon-home" aria-label="Home"></a></li>
-          <li class="breadcrumb-item"><a href="index.html">Case Control System Part 1: Basic Usage</a></li>
+          <li class="breadcrumb-item"><a href="index.html">Using the Case Control System</a></li>
       <li class="breadcrumb-item active"><span class="section-number">3. </span>Model grids</li>
       <li class="wy-breadcrumbs-aside">
             <a href="../_sources/users_guide/grids.rst.txt" rel="nofollow"> View page source</a>
diff --git a/versions/master/html/users_guide/index.html b/versions/master/html/users_guide/index.html
index 35bba69e6d0..11def217896 100644
--- a/versions/master/html/users_guide/index.html
+++ b/versions/master/html/users_guide/index.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Case Control System Part 1: Basic Usage &mdash; CIME master documentation</title>
+  <title>Using the Case Control System &mdash; CIME master documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
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@@ -50,7 +50,7 @@
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               <ul class="current">
 <li class="toctree-l1"><a class="reference internal" href="../what_cime/index.html">What is CIME?</a></li>
-<li class="toctree-l1 current"><a class="current reference internal" href="#">Case Control System Part 1: Basic Usage</a><ul>
+<li class="toctree-l1 current"><a class="current reference internal" href="#">Using the Case Control System</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="introduction-and-overview.html">1. Introduction</a></li>
 <li class="toctree-l2"><a class="reference internal" href="create-a-case.html">2. Creating a Case</a></li>
 <li class="toctree-l2"><a class="reference internal" href="setting-up-a-case.html">3. Setting up a Case</a></li>
@@ -60,22 +60,21 @@
 <li class="toctree-l2"><a class="reference internal" href="cime-change-namelist.html">7. Customizing your input variables</a></li>
 <li class="toctree-l2"><a class="reference internal" href="cime-config.html">8. CIME user config directory</a></li>
 <li class="toctree-l2"><a class="reference internal" href="cime-customize.html">9. CIME config and hooks</a></li>
-<li class="toctree-l2"><a class="reference internal" href="troubleshooting.html">10. Troubleshooting</a></li>
+<li class="toctree-l2"><a class="reference internal" href="testing.html">10. Testing</a></li>
+<li class="toctree-l2"><a class="reference internal" href="troubleshooting.html">11. Troubleshooting</a></li>
 </ul>
 </li>
-<li class="toctree-l1"><a class="reference internal" href="#case-control-system-part-2-configuration-porting-testing-and-use-cases">Case Control System Part 2: Configuration, Porting, Testing and Use Cases</a><ul>
+<li class="toctree-l1"><a class="reference internal" href="#configuring-the-case-control-system">Configuring the Case Control System</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="cime-internals.html">1. Main Configuration File</a></li>
 <li class="toctree-l2"><a class="reference internal" href="compsets.html">2. Component sets</a></li>
 <li class="toctree-l2"><a class="reference internal" href="grids.html">3. Model grids</a></li>
 <li class="toctree-l2"><a class="reference internal" href="machine.html">4. Defining the machine</a></li>
 <li class="toctree-l2"><a class="reference internal" href="pes-threads.html">5. Controlling processors and threads</a></li>
 <li class="toctree-l2"><a class="reference internal" href="porting-cime.html">6. Porting and validating CIME on a new platform</a></li>
-<li class="toctree-l2"><a class="reference internal" href="timers.html">7. Timers and timing</a></li>
-<li class="toctree-l2"><a class="reference internal" href="testing.html">8. Testing</a></li>
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-<li class="toctree-l2"><a class="reference internal" href="multi-instance.html">10. Multi-instance component functionality</a></li>
-<li class="toctree-l2"><a class="reference internal" href="workflows.html">11. Workflows</a></li>
-<li class="toctree-l2"><a class="reference internal" href="cime-dir.html">12. Directory content</a></li>
+<li class="toctree-l2"><a class="reference internal" href="unit_testing.html">7. Fortran Unit Testing</a></li>
+<li class="toctree-l2"><a class="reference internal" href="multi-instance.html">8. Multi-instance component functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="workflows.html">9. Workflows</a></li>
+<li class="toctree-l2"><a class="reference internal" href="cime-dir.html">10. Directory content</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#indices-and-tables">Indices and tables</a></li>
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@@ -104,7 +103,7 @@
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       <li><a href="../index.html" class="icon icon-home" aria-label="Home"></a></li>
-      <li class="breadcrumb-item active">Case Control System Part 1: Basic Usage</li>
+      <li class="breadcrumb-item active">Using the Case Control System</li>
       <li class="wy-breadcrumbs-aside">
             <a href="../_sources/users_guide/index.rst.txt" rel="nofollow"> View page source</a>
       </li>
@@ -114,16 +113,16 @@
           <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
            <div itemprop="articleBody">
              
-  <section id="case-control-system-part-1-basic-usage">
-<span id="users-guide1"></span><h1>Case Control System Part 1: Basic Usage<a class="headerlink" href="#case-control-system-part-1-basic-usage" title="Link to this heading"></a></h1>
+  <section id="using-the-case-control-system">
+<span id="users-guide1"></span><h1>Using the Case Control System<a class="headerlink" href="#using-the-case-control-system" title="Link to this heading"></a></h1>
 <div class="toctree-wrapper compound">
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="introduction-and-overview.html">1. Introduction</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="introduction-and-overview.html#prerequisites">1.1. Prerequisites</a></li>
 <li class="toctree-l2"><a class="reference internal" href="introduction-and-overview.html#key-terms-and-concepts">1.2. Key Terms and concepts</a></li>
-<li class="toctree-l2"><a class="reference internal" href="introduction-and-overview.html#cime-and-your-environment">1.3. CIME and your environment</a></li>
+<li class="toctree-l2"><a class="reference internal" href="introduction-and-overview.html#ccs-and-your-environment">1.3. CCS and your environment</a></li>
 <li class="toctree-l2"><a class="reference internal" href="introduction-and-overview.html#quick-start">1.4. Quick start</a></li>
-<li class="toctree-l2"><a class="reference internal" href="introduction-and-overview.html#discovering-available-cases-with-query-config">1.5. Discovering available cases with <strong>query_config</strong></a></li>
+<li class="toctree-l2"><a class="reference internal" href="introduction-and-overview.html#discovering-available-pre-defined-compsets-with-query-config">1.5. Discovering available pre-defined compsets with <strong>query_config</strong></a></li>
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="create-a-case.html">2. Creating a Case</a><ul>
@@ -167,18 +166,27 @@
 <li class="toctree-l2"><a class="reference internal" href="cime-customize.html#cime-hooks">9.3. CIME hooks</a></li>
 </ul>
 </li>
-<li class="toctree-l1"><a class="reference internal" href="troubleshooting.html">10. Troubleshooting</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="troubleshooting.html#troubleshooting-case-creation">10.1. Troubleshooting case creation</a></li>
-<li class="toctree-l2"><a class="reference internal" href="troubleshooting.html#troubleshooting-problems-in-cime-scripts">10.2. Troubleshooting problems in cime scripts</a></li>
-<li class="toctree-l2"><a class="reference internal" href="troubleshooting.html#troubleshooting-job-submission">10.3. Troubleshooting job submission</a></li>
-<li class="toctree-l2"><a class="reference internal" href="troubleshooting.html#troubleshooting-runtime-problems">10.4. Troubleshooting runtime problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="testing.html">10. Testing</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="testing.html#testname-syntax">10.1. Testname syntax</a></li>
+<li class="toctree-l2"><a class="reference internal" href="testing.html#query-testlists">10.2. Query_testlists</a></li>
+<li class="toctree-l2"><a class="reference internal" href="testing.html#using-create-test-e3sm">10.3. Using <strong>create_test</strong> (E3SM)</a></li>
+<li class="toctree-l2"><a class="reference internal" href="testing.html#baselines">10.4. Baselines</a></li>
+<li class="toctree-l2"><a class="reference internal" href="testing.html#adding-tests">10.5. Adding tests</a></li>
+<li class="toctree-l2"><a class="reference internal" href="testing.html#cime-developer-s-guide">10.6. CIME Developer’s guide</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="troubleshooting.html">11. Troubleshooting</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="troubleshooting.html#troubleshooting-case-creation">11.1. Troubleshooting case creation</a></li>
+<li class="toctree-l2"><a class="reference internal" href="troubleshooting.html#troubleshooting-problems-in-cime-scripts">11.2. Troubleshooting problems in cime scripts</a></li>
+<li class="toctree-l2"><a class="reference internal" href="troubleshooting.html#troubleshooting-job-submission">11.3. Troubleshooting job submission</a></li>
+<li class="toctree-l2"><a class="reference internal" href="troubleshooting.html#troubleshooting-runtime-problems">11.4. Troubleshooting runtime problems</a></li>
 </ul>
 </li>
 </ul>
 </div>
 </section>
-<section id="case-control-system-part-2-configuration-porting-testing-and-use-cases">
-<span id="users-guide2"></span><h1>Case Control System Part 2: Configuration, Porting, Testing and Use Cases<a class="headerlink" href="#case-control-system-part-2-configuration-porting-testing-and-use-cases" title="Link to this heading"></a></h1>
+<section id="configuring-the-case-control-system">
+<span id="users-guide2"></span><h1>Configuring the Case Control System<a class="headerlink" href="#configuring-the-case-control-system" title="Link to this heading"></a></h1>
 <div class="toctree-wrapper compound">
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="cime-internals.html">1. Main Configuration File</a></li>
@@ -217,34 +225,19 @@
 <li class="toctree-l2"><a class="reference internal" href="porting-cime.html#performance-tuning-of-a-cesm-port">6.6. Performance tuning of a CESM port</a></li>
 </ul>
 </li>
-<li class="toctree-l1"><a class="reference internal" href="timers.html">7. Timers and timing</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="timers.html#model-timing-data">7.1. Model timing data</a></li>
-<li class="toctree-l2"><a class="reference internal" href="timers.html#controlling-timers">7.2. Controlling timers</a></li>
-<li class="toctree-l2"><a class="reference internal" href="timers.html#advice-on-setting-your-wallclock-time">7.3. Advice on setting your wallclock time</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="testing.html">8. Testing</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="testing.html#testname-syntax">8.1. Testname syntax</a></li>
-<li class="toctree-l2"><a class="reference internal" href="testing.html#query-testlists">8.2. Query_testlists</a></li>
-<li class="toctree-l2"><a class="reference internal" href="testing.html#using-create-test-e3sm">8.3. Using <strong>create_test</strong> (E3SM)</a></li>
-<li class="toctree-l2"><a class="reference internal" href="testing.html#baselines">8.4. Baselines</a></li>
-<li class="toctree-l2"><a class="reference internal" href="testing.html#adding-tests">8.5. Adding tests</a></li>
-<li class="toctree-l2"><a class="reference internal" href="testing.html#cime-developer-s-guide">8.6. CIME Developer’s guide</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="unit_testing.html">9. Fortran Unit Testing</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="unit_testing.html#introduction">9.1. Introduction</a></li>
-<li class="toctree-l2"><a class="reference internal" href="unit_testing.html#running-cime-s-fortran-unit-tests">9.2. Running CIME’s Fortran unit tests</a></li>
-<li class="toctree-l2"><a class="reference internal" href="unit_testing.html#how-to-add-unit-testing-support-on-your-machine">9.3. How to add unit testing support on your machine</a></li>
-<li class="toctree-l2"><a class="reference internal" href="unit_testing.html#how-to-write-a-new-unit-test">9.4. How to write a new unit test</a></li>
-<li class="toctree-l2"><a class="reference internal" href="unit_testing.html#general-guidelines-for-writing-unit-tests">9.5. General guidelines for writing unit tests</a></li>
-<li class="toctree-l2"><a class="reference internal" href="unit_testing.html#more-details-on-writing-pfunit-based-unit-tests">9.6. More details on writing pFUnit-based unit tests</a></li>
-<li class="toctree-l2"><a class="reference internal" href="unit_testing.html#finding-more-documentation-and-examples">9.7. Finding more documentation and examples</a></li>
+<li class="toctree-l1"><a class="reference internal" href="unit_testing.html">7. Fortran Unit Testing</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="unit_testing.html#introduction">7.1. Introduction</a></li>
+<li class="toctree-l2"><a class="reference internal" href="unit_testing.html#running-cime-s-fortran-unit-tests">7.2. Running CIME’s Fortran unit tests</a></li>
+<li class="toctree-l2"><a class="reference internal" href="unit_testing.html#how-to-add-unit-testing-support-on-your-machine">7.3. How to add unit testing support on your machine</a></li>
+<li class="toctree-l2"><a class="reference internal" href="unit_testing.html#how-to-write-a-new-unit-test">7.4. How to write a new unit test</a></li>
+<li class="toctree-l2"><a class="reference internal" href="unit_testing.html#general-guidelines-for-writing-unit-tests">7.5. General guidelines for writing unit tests</a></li>
+<li class="toctree-l2"><a class="reference internal" href="unit_testing.html#more-details-on-writing-pfunit-based-unit-tests">7.6. More details on writing pFUnit-based unit tests</a></li>
+<li class="toctree-l2"><a class="reference internal" href="unit_testing.html#finding-more-documentation-and-examples">7.7. Finding more documentation and examples</a></li>
 </ul>
 </li>
-<li class="toctree-l1"><a class="reference internal" href="multi-instance.html">10. Multi-instance component functionality</a></li>
-<li class="toctree-l1"><a class="reference internal" href="workflows.html">11. Workflows</a></li>
-<li class="toctree-l1"><a class="reference internal" href="cime-dir.html">12. Directory content</a></li>
+<li class="toctree-l1"><a class="reference internal" href="multi-instance.html">8. Multi-instance component functionality</a></li>
+<li class="toctree-l1"><a class="reference internal" href="workflows.html">9. Workflows</a></li>
+<li class="toctree-l1"><a class="reference internal" href="cime-dir.html">10. Directory content</a></li>
 </ul>
 </div>
 <section id="indices-and-tables">
diff --git a/versions/master/html/users_guide/introduction-and-overview.html b/versions/master/html/users_guide/introduction-and-overview.html
index 127f9de491b..ce7d1b694a9 100644
--- a/versions/master/html/users_guide/introduction-and-overview.html
+++ b/versions/master/html/users_guide/introduction-and-overview.html
@@ -23,7 +23,7 @@
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="2. Creating a Case" href="create-a-case.html" />
-    <link rel="prev" title="Case Control System Part 1: Basic Usage" href="index.html" /> 
+    <link rel="prev" title="Using the Case Control System" href="index.html" /> 
 </head>
 
 <body class="wy-body-for-nav"> 
@@ -50,13 +50,13 @@
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
               <ul class="current">
 <li class="toctree-l1"><a class="reference internal" href="../what_cime/index.html">What is CIME?</a></li>
-<li class="toctree-l1 current"><a class="reference internal" href="index.html">Case Control System Part 1: Basic Usage</a><ul class="current">
+<li class="toctree-l1 current"><a class="reference internal" href="index.html">Using the Case Control System</a><ul class="current">
 <li class="toctree-l2 current"><a class="current reference internal" href="#">1. Introduction</a><ul>
 <li class="toctree-l3"><a class="reference internal" href="#prerequisites">1.1. Prerequisites</a></li>
 <li class="toctree-l3"><a class="reference internal" href="#key-terms-and-concepts">1.2. Key Terms and concepts</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#cime-and-your-environment">1.3. CIME and your environment</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#ccs-and-your-environment">1.3. CCS and your environment</a></li>
 <li class="toctree-l3"><a class="reference internal" href="#quick-start">1.4. Quick start</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#discovering-available-cases-with-query-config">1.5. Discovering available cases with <strong>query_config</strong></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#discovering-available-pre-defined-compsets-with-query-config">1.5. Discovering available pre-defined compsets with <strong>query_config</strong></a></li>
 </ul>
 </li>
 <li class="toctree-l2"><a class="reference internal" href="create-a-case.html">2. Creating a Case</a></li>
@@ -67,10 +67,11 @@
 <li class="toctree-l2"><a class="reference internal" href="cime-change-namelist.html">7. Customizing your input variables</a></li>
 <li class="toctree-l2"><a class="reference internal" href="cime-config.html">8. CIME user config directory</a></li>
 <li class="toctree-l2"><a class="reference internal" href="cime-customize.html">9. CIME config and hooks</a></li>
-<li class="toctree-l2"><a class="reference internal" href="troubleshooting.html">10. Troubleshooting</a></li>
+<li class="toctree-l2"><a class="reference internal" href="testing.html">10. Testing</a></li>
+<li class="toctree-l2"><a class="reference internal" href="troubleshooting.html">11. Troubleshooting</a></li>
 </ul>
 </li>
-<li class="toctree-l1"><a class="reference internal" href="index.html#case-control-system-part-2-configuration-porting-testing-and-use-cases">Case Control System Part 2: Configuration, Porting, Testing and Use Cases</a></li>
+<li class="toctree-l1"><a class="reference internal" href="index.html#configuring-the-case-control-system">Configuring the Case Control System</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../build_cpl/index.html">Building a Coupled Model with CIME</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../misc_tools/index.html">Miscellaneous Tools</a></li>
 </ul>
@@ -96,7 +97,7 @@
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
       <li><a href="../index.html" class="icon icon-home" aria-label="Home"></a></li>
-          <li class="breadcrumb-item"><a href="index.html">Case Control System Part 1: Basic Usage</a></li>
+          <li class="breadcrumb-item"><a href="index.html">Using the Case Control System</a></li>
       <li class="breadcrumb-item active"><span class="section-number">1. </span>Introduction</li>
       <li class="wy-breadcrumbs-aside">
             <a href="../_sources/users_guide/introduction-and-overview.rst.txt" rel="nofollow"> View page source</a>
@@ -123,7 +124,7 @@ <h2><span class="section-number">1.1. </span>Prerequisites<a class="headerlink"
 </ul>
 <p>CIME’s commands are Python scripts and require a correct version of
 the Python interpreter to be installed. The Python version must be
-greater than 2.7.  Determine which version you have
+greater than 2.11.  Determine which version you have
 like this:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="o">&gt;</span> <span class="n">python</span> <span class="o">--</span><span class="n">version</span>
 </pre></div>
@@ -132,7 +133,7 @@ <h2><span class="section-number">1.1. </span>Prerequisites<a class="headerlink"
 </section>
 <section id="key-terms-and-concepts">
 <h2><span class="section-number">1.2. </span>Key Terms and concepts<a class="headerlink" href="#key-terms-and-concepts" title="Link to this heading"></a></h2>
-<p>The following key terms and concepts are ingrained in CIME and used frequently in this documentation.
+<p>The following key terms and concepts are ingrained in the CCS and used frequently in this documentation.
 See the <a class="reference internal" href="../glossary/index.html#glossary"><span class="std std-ref">Glossary</span></a> for a more complete list of terms.</p>
 <p><strong>components</strong></p>
 <blockquote>
@@ -152,24 +153,87 @@ <h2><span class="section-number">1.2. </span>Key Terms and concepts<a class="hea
 These can be full General Circulation Models. Multiple active models might be available (for example POP and MPAS-ocean to represent the global ocean) but only one ocean or atmosphere model at a time can be used in a component set.</p>
 <p><em>data</em>: For some climate problems, it is necessary to reduce feedbacks within the system by replacing an active model with a
 version that sends and receives the same variables to and from other models, but with the values read from files rather
-than computed from the equations. The values received are ignored. These active-model substitutes are called <em>data models</em>.
-CIME provides data models for each of the possible components.  You could add your own data model implementation of a component
-but as for active models only one at a time can be used.</p>
-<p><em>stub</em>: For some configurations, no data model is needed, so CIME provides <em>stub</em> versions that simply occupy the
-required place in the driver and do not send or receive any data.</p>
+than computed from the equations. The values received are ignored. These active-model substitutes are called <em>data models</em>.</p>
+<p><em>stub</em>: For some configurations, no data model is needed and one instead uses a <em>stub</em> version that simply occupies the
+required place in the driver and does not send or receive any data.  For example, if you are setting up an aqua-planet case
+you would only need a stub for the land model.</p>
+</div></blockquote>
+<p><strong>component set</strong> or <strong>compset</strong>:</p>
+<blockquote>
+<div><p>The particular combination of active, data and stub versions of the 7 components is referred to
+as a <em>component set</em> or  <em>compset</em>.  The Case Control System allows one to define
+several possible compsets and configure and run them on supported platforms.
+Here is an example of a component set <em>longname</em> from E3SM for a fully coupled active case:</p>
+</div></blockquote>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="mi">1850</span><span class="n">SOI_EAM</span><span class="o">%</span><span class="n">CMIP6_ELM</span><span class="o">%</span><span class="n">CNPRDCTCBCTOP_MPASSI_MPASO_MOSART_SGLC_SWAV</span>
+</pre></div>
+</div>
+<p>See <a class="reference internal" href="compsets.html#compsets"><span class="std std-ref">Component Sets</span></a> for more information. “GLC” originally meant “glacier model” and is now an ice-sheet model but the GLC letters have stuck.</p>
+<p><strong>compset alias</strong>:</p>
+<blockquote>
+<div><p>Typing a compset longname like the above can be exhausting so the CCS allows defining a shorter <em>compset alias</em>
+which is a short string that substitutes for the longname. In E3SM, the above longname can be reffered to as “WCYCL1850”.</p>
+</div></blockquote>
+<div class="admonition note">
+<p class="admonition-title">Note</p>
+<blockquote>
+<div><p>Long ago, CESM established a convention for the first letter in a compset alias based
+on the combination of active, data and stub components.
+If you see mention of “B-case” or “F-case”, it comes from these conventions.
+They pre-date the introduction of a wave model as an option.</p>
+</div></blockquote>
+<table class="docutils align-default">
+<tbody>
+<tr class="row-odd"><td><p>A</p></td>
+<td><p>All data models</p></td>
+</tr>
+<tr class="row-even"><td><p>B</p></td>
+<td><p>All models fully active with stub glc</p></td>
+</tr>
+<tr class="row-odd"><td><p>C</p></td>
+<td><p>Active ocean with data atm, river and sea ice. stub lnd, glc</p></td>
+</tr>
+<tr class="row-even"><td><p>D</p></td>
+<td><p>Active sea ice with data atm, ocean (slab) and river. stub lnd, glc</p></td>
+</tr>
+<tr class="row-odd"><td><p>E</p></td>
+<td><p>Active atm, lnd, sea-ice, river, data ocean (slab), stub glc</p></td>
+</tr>
+<tr class="row-even"><td><p>F</p></td>
+<td><p>Active atm, lnd, river, sea-ice (thermodynamics only), data ocean (fixed SST), stub glc</p></td>
+</tr>
+<tr class="row-odd"><td><p>G</p></td>
+<td><p>Active ocean and sea ice, data atmosphere and river, stub lnd and glc</p></td>
+</tr>
+<tr class="row-even"><td><p>H</p></td>
+<td><p>Active ocean and sea ice, data atmosphere, stub lnd, river and glc</p></td>
+</tr>
+<tr class="row-odd"><td><p>I</p></td>
+<td><p>Active land and river model, data atmosphere, stub ocn, sea-ice, glc</p></td>
+</tr>
+<tr class="row-even"><td><p>IG</p></td>
+<td><p>Active land, river and ice-sheet, data atmosphere, stub ocn, sea-ice</p></td>
+</tr>
+<tr class="row-odd"><td><p>S</p></td>
+<td><p>All stub models (for testing only)</p></td>
+</tr>
+<tr class="row-even"><td><p>X</p></td>
+<td><p>All x-compsets (2D sine waves for each component except stub glc; for testing only)</p></td>
+</tr>
+</tbody>
+</table>
+</div>
+<p><strong>grid set</strong>:</p>
+<blockquote>
+<div><p>Each active model must solve its equations on a numerical grid. CIME allows models within the system to have
+different grids. The resulting set of all numerical grids is called the <em>grid set</em> or usually just the <em>grid</em>. Like
+the compset longnamme, the CCS allows one to define an alias to represent a grid set.  This alias is also referred to
+as the <em>grid</em> or sometimes the <em>resolution</em>.</p>
 </div></blockquote>
 <dl class="simple">
-<dt><strong>component set</strong> or <strong>compset</strong>:   The particular combination of active, data and stub versions of the 7 components is referred to</dt><dd><p>as a <em>component set</em> or  <em>compset</em>.  The Case Control System allows one to define
-several possible compsets and configure and run them on supported platforms. See <a class="reference internal" href="compsets.html#compsets"><span class="std std-ref">Component Sets</span></a> for more information.</p>
-</dd>
-<dt><strong>grid</strong> or <strong>model grid</strong>:</dt><dd><p>Each active model must solve its equations on a numerical grid. CIME allows models within the system to have
-different grids. The resulting set of all numerical grids is called the <em>model grid</em> or sometimes just the <em>grid</em>, where
-<em>grid</em> is a unique name that denotes a set of numerical grids. Sometimes the <em>resolution</em> also refers to a specific set
-of grids.</p>
-</dd>
 <dt><strong>machine and compilers</strong>:</dt><dd><p>The <em>machine</em> is the computer you are using to run CIME and build and run the climate model. It could be a workstation
 or a national supercomputer. The exact name of  <em>machine</em> is typically the UNIX hostname but it could be any string.  A machine
-may have one more more versions of Fortran, C and C++ <em>compilers</em> that are needed to compile the model’s source code and CIME</p>
+may have one more more versions of Fortran, C and C++ <em>compilers</em> that are needed to compile the model’s source code and CIME.</p>
 </dd>
 <dt><strong>case</strong>:</dt><dd><p>To build and execute a CIME-enabled climate model, you have to make choices of compset, model grid,
 machine and compiler. The collection of these choices, and any additional
@@ -182,9 +246,9 @@ <h2><span class="section-number">1.2. </span>Key Terms and concepts<a class="hea
 </dd>
 </dl>
 </section>
-<section id="cime-and-your-environment">
-<h2><span class="section-number">1.3. </span>CIME and your environment<a class="headerlink" href="#cime-and-your-environment" title="Link to this heading"></a></h2>
-<p>Before using any CIME commands, set the <code class="docutils literal notranslate"><span class="pre">CIME_MODEL</span></code> environment variable. In bash, use <strong>export</strong> as shown and replace
+<section id="ccs-and-your-environment">
+<h2><span class="section-number">1.3. </span>CCS and your environment<a class="headerlink" href="#ccs-and-your-environment" title="Link to this heading"></a></h2>
+<p>Before using any CCS commands, set the <code class="docutils literal notranslate"><span class="pre">CIME_MODEL</span></code> environment variable. In bash, use <strong>export</strong> as shown and replace
 <strong>&lt;model&gt;</strong> with the appropriate text. Current possibilities are “e3sm” or “cesm.”</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="o">&gt;</span> <span class="n">export</span> <span class="n">CIME_MODEL</span><span class="o">=&lt;</span><span class="n">model</span><span class="o">&gt;</span>
 </pre></div>
@@ -216,12 +280,11 @@ <h2><span class="section-number">1.4. </span>Quick start<a class="headerlink" hr
 </div>
 <p>Repeat the command until you see the message <code class="docutils literal notranslate"><span class="pre">case.run</span> <span class="pre">success</span></code>.</p>
 </section>
-<section id="discovering-available-cases-with-query-config">
-<h2><span class="section-number">1.5. </span>Discovering available cases with <strong>query_config</strong><a class="headerlink" href="#discovering-available-cases-with-query-config" title="Link to this heading"></a></h2>
-<p>Your CIME-driven model has many more possible cases besides the simple one in the above Quick Start.</p>
+<section id="discovering-available-pre-defined-compsets-with-query-config">
+<h2><span class="section-number">1.5. </span>Discovering available pre-defined compsets with <strong>query_config</strong><a class="headerlink" href="#discovering-available-pre-defined-compsets-with-query-config" title="Link to this heading"></a></h2>
+<p>Your CIME-driven model likely has many compset and gridset aliases defined for cases that are widely used by the
+model developers.</p>
 <p>Use the utility <a class="reference external" href="../Tools_user/query_config.html">query_config</a>  to see which out-of-the-box compsets, components, grids and machines are available for your model.</p>
-<p>If CIME is downloaded in standalone mode, only standalone CIME compsets can be queried.</p>
-<p>If CIME is part of a CIME-driven model, <a class="reference external" href="../Tools_user/query_config.html">query_config</a> will allow you to query all prognostic component compsets.</p>
 <p>To see lists of available compsets, components, grids and machines, look at the <strong>help</strong> text:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="o">&gt;</span> <span class="n">query_config</span> <span class="o">--</span><span class="n">help</span>
 </pre></div>
@@ -285,7 +348,7 @@ <h2><span class="section-number">1.5. </span>Discovering available cases with <s
            </div>
           </div>
           <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
-        <a href="index.html" class="btn btn-neutral float-left" title="Case Control System Part 1: Basic Usage" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
+        <a href="index.html" class="btn btn-neutral float-left" title="Using the Case Control System" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
         <a href="create-a-case.html" class="btn btn-neutral float-right" title="2. Creating a Case" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
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diff --git a/versions/master/html/users_guide/machine.html b/versions/master/html/users_guide/machine.html
index b112320fc4b..20adc3a4e9a 100644
--- a/versions/master/html/users_guide/machine.html
+++ b/versions/master/html/users_guide/machine.html
@@ -50,8 +50,8 @@
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
               <ul class="current">
 <li class="toctree-l1"><a class="reference internal" href="../what_cime/index.html">What is CIME?</a></li>
-<li class="toctree-l1"><a class="reference internal" href="index.html">Case Control System Part 1: Basic Usage</a></li>
-<li class="toctree-l1 current"><a class="reference internal" href="index.html#case-control-system-part-2-configuration-porting-testing-and-use-cases">Case Control System Part 2: Configuration, Porting, Testing and Use Cases</a><ul class="current">
+<li class="toctree-l1"><a class="reference internal" href="index.html">Using the Case Control System</a></li>
+<li class="toctree-l1 current"><a class="reference internal" href="index.html#configuring-the-case-control-system">Configuring the Case Control System</a><ul class="current">
 <li class="toctree-l2"><a class="reference internal" href="cime-internals.html">1. Main Configuration File</a></li>
 <li class="toctree-l2"><a class="reference internal" href="compsets.html">2. Component sets</a></li>
 <li class="toctree-l2"><a class="reference internal" href="grids.html">3. Model grids</a></li>
@@ -65,12 +65,10 @@
 </li>
 <li class="toctree-l2"><a class="reference internal" href="pes-threads.html">5. Controlling processors and threads</a></li>
 <li class="toctree-l2"><a class="reference internal" href="porting-cime.html">6. Porting and validating CIME on a new platform</a></li>
-<li class="toctree-l2"><a class="reference internal" href="timers.html">7. Timers and timing</a></li>
-<li class="toctree-l2"><a class="reference internal" href="testing.html">8. Testing</a></li>
-<li class="toctree-l2"><a class="reference internal" href="unit_testing.html">9. Fortran Unit Testing</a></li>
-<li class="toctree-l2"><a class="reference internal" href="multi-instance.html">10. Multi-instance component functionality</a></li>
-<li class="toctree-l2"><a class="reference internal" href="workflows.html">11. Workflows</a></li>
-<li class="toctree-l2"><a class="reference internal" href="cime-dir.html">12. Directory content</a></li>
+<li class="toctree-l2"><a class="reference internal" href="unit_testing.html">7. Fortran Unit Testing</a></li>
+<li class="toctree-l2"><a class="reference internal" href="multi-instance.html">8. Multi-instance component functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="workflows.html">9. Workflows</a></li>
+<li class="toctree-l2"><a class="reference internal" href="cime-dir.html">10. Directory content</a></li>
 <li class="toctree-l2"><a class="reference internal" href="index.html#indices-and-tables">Indices and tables</a></li>
 </ul>
 </li>
@@ -99,7 +97,7 @@
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
       <li><a href="../index.html" class="icon icon-home" aria-label="Home"></a></li>
-          <li class="breadcrumb-item"><a href="index.html">Case Control System Part 1: Basic Usage</a></li>
+          <li class="breadcrumb-item"><a href="index.html">Using the Case Control System</a></li>
       <li class="breadcrumb-item active"><span class="section-number">4. </span>Defining the machine</li>
       <li class="wy-breadcrumbs-aside">
             <a href="../_sources/users_guide/machine.rst.txt" rel="nofollow"> View page source</a>
diff --git a/versions/master/html/users_guide/multi-instance.html b/versions/master/html/users_guide/multi-instance.html
index d3779c8fdd8..797d2b3e871 100644
--- a/versions/master/html/users_guide/multi-instance.html
+++ b/versions/master/html/users_guide/multi-instance.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>10. Multi-instance component functionality &mdash; CIME master documentation</title>
+  <title>8. Multi-instance component functionality &mdash; CIME master documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../_static/custom.css" />
@@ -22,8 +22,8 @@
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
-    <link rel="next" title="11. Workflows" href="workflows.html" />
-    <link rel="prev" title="9. Fortran Unit Testing" href="unit_testing.html" /> 
+    <link rel="next" title="9. Workflows" href="workflows.html" />
+    <link rel="prev" title="7. Fortran Unit Testing" href="unit_testing.html" /> 
 </head>
 
 <body class="wy-body-for-nav"> 
@@ -50,20 +50,18 @@
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               <ul class="current">
 <li class="toctree-l1"><a class="reference internal" href="../what_cime/index.html">What is CIME?</a></li>
-<li class="toctree-l1"><a class="reference internal" href="index.html">Case Control System Part 1: Basic Usage</a></li>
-<li class="toctree-l1 current"><a class="reference internal" href="index.html#case-control-system-part-2-configuration-porting-testing-and-use-cases">Case Control System Part 2: Configuration, Porting, Testing and Use Cases</a><ul class="current">
+<li class="toctree-l1"><a class="reference internal" href="index.html">Using the Case Control System</a></li>
+<li class="toctree-l1 current"><a class="reference internal" href="index.html#configuring-the-case-control-system">Configuring the Case Control System</a><ul class="current">
 <li class="toctree-l2"><a class="reference internal" href="cime-internals.html">1. Main Configuration File</a></li>
 <li class="toctree-l2"><a class="reference internal" href="compsets.html">2. Component sets</a></li>
 <li class="toctree-l2"><a class="reference internal" href="grids.html">3. Model grids</a></li>
 <li class="toctree-l2"><a class="reference internal" href="machine.html">4. Defining the machine</a></li>
 <li class="toctree-l2"><a class="reference internal" href="pes-threads.html">5. Controlling processors and threads</a></li>
 <li class="toctree-l2"><a class="reference internal" href="porting-cime.html">6. Porting and validating CIME on a new platform</a></li>
-<li class="toctree-l2"><a class="reference internal" href="timers.html">7. Timers and timing</a></li>
-<li class="toctree-l2"><a class="reference internal" href="testing.html">8. Testing</a></li>
-<li class="toctree-l2"><a class="reference internal" href="unit_testing.html">9. Fortran Unit Testing</a></li>
-<li class="toctree-l2 current"><a class="current reference internal" href="#">10. Multi-instance component functionality</a></li>
-<li class="toctree-l2"><a class="reference internal" href="workflows.html">11. Workflows</a></li>
-<li class="toctree-l2"><a class="reference internal" href="cime-dir.html">12. Directory content</a></li>
+<li class="toctree-l2"><a class="reference internal" href="unit_testing.html">7. Fortran Unit Testing</a></li>
+<li class="toctree-l2 current"><a class="current reference internal" href="#">8. Multi-instance component functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="workflows.html">9. Workflows</a></li>
+<li class="toctree-l2"><a class="reference internal" href="cime-dir.html">10. Directory content</a></li>
 <li class="toctree-l2"><a class="reference internal" href="index.html#indices-and-tables">Indices and tables</a></li>
 </ul>
 </li>
@@ -92,8 +90,8 @@
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
       <li><a href="../index.html" class="icon icon-home" aria-label="Home"></a></li>
-          <li class="breadcrumb-item"><a href="index.html">Case Control System Part 1: Basic Usage</a></li>
-      <li class="breadcrumb-item active"><span class="section-number">10. </span>Multi-instance component functionality</li>
+          <li class="breadcrumb-item"><a href="index.html">Using the Case Control System</a></li>
+      <li class="breadcrumb-item active"><span class="section-number">8. </span>Multi-instance component functionality</li>
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             <a href="../_sources/users_guide/multi-instance.rst.txt" rel="nofollow"> View page source</a>
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@@ -104,7 +102,7 @@
            <div itemprop="articleBody">
              
   <section id="multi-instance-component-functionality">
-<span id="multi-instance"></span><h1><span class="section-number">10. </span>Multi-instance component functionality<a class="headerlink" href="#multi-instance-component-functionality" title="Link to this heading"></a></h1>
+<span id="multi-instance"></span><h1><span class="section-number">8. </span>Multi-instance component functionality<a class="headerlink" href="#multi-instance-component-functionality" title="Link to this heading"></a></h1>
 <p>The CIME coupling infrastructure is capable of running multiple
 component instances (ensembles) under one model executable.  There are
 two modes of ensemble capability, single driver in which all component
@@ -197,8 +195,8 @@
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           </div>
           <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
-        <a href="unit_testing.html" class="btn btn-neutral float-left" title="9. Fortran Unit Testing" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
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+        <a href="unit_testing.html" class="btn btn-neutral float-left" title="7. Fortran Unit Testing" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
+        <a href="workflows.html" class="btn btn-neutral float-right" title="9. Workflows" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
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diff --git a/versions/master/html/users_guide/pes-threads.html b/versions/master/html/users_guide/pes-threads.html
index 3c691ef9e4e..65e7ea328ce 100644
--- a/versions/master/html/users_guide/pes-threads.html
+++ b/versions/master/html/users_guide/pes-threads.html
@@ -50,8 +50,8 @@
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
               <ul class="current">
 <li class="toctree-l1"><a class="reference internal" href="../what_cime/index.html">What is CIME?</a></li>
-<li class="toctree-l1"><a class="reference internal" href="index.html">Case Control System Part 1: Basic Usage</a></li>
-<li class="toctree-l1 current"><a class="reference internal" href="index.html#case-control-system-part-2-configuration-porting-testing-and-use-cases">Case Control System Part 2: Configuration, Porting, Testing and Use Cases</a><ul class="current">
+<li class="toctree-l1"><a class="reference internal" href="index.html">Using the Case Control System</a></li>
+<li class="toctree-l1 current"><a class="reference internal" href="index.html#configuring-the-case-control-system">Configuring the Case Control System</a><ul class="current">
 <li class="toctree-l2"><a class="reference internal" href="cime-internals.html">1. Main Configuration File</a></li>
 <li class="toctree-l2"><a class="reference internal" href="compsets.html">2. Component sets</a></li>
 <li class="toctree-l2"><a class="reference internal" href="grids.html">3. Model grids</a></li>
@@ -64,12 +64,10 @@
 </ul>
 </li>
 <li class="toctree-l2"><a class="reference internal" href="porting-cime.html">6. Porting and validating CIME on a new platform</a></li>
-<li class="toctree-l2"><a class="reference internal" href="timers.html">7. Timers and timing</a></li>
-<li class="toctree-l2"><a class="reference internal" href="testing.html">8. Testing</a></li>
-<li class="toctree-l2"><a class="reference internal" href="unit_testing.html">9. Fortran Unit Testing</a></li>
-<li class="toctree-l2"><a class="reference internal" href="multi-instance.html">10. Multi-instance component functionality</a></li>
-<li class="toctree-l2"><a class="reference internal" href="workflows.html">11. Workflows</a></li>
-<li class="toctree-l2"><a class="reference internal" href="cime-dir.html">12. Directory content</a></li>
+<li class="toctree-l2"><a class="reference internal" href="unit_testing.html">7. Fortran Unit Testing</a></li>
+<li class="toctree-l2"><a class="reference internal" href="multi-instance.html">8. Multi-instance component functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="workflows.html">9. Workflows</a></li>
+<li class="toctree-l2"><a class="reference internal" href="cime-dir.html">10. Directory content</a></li>
 <li class="toctree-l2"><a class="reference internal" href="index.html#indices-and-tables">Indices and tables</a></li>
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@@ -98,7 +96,7 @@
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+          <li class="breadcrumb-item"><a href="index.html">Using the Case Control System</a></li>
       <li class="breadcrumb-item active"><span class="section-number">5. </span>Controlling processors and threads</li>
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diff --git a/versions/master/html/users_guide/porting-cime.html b/versions/master/html/users_guide/porting-cime.html
index bb058f83ec1..df3e115af38 100644
--- a/versions/master/html/users_guide/porting-cime.html
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 <li class="toctree-l1"><a class="reference internal" href="../what_cime/index.html">What is CIME?</a></li>
-<li class="toctree-l1"><a class="reference internal" href="index.html">Case Control System Part 1: Basic Usage</a></li>
-<li class="toctree-l1 current"><a class="reference internal" href="index.html#case-control-system-part-2-configuration-porting-testing-and-use-cases">Case Control System Part 2: Configuration, Porting, Testing and Use Cases</a><ul class="current">
+<li class="toctree-l1"><a class="reference internal" href="index.html">Using the Case Control System</a></li>
+<li class="toctree-l1 current"><a class="reference internal" href="index.html#configuring-the-case-control-system">Configuring the Case Control System</a><ul class="current">
 <li class="toctree-l2"><a class="reference internal" href="cime-internals.html">1. Main Configuration File</a></li>
 <li class="toctree-l2"><a class="reference internal" href="compsets.html">2. Component sets</a></li>
 <li class="toctree-l2"><a class="reference internal" href="grids.html">3. Model grids</a></li>
@@ -66,12 +66,10 @@
 <li class="toctree-l3"><a class="reference internal" href="#performance-tuning-of-a-cesm-port">6.6. Performance tuning of a CESM port</a></li>
 </ul>
 </li>
-<li class="toctree-l2"><a class="reference internal" href="timers.html">7. Timers and timing</a></li>
-<li class="toctree-l2"><a class="reference internal" href="testing.html">8. Testing</a></li>
-<li class="toctree-l2"><a class="reference internal" href="unit_testing.html">9. Fortran Unit Testing</a></li>
-<li class="toctree-l2"><a class="reference internal" href="multi-instance.html">10. Multi-instance component functionality</a></li>
-<li class="toctree-l2"><a class="reference internal" href="workflows.html">11. Workflows</a></li>
-<li class="toctree-l2"><a class="reference internal" href="cime-dir.html">12. Directory content</a></li>
+<li class="toctree-l2"><a class="reference internal" href="unit_testing.html">7. Fortran Unit Testing</a></li>
+<li class="toctree-l2"><a class="reference internal" href="multi-instance.html">8. Multi-instance component functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="workflows.html">9. Workflows</a></li>
+<li class="toctree-l2"><a class="reference internal" href="cime-dir.html">10. Directory content</a></li>
 <li class="toctree-l2"><a class="reference internal" href="index.html#indices-and-tables">Indices and tables</a></li>
 </ul>
 </li>
@@ -100,7 +98,7 @@
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
       <li><a href="../index.html" class="icon icon-home" aria-label="Home"></a></li>
-          <li class="breadcrumb-item"><a href="index.html">Case Control System Part 1: Basic Usage</a></li>
+          <li class="breadcrumb-item"><a href="index.html">Using the Case Control System</a></li>
       <li class="breadcrumb-item active"><span class="section-number">6. </span>Porting and validating CIME on a new platform</li>
       <li class="wy-breadcrumbs-aside">
             <a href="../_sources/users_guide/porting-cime.rst.txt" rel="nofollow"> View page source</a>
@@ -287,7 +285,7 @@ <h2><span class="section-number">6.6. </span>Performance tuning of a CESM port<a
           </div>
           <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
         <a href="pes-threads.html" class="btn btn-neutral float-left" title="5. Controlling processors and threads" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
-        <a href="timers.html" class="btn btn-neutral float-right" title="7. Timers and timing" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
+        <a href="unit_testing.html" class="btn btn-neutral float-right" title="7. Fortran Unit Testing" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
     </div>
 
   <hr/>
diff --git a/versions/master/html/users_guide/running-a-case.html b/versions/master/html/users_guide/running-a-case.html
index 5c28eb6dfc3..d2f0c0e7c4b 100644
--- a/versions/master/html/users_guide/running-a-case.html
+++ b/versions/master/html/users_guide/running-a-case.html
@@ -50,7 +50,7 @@
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
               <ul class="current">
 <li class="toctree-l1"><a class="reference internal" href="../what_cime/index.html">What is CIME?</a></li>
-<li class="toctree-l1 current"><a class="reference internal" href="index.html">Case Control System Part 1: Basic Usage</a><ul class="current">
+<li class="toctree-l1 current"><a class="reference internal" href="index.html">Using the Case Control System</a><ul class="current">
 <li class="toctree-l2"><a class="reference internal" href="introduction-and-overview.html">1. Introduction</a></li>
 <li class="toctree-l2"><a class="reference internal" href="create-a-case.html">2. Creating a Case</a></li>
 <li class="toctree-l2"><a class="reference internal" href="setting-up-a-case.html">3. Setting up a Case</a></li>
@@ -93,10 +93,11 @@
 <li class="toctree-l2"><a class="reference internal" href="cime-change-namelist.html">7. Customizing your input variables</a></li>
 <li class="toctree-l2"><a class="reference internal" href="cime-config.html">8. CIME user config directory</a></li>
 <li class="toctree-l2"><a class="reference internal" href="cime-customize.html">9. CIME config and hooks</a></li>
-<li class="toctree-l2"><a class="reference internal" href="troubleshooting.html">10. Troubleshooting</a></li>
+<li class="toctree-l2"><a class="reference internal" href="testing.html">10. Testing</a></li>
+<li class="toctree-l2"><a class="reference internal" href="troubleshooting.html">11. Troubleshooting</a></li>
 </ul>
 </li>
-<li class="toctree-l1"><a class="reference internal" href="index.html#case-control-system-part-2-configuration-porting-testing-and-use-cases">Case Control System Part 2: Configuration, Porting, Testing and Use Cases</a></li>
+<li class="toctree-l1"><a class="reference internal" href="index.html#configuring-the-case-control-system">Configuring the Case Control System</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../build_cpl/index.html">Building a Coupled Model with CIME</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../misc_tools/index.html">Miscellaneous Tools</a></li>
 </ul>
@@ -122,7 +123,7 @@
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
       <li><a href="../index.html" class="icon icon-home" aria-label="Home"></a></li>
-          <li class="breadcrumb-item"><a href="index.html">Case Control System Part 1: Basic Usage</a></li>
+          <li class="breadcrumb-item"><a href="index.html">Using the Case Control System</a></li>
       <li class="breadcrumb-item active"><span class="section-number">5. </span>Running a Case</li>
       <li class="wy-breadcrumbs-aside">
             <a href="../_sources/users_guide/running-a-case.rst.txt" rel="nofollow"> View page source</a>
diff --git a/versions/master/html/users_guide/setting-up-a-case.html b/versions/master/html/users_guide/setting-up-a-case.html
index ab9ea17d2ec..e8ce2862002 100644
--- a/versions/master/html/users_guide/setting-up-a-case.html
+++ b/versions/master/html/users_guide/setting-up-a-case.html
@@ -50,7 +50,7 @@
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
               <ul class="current">
 <li class="toctree-l1"><a class="reference internal" href="../what_cime/index.html">What is CIME?</a></li>
-<li class="toctree-l1 current"><a class="reference internal" href="index.html">Case Control System Part 1: Basic Usage</a><ul class="current">
+<li class="toctree-l1 current"><a class="reference internal" href="index.html">Using the Case Control System</a><ul class="current">
 <li class="toctree-l2"><a class="reference internal" href="introduction-and-overview.html">1. Introduction</a></li>
 <li class="toctree-l2"><a class="reference internal" href="create-a-case.html">2. Creating a Case</a></li>
 <li class="toctree-l2 current"><a class="current reference internal" href="#">3. Setting up a Case</a><ul>
@@ -63,10 +63,11 @@
 <li class="toctree-l2"><a class="reference internal" href="cime-change-namelist.html">7. Customizing your input variables</a></li>
 <li class="toctree-l2"><a class="reference internal" href="cime-config.html">8. CIME user config directory</a></li>
 <li class="toctree-l2"><a class="reference internal" href="cime-customize.html">9. CIME config and hooks</a></li>
-<li class="toctree-l2"><a class="reference internal" href="troubleshooting.html">10. Troubleshooting</a></li>
+<li class="toctree-l2"><a class="reference internal" href="testing.html">10. Testing</a></li>
+<li class="toctree-l2"><a class="reference internal" href="troubleshooting.html">11. Troubleshooting</a></li>
 </ul>
 </li>
-<li class="toctree-l1"><a class="reference internal" href="index.html#case-control-system-part-2-configuration-porting-testing-and-use-cases">Case Control System Part 2: Configuration, Porting, Testing and Use Cases</a></li>
+<li class="toctree-l1"><a class="reference internal" href="index.html#configuring-the-case-control-system">Configuring the Case Control System</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../build_cpl/index.html">Building a Coupled Model with CIME</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../misc_tools/index.html">Miscellaneous Tools</a></li>
 </ul>
@@ -92,7 +93,7 @@
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
       <li><a href="../index.html" class="icon icon-home" aria-label="Home"></a></li>
-          <li class="breadcrumb-item"><a href="index.html">Case Control System Part 1: Basic Usage</a></li>
+          <li class="breadcrumb-item"><a href="index.html">Using the Case Control System</a></li>
       <li class="breadcrumb-item active"><span class="section-number">3. </span>Setting up a Case</li>
       <li class="wy-breadcrumbs-aside">
             <a href="../_sources/users_guide/setting-up-a-case.rst.txt" rel="nofollow"> View page source</a>
@@ -116,48 +117,63 @@ <h2><span class="section-number">3.1. </span>Calling <strong>case.setup</strong>
 <div><table class="docutils align-default">
 <tbody>
 <tr class="row-odd"><td><p>.case.run</p></td>
-<td><p>A (hidden) file with the commands that will be used to run the model (such as “mpirun”) and any batch directives needed.
-The directive values are generated using the contents
-of <strong>env_mach_pes.xml</strong>. Running <a class="reference external" href="../Tools_user/case.setup.html">case.setup –clean</a>  will remove this file.
-This file should not be edited directly and instead controlled through XML variables in <strong>env_batch.xml</strong>. It should also
-<em>never</em> be run directly.</p></td>
+<td><p>A (hidden) file with the commands that will be used to run the model (such as “mpirun”)</p>
+<p>and any batch directives needed.  The directive values are generated using the contents</p>
+<p>of <strong>env_mach_pes.xml</strong>. Running <a class="reference external" href="../Tools_user/case.setup.html">case.setup –clean</a></p>
+<p>will remove this file.  This file should not be edited directly and instead controlled</p>
+<p>through XML variables in <strong>env_batch.xml</strong>. It should also <em>never</em> be run directly.</p>
+</td>
+</tr>
+<tr class="row-even"><td><p>CaseStatus</p></td>
+<td><p>File containing a list of operations done in the current case.</p></td>
 </tr>
-<tr class="row-even"><td><p>Macros.make</p></td>
-<td><p>File containing machine-specific makefile directives for your target platform/compiler.
-This file is created if it does not already exist.</p>
-<p>The user can modify the file to change certain aspects of the build, such as compiler flags.
-Running <a class="reference external" href="../Tools_user/case.setup.html">case.setup –clean</a>  will not remove the file once it has been created.
-However. if you remove or rename the Macros.make file, running <a class="reference external" href="../Tools_user/case.setup.html">case.setup</a> recreates it.</p>
+<tr class="row-odd"><td><p>case.st_archive</p></td>
+<td><p>Script to perform short term archiving to disk for your case</p>
+<p>output. Note that this script is run automatically by the normal CIME workflow.</p>
 </td>
 </tr>
-<tr class="row-odd"><td><p>user_nl_xxx[_NNNN]</p></td>
+<tr class="row-even"><td><p>Depends.*</p></td>
+<td><p>Lists of source code files that needs special build options.</p></td>
+</tr>
+<tr class="row-odd"><td><p>Macros.cmake</p></td>
+<td><p>File containing machine-specific makefile directives for your target platform/compiler.</p>
+<p>This file is created if it does not already exist.</p>
+<p>The user can modify the file to change certain aspects of the build, such as compiler flags.</p>
+<p>Running <a class="reference external" href="../Tools_user/case.setup.html">case.setup –clean</a>  will not remove the file once it has been created.
+However. if you remove or rename the Macros.make file, running</p>
+<p><a class="reference external" href="../Tools_user/case.setup.html">case.setup</a> recreates it.</p>
+</td>
+</tr>
+<tr class="row-even"><td><p>user_nl_xxx[_NNNN]</p></td>
 <td><p>Files where all user modifications to component namelists are made.</p>
-<p><strong>xxx</strong> is any one of the set of components targeted for the case.
-For example, for a full active CESM compset, <strong>xxx</strong> is cam, clm or rtm, and so on.</p>
+<p><strong>xxx</strong> is any one of the set of components targeted for the case.</p>
+<p>For example, for a full active CESM compset, <strong>xxx</strong> is cam, clm or rtm, and so on.</p>
 <p>NNNN goes from 0001 to the number of instances of that component.
 (See <a class="reference internal" href="multi-instance.html#multi-instance"><span class="std std-ref">multiple instances</span></a>)</p>
 <p>For a case with 1 instance of each component (default), NNNN will not appear
 in the user_nl file names.</p>
 <p>A user_nl file of a given name is created only once.</p>
 <p>Calling <a class="reference external" href="../Tools_user/case.setup.html">case.setup –clean</a> will <em>not remove</em> any user_nl files.</p>
-<p>Changing the number of instances in the <strong>env_mach_pes.xml</strong> file will cause only
-new user_nl files to be added to <code class="docutils literal notranslate"><span class="pre">$CASEROOT</span></code>.</p>
+<p>Changing the number of instances in the <strong>env_mach_pes.xml</strong> file will cause only</p>
+<p>new user_nl files to be added to <code class="docutils literal notranslate"><span class="pre">$CASEROOT</span></code>.</p>
 </td>
 </tr>
-<tr class="row-even"><td><p>CaseDocs/</p></td>
+<tr class="row-odd"><td><p>CaseDocs/</p></td>
 <td><p>Directory that contains all the component namelists for the run.</p>
-<p>This is for reference only and files in this directory SHOULD NOT BE EDITED since they will
-be overwritten at build time and runtime.</p>
+<p>This is for reference only and files in this directory SHOULD NOT BE EDITED since they will</p>
+<p>be overwritten at build time and runtime.</p>
 </td>
 </tr>
-<tr class="row-odd"><td><p>.env_mach_specific.*</p></td>
-<td><p>Files summarizing the <strong>module load</strong> commands and environment variables that are set when
-the scripts in <code class="docutils literal notranslate"><span class="pre">$CASEROOT</span></code> are called. These files are not used by the case but can be
-useful for debugging <strong>module load</strong> and environment settings.</p></td>
+<tr class="row-even"><td><p>.env_mach_specific.*</p></td>
+<td><p>Files summarizing the <strong>module load</strong> commands and environment variables that are set when</p>
+<p>the scripts in <code class="docutils literal notranslate"><span class="pre">$CASEROOT</span></code> are called. These files are not used by the case but can be</p>
+<p>useful for debugging <strong>module load</strong> and environment settings.</p>
+</td>
 </tr>
-<tr class="row-even"><td><p>software_environment.txt</p></td>
-<td><p>This file records some aspects of the computing system on which the case is built,
-such as the shell environment.</p></td>
+<tr class="row-odd"><td><p>software_environment.txt</p></td>
+<td><p>This file records some aspects of the computing system on which the case is built,</p>
+<p>such as the shell environment.</p>
+</td>
 </tr>
 </tbody>
 </table>
diff --git a/versions/master/html/users_guide/testing.html b/versions/master/html/users_guide/testing.html
index 01176d35c2f..56d5487ea33 100644
--- a/versions/master/html/users_guide/testing.html
+++ b/versions/master/html/users_guide/testing.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>8. Testing &mdash; CIME master documentation</title>
+  <title>10. Testing &mdash; CIME master documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../_static/custom.css" />
@@ -22,8 +22,8 @@
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
-    <link rel="next" title="9. Fortran Unit Testing" href="unit_testing.html" />
-    <link rel="prev" title="7. Timers and timing" href="timers.html" /> 
+    <link rel="next" title="11. Troubleshooting" href="troubleshooting.html" />
+    <link rel="prev" title="9. CIME config and hooks" href="cime-customize.html" /> 
 </head>
 
 <body class="wy-body-for-nav"> 
@@ -50,37 +50,35 @@
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
               <ul class="current">
 <li class="toctree-l1"><a class="reference internal" href="../what_cime/index.html">What is CIME?</a></li>
-<li class="toctree-l1"><a class="reference internal" href="index.html">Case Control System Part 1: Basic Usage</a></li>
-<li class="toctree-l1 current"><a class="reference internal" href="index.html#case-control-system-part-2-configuration-porting-testing-and-use-cases">Case Control System Part 2: Configuration, Porting, Testing and Use Cases</a><ul class="current">
-<li class="toctree-l2"><a class="reference internal" href="cime-internals.html">1. Main Configuration File</a></li>
-<li class="toctree-l2"><a class="reference internal" href="compsets.html">2. Component sets</a></li>
-<li class="toctree-l2"><a class="reference internal" href="grids.html">3. Model grids</a></li>
-<li class="toctree-l2"><a class="reference internal" href="machine.html">4. Defining the machine</a></li>
-<li class="toctree-l2"><a class="reference internal" href="pes-threads.html">5. Controlling processors and threads</a></li>
-<li class="toctree-l2"><a class="reference internal" href="porting-cime.html">6. Porting and validating CIME on a new platform</a></li>
-<li class="toctree-l2"><a class="reference internal" href="timers.html">7. Timers and timing</a></li>
-<li class="toctree-l2 current"><a class="current reference internal" href="#">8. Testing</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="#testname-syntax">8.1. Testname syntax</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#query-testlists">8.2. Query_testlists</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#using-create-test-e3sm">8.3. Using <strong>create_test</strong> (E3SM)</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#baselines">8.4. Baselines</a><ul>
-<li class="toctree-l4"><a class="reference internal" href="#creating-a-baseline">8.4.1. Creating a baseline</a></li>
-<li class="toctree-l4"><a class="reference internal" href="#comparing-a-baseline">8.4.2. Comparing a baseline</a></li>
-<li class="toctree-l4"><a class="reference internal" href="#managing-baselines">8.4.3. Managing baselines</a></li>
-<li class="toctree-l4"><a class="reference internal" href="#performance-baselines">8.4.4. Performance baselines</a></li>
+<li class="toctree-l1 current"><a class="reference internal" href="index.html">Using the Case Control System</a><ul class="current">
+<li class="toctree-l2"><a class="reference internal" href="introduction-and-overview.html">1. Introduction</a></li>
+<li class="toctree-l2"><a class="reference internal" href="create-a-case.html">2. Creating a Case</a></li>
+<li class="toctree-l2"><a class="reference internal" href="setting-up-a-case.html">3. Setting up a Case</a></li>
+<li class="toctree-l2"><a class="reference internal" href="building-a-case.html">4. Building a Case</a></li>
+<li class="toctree-l2"><a class="reference internal" href="running-a-case.html">5. Running a Case</a></li>
+<li class="toctree-l2"><a class="reference internal" href="cloning-a-case.html">6. Cloning a Case</a></li>
+<li class="toctree-l2"><a class="reference internal" href="cime-change-namelist.html">7. Customizing your input variables</a></li>
+<li class="toctree-l2"><a class="reference internal" href="cime-config.html">8. CIME user config directory</a></li>
+<li class="toctree-l2"><a class="reference internal" href="cime-customize.html">9. CIME config and hooks</a></li>
+<li class="toctree-l2 current"><a class="current reference internal" href="#">10. Testing</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#testname-syntax">10.1. Testname syntax</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#query-testlists">10.2. Query_testlists</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#using-create-test-e3sm">10.3. Using <strong>create_test</strong> (E3SM)</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#baselines">10.4. Baselines</a><ul>
+<li class="toctree-l4"><a class="reference internal" href="#creating-a-baseline">10.4.1. Creating a baseline</a></li>
+<li class="toctree-l4"><a class="reference internal" href="#comparing-a-baseline">10.4.2. Comparing a baseline</a></li>
+<li class="toctree-l4"><a class="reference internal" href="#managing-baselines">10.4.3. Managing baselines</a></li>
+<li class="toctree-l4"><a class="reference internal" href="#performance-baselines">10.4.4. Performance baselines</a></li>
 </ul>
 </li>
-<li class="toctree-l3"><a class="reference internal" href="#adding-tests">8.5. Adding tests</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#cime-developer-s-guide">8.6. CIME Developer’s guide</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#adding-tests">10.5. Adding tests</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#cime-developer-s-guide">10.6. CIME Developer’s guide</a></li>
 </ul>
 </li>
-<li class="toctree-l2"><a class="reference internal" href="unit_testing.html">9. Fortran Unit Testing</a></li>
-<li class="toctree-l2"><a class="reference internal" href="multi-instance.html">10. Multi-instance component functionality</a></li>
-<li class="toctree-l2"><a class="reference internal" href="workflows.html">11. Workflows</a></li>
-<li class="toctree-l2"><a class="reference internal" href="cime-dir.html">12. Directory content</a></li>
-<li class="toctree-l2"><a class="reference internal" href="index.html#indices-and-tables">Indices and tables</a></li>
+<li class="toctree-l2"><a class="reference internal" href="troubleshooting.html">11. Troubleshooting</a></li>
 </ul>
 </li>
+<li class="toctree-l1"><a class="reference internal" href="index.html#configuring-the-case-control-system">Configuring the Case Control System</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../build_cpl/index.html">Building a Coupled Model with CIME</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../misc_tools/index.html">Miscellaneous Tools</a></li>
 </ul>
@@ -106,8 +104,8 @@
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
       <li><a href="../index.html" class="icon icon-home" aria-label="Home"></a></li>
-          <li class="breadcrumb-item"><a href="index.html">Case Control System Part 1: Basic Usage</a></li>
-      <li class="breadcrumb-item active"><span class="section-number">8. </span>Testing</li>
+          <li class="breadcrumb-item"><a href="index.html">Using the Case Control System</a></li>
+      <li class="breadcrumb-item active"><span class="section-number">10. </span>Testing</li>
       <li class="wy-breadcrumbs-aside">
             <a href="../_sources/users_guide/testing.rst.txt" rel="nofollow"> View page source</a>
       </li>
@@ -118,7 +116,7 @@
            <div itemprop="articleBody">
              
   <section id="testing">
-<span id="id1"></span><h1><span class="section-number">8. </span>Testing<a class="headerlink" href="#testing" title="Link to this heading"></a></h1>
+<span id="id1"></span><h1><span class="section-number">10. </span>Testing<a class="headerlink" href="#testing" title="Link to this heading"></a></h1>
 <p><a class="reference external" href="../Tools_user/create_test.html">create_test</a>
 is the tool we use to test both CIME and CIME-driven models.
 It can be used as an easy way to run a single basic test or an entire suite of tests.
@@ -164,7 +162,7 @@
 </pre></div>
 </div>
 <section id="testname-syntax">
-<h2><span class="section-number">8.1. </span>Testname syntax<a class="headerlink" href="#testname-syntax" title="Link to this heading"></a></h2>
+<h2><span class="section-number">10.1. </span>Testname syntax<a class="headerlink" href="#testname-syntax" title="Link to this heading"></a></h2>
 <p id="test-naming">Tests must be named with the following forms, [ ]=optional:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">TESTTYPE</span><span class="p">[</span><span class="n">_MODIFIERS</span><span class="p">]</span><span class="o">.</span><span class="n">GRID</span><span class="o">.</span><span class="n">COMPSET</span><span class="p">[</span><span class="o">.</span><span class="n">MACHINE_COMPILER</span><span class="p">][</span><span class="o">.</span><span class="n">GROUP</span><span class="o">-</span><span class="n">TESTMODS</span><span class="p">]</span>
 </pre></div>
@@ -499,7 +497,7 @@ <h2><span class="section-number">8.1. </span>Testname syntax<a class="headerlink
 current status of all your tests.</p>
 </section>
 <section id="query-testlists">
-<h2><span class="section-number">8.2. </span>Query_testlists<a class="headerlink" href="#query-testlists" title="Link to this heading"></a></h2>
+<h2><span class="section-number">10.2. </span>Query_testlists<a class="headerlink" href="#query-testlists" title="Link to this heading"></a></h2>
 <p id="id5"><strong>$CIMEROOT/scripts/query_testlists</strong> gathers descriptions of the tests and testlists available
 for CESM, the components, and projects.</p>
 <p>The <code class="docutils literal notranslate"><span class="pre">--xml-{compiler,machine,category,testlist}</span></code> arguments can be used
@@ -513,7 +511,7 @@ <h2><span class="section-number">8.2. </span>Query_testlists<a class="headerlink
 such as queue, walltime, etc..</p>
 </section>
 <section id="using-create-test-e3sm">
-<h2><span class="section-number">8.3. </span>Using <strong>create_test</strong> (E3SM)<a class="headerlink" href="#using-create-test-e3sm" title="Link to this heading"></a></h2>
+<h2><span class="section-number">10.3. </span>Using <strong>create_test</strong> (E3SM)<a class="headerlink" href="#using-create-test-e3sm" title="Link to this heading"></a></h2>
 <p id="id6">Usage will differ slightly depending on if you’re using E3SM or CESM.</p>
 <p>Using examples to illustrate common use cases</p>
 <p>To run a test:</p>
@@ -593,24 +591,24 @@ <h2><span class="section-number">8.3. </span>Using <strong>create_test</strong>
 of the various test phases.</p>
 </section>
 <section id="baselines">
-<h2><span class="section-number">8.4. </span>Baselines<a class="headerlink" href="#baselines" title="Link to this heading"></a></h2>
+<h2><span class="section-number">10.4. </span>Baselines<a class="headerlink" href="#baselines" title="Link to this heading"></a></h2>
 <p id="id8">A big part of testing is managing your baselines (sometimes called gold results). We have provided tools to help the user do this without having to repeat full runs of test cases with <a class="reference external" href="../Tools_user/create_test.html">create_test</a> .</p>
 <section id="creating-a-baseline">
-<h3><span class="section-number">8.4.1. </span>Creating a baseline<a class="headerlink" href="#creating-a-baseline" title="Link to this heading"></a></h3>
+<h3><span class="section-number">10.4.1. </span>Creating a baseline<a class="headerlink" href="#creating-a-baseline" title="Link to this heading"></a></h3>
 <p id="id10">A baseline can be generated by passing <code class="docutils literal notranslate"><span class="pre">-g</span></code> to <a class="reference external" href="../Tools_user/create_test.html">create_test</a>. There are additional options to control generating baselines.:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="o">./</span><span class="n">scripts</span><span class="o">/</span><span class="n">create_test</span> <span class="o">-</span><span class="n">b</span> <span class="n">master</span> <span class="o">-</span><span class="n">g</span> <span class="n">SMS</span><span class="o">.</span><span class="n">ne30_f19_g16_rx1</span><span class="o">.</span><span class="n">A</span>
 </pre></div>
 </div>
 </section>
 <section id="comparing-a-baseline">
-<h3><span class="section-number">8.4.2. </span>Comparing a baseline<a class="headerlink" href="#comparing-a-baseline" title="Link to this heading"></a></h3>
+<h3><span class="section-number">10.4.2. </span>Comparing a baseline<a class="headerlink" href="#comparing-a-baseline" title="Link to this heading"></a></h3>
 <p id="id12">Comparing the output of a test to a baseline is achieved by passing <code class="docutils literal notranslate"><span class="pre">-c</span></code> to <a class="reference external" href="../Tools_user/create_test.html">create_test</a>.:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="o">./</span><span class="n">scripts</span><span class="o">/</span><span class="n">create_test</span> <span class="o">-</span><span class="n">b</span> <span class="n">master</span> <span class="o">-</span><span class="n">c</span> <span class="n">SMS</span><span class="o">.</span><span class="n">ne30_f19_g16_rx1</span><span class="o">.</span><span class="n">A</span>
 </pre></div>
 </div>
 </section>
 <section id="managing-baselines">
-<h3><span class="section-number">8.4.3. </span>Managing baselines<a class="headerlink" href="#managing-baselines" title="Link to this heading"></a></h3>
+<h3><span class="section-number">10.4.3. </span>Managing baselines<a class="headerlink" href="#managing-baselines" title="Link to this heading"></a></h3>
 <p id="id14">Once a baseline has been generated it can be managed using the <a class="reference external" href="../Tools_user/bless_test_results.html">bless_test_results</a> tool. The tool provides the ability to bless different features of the baseline. The currently supported features are namelist files, history files, and performance metrics. The performance metrics are separated into throughput and memory usage.</p>
 <p>The following command can be used to compare a test to a baseline and bless an update to the history file.:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="o">./</span><span class="n">CIME</span><span class="o">/</span><span class="n">Tools</span><span class="o">/</span><span class="n">bless_test_results</span> <span class="o">-</span><span class="n">b</span> <span class="n">master</span> <span class="o">--</span><span class="n">hist</span><span class="o">-</span><span class="n">only</span> <span class="n">SMS</span><span class="o">.</span><span class="n">ne30_f19_g16_rx1</span><span class="o">.</span><span class="n">A</span>
@@ -622,7 +620,7 @@ <h3><span class="section-number">8.4.3. </span>Managing baselines<a class="heade
 </div>
 </section>
 <section id="performance-baselines">
-<h3><span class="section-number">8.4.4. </span>Performance baselines<a class="headerlink" href="#performance-baselines" title="Link to this heading"></a></h3>
+<h3><span class="section-number">10.4.4. </span>Performance baselines<a class="headerlink" href="#performance-baselines" title="Link to this heading"></a></h3>
 <p id="id15">By default performance baselines are generated by parsing the coupler log and comparing the throughput in SYPD (Simulated Years Per Day) and the memory usage high water.</p>
 <p>This can be customized by creating a python module under <code class="docutils literal notranslate"><span class="pre">$DRIVER_ROOT/cime_config/customize</span></code>. There are four hooks that can be used to customize the generation and comparison.</p>
 <ul class="simple">
@@ -726,7 +724,7 @@ <h3><span class="section-number">8.4.4. </span>Performance baselines<a class="he
 </section>
 </section>
 <section id="adding-tests">
-<h2><span class="section-number">8.5. </span>Adding tests<a class="headerlink" href="#adding-tests" title="Link to this heading"></a></h2>
+<h2><span class="section-number">10.5. </span>Adding tests<a class="headerlink" href="#adding-tests" title="Link to this heading"></a></h2>
 <p id="id16">E3SM</p>
 <p>Open the config/e3sm/tests.py file, you’ll see a python dict at the top
 of the file called _TESTS, find the test category you want to
@@ -771,7 +769,7 @@ <h2><span class="section-number">8.5. </span>Adding tests<a class="headerlink" h
 If you want this test to be part of a suite, then it must be described in the relevant testlists_YYY.xml file.</p>
 </section>
 <section id="cime-developer-s-guide">
-<h2><span class="section-number">8.6. </span>CIME Developer’s guide<a class="headerlink" href="#cime-developer-s-guide" title="Link to this heading"></a></h2>
+<h2><span class="section-number">10.6. </span>CIME Developer’s guide<a class="headerlink" href="#cime-developer-s-guide" title="Link to this heading"></a></h2>
 <p id="id17">The CIME Developer’s guide can be found on the project’s GitHub <a class="reference external" href="https://github.com/ESMCI/cime/wiki/CIME-Developers-Guide">wiki</a>.</p>
 </section>
 </section>
@@ -780,8 +778,8 @@ <h2><span class="section-number">8.6. </span>CIME Developer’s guide<a class="h
            </div>
           </div>
           <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
-        <a href="timers.html" class="btn btn-neutral float-left" title="7. Timers and timing" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
-        <a href="unit_testing.html" class="btn btn-neutral float-right" title="9. Fortran Unit Testing" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
+        <a href="cime-customize.html" class="btn btn-neutral float-left" title="9. CIME config and hooks" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
+        <a href="troubleshooting.html" class="btn btn-neutral float-right" title="11. Troubleshooting" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
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   <hr/>
diff --git a/versions/master/html/users_guide/timers.html b/versions/master/html/users_guide/timers.html
index f91a17a9bf9..7bc0ac1c5e2 100644
--- a/versions/master/html/users_guide/timers.html
+++ b/versions/master/html/users_guide/timers.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>7. Timers and timing &mdash; CIME master documentation</title>
+  <title>Timers and timing &mdash; CIME master documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../_static/custom.css" />
@@ -21,9 +21,7 @@
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     <script src="../_static/js/theme.js"></script>
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-    <link rel="next" title="8. Testing" href="testing.html" />
-    <link rel="prev" title="6. Porting and validating CIME on a new platform" href="porting-cime.html" /> 
+    <link rel="search" title="Search" href="../search.html" /> 
 </head>
 
 <body class="wy-body-for-nav"> 
@@ -48,30 +46,10 @@
   </form>
 </div>
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
-              <ul class="current">
+              <ul>
 <li class="toctree-l1"><a class="reference internal" href="../what_cime/index.html">What is CIME?</a></li>
-<li class="toctree-l1"><a class="reference internal" href="index.html">Case Control System Part 1: Basic Usage</a></li>
-<li class="toctree-l1 current"><a class="reference internal" href="index.html#case-control-system-part-2-configuration-porting-testing-and-use-cases">Case Control System Part 2: Configuration, Porting, Testing and Use Cases</a><ul class="current">
-<li class="toctree-l2"><a class="reference internal" href="cime-internals.html">1. Main Configuration File</a></li>
-<li class="toctree-l2"><a class="reference internal" href="compsets.html">2. Component sets</a></li>
-<li class="toctree-l2"><a class="reference internal" href="grids.html">3. Model grids</a></li>
-<li class="toctree-l2"><a class="reference internal" href="machine.html">4. Defining the machine</a></li>
-<li class="toctree-l2"><a class="reference internal" href="pes-threads.html">5. Controlling processors and threads</a></li>
-<li class="toctree-l2"><a class="reference internal" href="porting-cime.html">6. Porting and validating CIME on a new platform</a></li>
-<li class="toctree-l2 current"><a class="current reference internal" href="#">7. Timers and timing</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="#model-timing-data">7.1. Model timing data</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#controlling-timers">7.2. Controlling timers</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#advice-on-setting-your-wallclock-time">7.3. Advice on setting your wallclock time</a></li>
-</ul>
-</li>
-<li class="toctree-l2"><a class="reference internal" href="testing.html">8. Testing</a></li>
-<li class="toctree-l2"><a class="reference internal" href="unit_testing.html">9. Fortran Unit Testing</a></li>
-<li class="toctree-l2"><a class="reference internal" href="multi-instance.html">10. Multi-instance component functionality</a></li>
-<li class="toctree-l2"><a class="reference internal" href="workflows.html">11. Workflows</a></li>
-<li class="toctree-l2"><a class="reference internal" href="cime-dir.html">12. Directory content</a></li>
-<li class="toctree-l2"><a class="reference internal" href="index.html#indices-and-tables">Indices and tables</a></li>
-</ul>
-</li>
+<li class="toctree-l1"><a class="reference internal" href="index.html">Using the Case Control System</a></li>
+<li class="toctree-l1"><a class="reference internal" href="index.html#configuring-the-case-control-system">Configuring the Case Control System</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../build_cpl/index.html">Building a Coupled Model with CIME</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../misc_tools/index.html">Miscellaneous Tools</a></li>
 </ul>
@@ -97,8 +75,7 @@
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
       <li><a href="../index.html" class="icon icon-home" aria-label="Home"></a></li>
-          <li class="breadcrumb-item"><a href="index.html">Case Control System Part 1: Basic Usage</a></li>
-      <li class="breadcrumb-item active"><span class="section-number">7. </span>Timers and timing</li>
+      <li class="breadcrumb-item active">Timers and timing</li>
       <li class="wy-breadcrumbs-aside">
             <a href="../_sources/users_guide/timers.rst.txt" rel="nofollow"> View page source</a>
       </li>
@@ -109,11 +86,11 @@
            <div itemprop="articleBody">
              
   <section id="timers-and-timing">
-<span id="timers"></span><h1><span class="section-number">7. </span>Timers and timing<a class="headerlink" href="#timers-and-timing" title="Link to this heading"></a></h1>
+<span id="timers"></span><h1>Timers and timing<a class="headerlink" href="#timers-and-timing" title="Link to this heading"></a></h1>
 <p>CIME includes a copy of the General Purpose Timing Library (GPTL) and timers are placed throughout the CIME driver.  CIME-driven models typically
 also have GPTL timers in their code and very detailed timing information can be obtained.</p>
 <section id="model-timing-data">
-<span id="id1"></span><h2><span class="section-number">7.1. </span>Model timing data<a class="headerlink" href="#model-timing-data" title="Link to this heading"></a></h2>
+<span id="id1"></span><h2>Model timing data<a class="headerlink" href="#model-timing-data" title="Link to this heading"></a></h2>
 <p>Every model run produces three types of timing output that you can examine:</p>
 <ol class="arabic">
 <li><p><strong>$CASEROOT/timing/$model_timing.$CASE.$datestamp</strong></p>
@@ -214,7 +191,7 @@
 <p>The xml variable <code class="docutils literal notranslate"><span class="pre">CHECK_TIMING</span></code>, if set to <code class="docutils literal notranslate"><span class="pre">TRUE</span></code> (the default) will produce the timing files in the <strong>$CASEROOT/timing</strong> directory.</p>
 </section>
 <section id="controlling-timers">
-<h2><span class="section-number">7.2. </span>Controlling timers<a class="headerlink" href="#controlling-timers" title="Link to this heading"></a></h2>
+<h2>Controlling timers<a class="headerlink" href="#controlling-timers" title="Link to this heading"></a></h2>
 <p>User customization of timers is done via the xml variables <code class="docutils literal notranslate"><span class="pre">TIMER_LEVEL</span></code> and <code class="docutils literal notranslate"><span class="pre">TIMER_DETAIL</span></code>.</p>
 <ul>
 <li><p><code class="docutils literal notranslate"><span class="pre">TIMER_LEVEL</span></code>:</p>
@@ -240,7 +217,7 @@ <h2><span class="section-number">7.2. </span>Controlling timers<a class="headerl
 </div>
 </section>
 <section id="advice-on-setting-your-wallclock-time">
-<h2><span class="section-number">7.3. </span>Advice on setting your wallclock time<a class="headerlink" href="#advice-on-setting-your-wallclock-time" title="Link to this heading"></a></h2>
+<h2>Advice on setting your wallclock time<a class="headerlink" href="#advice-on-setting-your-wallclock-time" title="Link to this heading"></a></h2>
 <dl>
 <dt>When you look at the <strong>$model_timing.$CASE.$datestamp</strong> file for “Model Throughput”, you will find output like this:</dt><dd><div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">Overall</span> <span class="n">Metrics</span><span class="p">:</span>
 <span class="n">Model</span> <span class="n">Cost</span><span class="p">:</span> <span class="mf">327.14</span> <span class="n">pe</span><span class="o">-</span><span class="n">hrs</span><span class="o">/</span><span class="n">simulated_year</span> <span class="p">(</span><span class="n">scale</span><span class="o">=</span> <span class="mf">0.50</span><span class="p">)</span>
@@ -273,10 +250,7 @@ <h2><span class="section-number">7.3. </span>Advice on setting your wallclock ti
 
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diff --git a/versions/master/html/users_guide/troubleshooting.html b/versions/master/html/users_guide/troubleshooting.html
index dc7e0449a5f..c72a5affc8f 100644
--- a/versions/master/html/users_guide/troubleshooting.html
+++ b/versions/master/html/users_guide/troubleshooting.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>10. Troubleshooting &mdash; CIME master documentation</title>
+  <title>11. Troubleshooting &mdash; CIME master documentation</title>
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+    <link rel="prev" title="10. Testing" href="testing.html" /> 
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-<li class="toctree-l1 current"><a class="reference internal" href="index.html">Case Control System Part 1: Basic Usage</a><ul class="current">
+<li class="toctree-l1 current"><a class="reference internal" href="index.html">Using the Case Control System</a><ul class="current">
 <li class="toctree-l2"><a class="reference internal" href="introduction-and-overview.html">1. Introduction</a></li>
 <li class="toctree-l2"><a class="reference internal" href="create-a-case.html">2. Creating a Case</a></li>
 <li class="toctree-l2"><a class="reference internal" href="setting-up-a-case.html">3. Setting up a Case</a></li>
@@ -60,16 +60,17 @@
 <li class="toctree-l2"><a class="reference internal" href="cime-change-namelist.html">7. Customizing your input variables</a></li>
 <li class="toctree-l2"><a class="reference internal" href="cime-config.html">8. CIME user config directory</a></li>
 <li class="toctree-l2"><a class="reference internal" href="cime-customize.html">9. CIME config and hooks</a></li>
-<li class="toctree-l2 current"><a class="current reference internal" href="#">10. Troubleshooting</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="#troubleshooting-case-creation">10.1. Troubleshooting case creation</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#troubleshooting-problems-in-cime-scripts">10.2. Troubleshooting problems in cime scripts</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#troubleshooting-job-submission">10.3. Troubleshooting job submission</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#troubleshooting-runtime-problems">10.4. Troubleshooting runtime problems</a></li>
+<li class="toctree-l2"><a class="reference internal" href="testing.html">10. Testing</a></li>
+<li class="toctree-l2 current"><a class="current reference internal" href="#">11. Troubleshooting</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#troubleshooting-case-creation">11.1. Troubleshooting case creation</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#troubleshooting-problems-in-cime-scripts">11.2. Troubleshooting problems in cime scripts</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#troubleshooting-job-submission">11.3. Troubleshooting job submission</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#troubleshooting-runtime-problems">11.4. Troubleshooting runtime problems</a></li>
 </ul>
 </li>
 </ul>
 </li>
-<li class="toctree-l1"><a class="reference internal" href="index.html#case-control-system-part-2-configuration-porting-testing-and-use-cases">Case Control System Part 2: Configuration, Porting, Testing and Use Cases</a></li>
+<li class="toctree-l1"><a class="reference internal" href="index.html#configuring-the-case-control-system">Configuring the Case Control System</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../build_cpl/index.html">Building a Coupled Model with CIME</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../misc_tools/index.html">Miscellaneous Tools</a></li>
 </ul>
@@ -95,8 +96,8 @@
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
       <li><a href="../index.html" class="icon icon-home" aria-label="Home"></a></li>
-          <li class="breadcrumb-item"><a href="index.html">Case Control System Part 1: Basic Usage</a></li>
-      <li class="breadcrumb-item active"><span class="section-number">10. </span>Troubleshooting</li>
+          <li class="breadcrumb-item"><a href="index.html">Using the Case Control System</a></li>
+      <li class="breadcrumb-item active"><span class="section-number">11. </span>Troubleshooting</li>
       <li class="wy-breadcrumbs-aside">
             <a href="../_sources/users_guide/troubleshooting.rst.txt" rel="nofollow"> View page source</a>
       </li>
@@ -107,9 +108,9 @@
            <div itemprop="articleBody">
              
   <section id="troubleshooting">
-<span id="id1"></span><h1><span class="section-number">10. </span>Troubleshooting<a class="headerlink" href="#troubleshooting" title="Link to this heading"></a></h1>
+<span id="id1"></span><h1><span class="section-number">11. </span>Troubleshooting<a class="headerlink" href="#troubleshooting" title="Link to this heading"></a></h1>
 <section id="troubleshooting-case-creation">
-<h2><span class="section-number">10.1. </span>Troubleshooting case creation<a class="headerlink" href="#troubleshooting-case-creation" title="Link to this heading"></a></h2>
+<h2><span class="section-number">11.1. </span>Troubleshooting case creation<a class="headerlink" href="#troubleshooting-case-creation" title="Link to this heading"></a></h2>
 <p>Generally, <a class="reference external" href="../Tools_user/create_newcase.html">create_newcase</a> errors are reported to the terminal and should provide some guidance about what caused them.</p>
 <p>If <a class="reference external" href="../Tools_user/create_newcase.html">create_newcase</a> fails on a relatively generic error, first check to make sure the command-line arguments match the interface’s specification. See the help text to review usage.</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="o">&gt;</span> <span class="n">create_newcase</span> <span class="o">--</span><span class="n">help</span>
@@ -117,11 +118,11 @@ <h2><span class="section-number">10.1. </span>Troubleshooting case creation<a cl
 </div>
 </section>
 <section id="troubleshooting-problems-in-cime-scripts">
-<h2><span class="section-number">10.2. </span>Troubleshooting problems in cime scripts<a class="headerlink" href="#troubleshooting-problems-in-cime-scripts" title="Link to this heading"></a></h2>
+<h2><span class="section-number">11.2. </span>Troubleshooting problems in cime scripts<a class="headerlink" href="#troubleshooting-problems-in-cime-scripts" title="Link to this heading"></a></h2>
 <p>If any of the python-based cime scripts are dying in a mysterious way, more information can be obtained by rerunning the script with the <code class="docutils literal notranslate"><span class="pre">--debug</span></code> option.</p>
 </section>
 <section id="troubleshooting-job-submission">
-<h2><span class="section-number">10.3. </span>Troubleshooting job submission<a class="headerlink" href="#troubleshooting-job-submission" title="Link to this heading"></a></h2>
+<h2><span class="section-number">11.3. </span>Troubleshooting job submission<a class="headerlink" href="#troubleshooting-job-submission" title="Link to this heading"></a></h2>
 <p>Most problems associated with submission or launch are site-specific.
 The batch and run aspects of the <a class="reference external" href="../Tools_user/case.submit.html">case.submit</a> script are created by parsing the variables in <strong>$CASEROOT/env_batch.xml</strong> file.</p>
 <p>Take these steps to check for problems:</p>
@@ -131,7 +132,7 @@ <h2><span class="section-number">10.3. </span>Troubleshooting job submission<a c
 </ol>
 </section>
 <section id="troubleshooting-runtime-problems">
-<h2><span class="section-number">10.4. </span>Troubleshooting runtime problems<a class="headerlink" href="#troubleshooting-runtime-problems" title="Link to this heading"></a></h2>
+<h2><span class="section-number">11.4. </span>Troubleshooting runtime problems<a class="headerlink" href="#troubleshooting-runtime-problems" title="Link to this heading"></a></h2>
 <p>To see if a run completed successfully, check the last several lines of the <strong>cpl.log</strong> file for a string like <code class="docutils literal notranslate"><span class="pre">SUCCESSFUL</span> <span class="pre">TERMINATION</span></code>. A successful job also usually copies the log files to the <strong>$CASEROOT/logs</strong> directory.</p>
 <p>Check these things first when a job fails:</p>
 <ul class="simple">
@@ -208,7 +209,7 @@ <h2><span class="section-number">10.4. </span>Troubleshooting runtime problems<a
            </div>
           </div>
           <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
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diff --git a/versions/master/html/users_guide/unit_testing.html b/versions/master/html/users_guide/unit_testing.html
index ddd6b9f13c7..fe4b7213b29 100644
--- a/versions/master/html/users_guide/unit_testing.html
+++ b/versions/master/html/users_guide/unit_testing.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>9. Fortran Unit Testing &mdash; CIME master documentation</title>
+  <title>7. Fortran Unit Testing &mdash; CIME master documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
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@@ -22,8 +22,8 @@
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     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
-    <link rel="next" title="10. Multi-instance component functionality" href="multi-instance.html" />
-    <link rel="prev" title="8. Testing" href="testing.html" /> 
+    <link rel="next" title="8. Multi-instance component functionality" href="multi-instance.html" />
+    <link rel="prev" title="6. Porting and validating CIME on a new platform" href="porting-cime.html" /> 
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@@ -50,47 +50,45 @@
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 <li class="toctree-l1"><a class="reference internal" href="../what_cime/index.html">What is CIME?</a></li>
-<li class="toctree-l1"><a class="reference internal" href="index.html">Case Control System Part 1: Basic Usage</a></li>
-<li class="toctree-l1 current"><a class="reference internal" href="index.html#case-control-system-part-2-configuration-porting-testing-and-use-cases">Case Control System Part 2: Configuration, Porting, Testing and Use Cases</a><ul class="current">
+<li class="toctree-l1"><a class="reference internal" href="index.html">Using the Case Control System</a></li>
+<li class="toctree-l1 current"><a class="reference internal" href="index.html#configuring-the-case-control-system">Configuring the Case Control System</a><ul class="current">
 <li class="toctree-l2"><a class="reference internal" href="cime-internals.html">1. Main Configuration File</a></li>
 <li class="toctree-l2"><a class="reference internal" href="compsets.html">2. Component sets</a></li>
 <li class="toctree-l2"><a class="reference internal" href="grids.html">3. Model grids</a></li>
 <li class="toctree-l2"><a class="reference internal" href="machine.html">4. Defining the machine</a></li>
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 <li class="toctree-l2"><a class="reference internal" href="porting-cime.html">6. Porting and validating CIME on a new platform</a></li>
-<li class="toctree-l2"><a class="reference internal" href="timers.html">7. Timers and timing</a></li>
-<li class="toctree-l2"><a class="reference internal" href="testing.html">8. Testing</a></li>
-<li class="toctree-l2 current"><a class="current reference internal" href="#">9. Fortran Unit Testing</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="#introduction">9.1. Introduction</a><ul>
-<li class="toctree-l4"><a class="reference internal" href="#what-is-a-unit-test">9.1.1. What is a unit test?</a></li>
-<li class="toctree-l4"><a class="reference internal" href="#overview-of-unit-test-support-in-cime">9.1.2. Overview of unit test support in CIME</a></li>
+<li class="toctree-l2 current"><a class="current reference internal" href="#">7. Fortran Unit Testing</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#introduction">7.1. Introduction</a><ul>
+<li class="toctree-l4"><a class="reference internal" href="#what-is-a-unit-test">7.1.1. What is a unit test?</a></li>
+<li class="toctree-l4"><a class="reference internal" href="#overview-of-unit-test-support-in-cime">7.1.2. Overview of unit test support in CIME</a></li>
 </ul>
 </li>
-<li class="toctree-l3"><a class="reference internal" href="#running-cime-s-fortran-unit-tests">9.2. Running CIME’s Fortran unit tests</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#how-to-add-unit-testing-support-on-your-machine">9.3. How to add unit testing support on your machine</a><ul>
-<li class="toctree-l4"><a class="reference internal" href="#building-pfunit">9.3.1. Building pFUnit</a></li>
-<li class="toctree-l4"><a class="reference internal" href="#adding-to-the-appropriate-cmake-file">9.3.2. Adding to the appropriate cmake file</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#running-cime-s-fortran-unit-tests">7.2. Running CIME’s Fortran unit tests</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#how-to-add-unit-testing-support-on-your-machine">7.3. How to add unit testing support on your machine</a><ul>
+<li class="toctree-l4"><a class="reference internal" href="#building-pfunit">7.3.1. Building pFUnit</a></li>
+<li class="toctree-l4"><a class="reference internal" href="#adding-to-the-appropriate-cmake-file">7.3.2. Adding to the appropriate cmake file</a></li>
 </ul>
 </li>
-<li class="toctree-l3"><a class="reference internal" href="#how-to-write-a-new-unit-test">9.4. How to write a new unit test</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#general-guidelines-for-writing-unit-tests">9.5. General guidelines for writing unit tests</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#more-details-on-writing-pfunit-based-unit-tests">9.6. More details on writing pFUnit-based unit tests</a><ul>
-<li class="toctree-l4"><a class="reference internal" href="#assertion-methods">9.6.1. Assertion methods</a></li>
-<li class="toctree-l4"><a class="reference internal" href="#defining-a-test-class-in-order-to-define-setup-and-teardown-methods">9.6.2. Defining a test class in order to define setUp and tearDown methods</a></li>
-<li class="toctree-l4"><a class="reference internal" href="#more-on-test-teardown">9.6.3. More on test teardown</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#how-to-write-a-new-unit-test">7.4. How to write a new unit test</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#general-guidelines-for-writing-unit-tests">7.5. General guidelines for writing unit tests</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#more-details-on-writing-pfunit-based-unit-tests">7.6. More details on writing pFUnit-based unit tests</a><ul>
+<li class="toctree-l4"><a class="reference internal" href="#assertion-methods">7.6.1. Assertion methods</a></li>
+<li class="toctree-l4"><a class="reference internal" href="#defining-a-test-class-in-order-to-define-setup-and-teardown-methods">7.6.2. Defining a test class in order to define setUp and tearDown methods</a></li>
+<li class="toctree-l4"><a class="reference internal" href="#more-on-test-teardown">7.6.3. More on test teardown</a></li>
 </ul>
 </li>
-<li class="toctree-l3"><a class="reference internal" href="#finding-more-documentation-and-examples">9.7. Finding more documentation and examples</a><ul>
-<li class="toctree-l4"><a class="reference internal" href="#more-detailed-examples-in-cime">9.7.1. More detailed examples in CIME</a></li>
-<li class="toctree-l4"><a class="reference internal" href="#other-pfunit-documentation-sources">9.7.2. Other pFUnit documentation sources</a></li>
-<li class="toctree-l4"><a class="reference internal" href="#documentation-of-the-unit-test-build-system">9.7.3. Documentation of the unit test build system</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#finding-more-documentation-and-examples">7.7. Finding more documentation and examples</a><ul>
+<li class="toctree-l4"><a class="reference internal" href="#more-detailed-examples-in-cime">7.7.1. More detailed examples in CIME</a></li>
+<li class="toctree-l4"><a class="reference internal" href="#other-pfunit-documentation-sources">7.7.2. Other pFUnit documentation sources</a></li>
+<li class="toctree-l4"><a class="reference internal" href="#documentation-of-the-unit-test-build-system">7.7.3. Documentation of the unit test build system</a></li>
 </ul>
 </li>
 </ul>
 </li>
-<li class="toctree-l2"><a class="reference internal" href="multi-instance.html">10. Multi-instance component functionality</a></li>
-<li class="toctree-l2"><a class="reference internal" href="workflows.html">11. Workflows</a></li>
-<li class="toctree-l2"><a class="reference internal" href="cime-dir.html">12. Directory content</a></li>
+<li class="toctree-l2"><a class="reference internal" href="multi-instance.html">8. Multi-instance component functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="workflows.html">9. Workflows</a></li>
+<li class="toctree-l2"><a class="reference internal" href="cime-dir.html">10. Directory content</a></li>
 <li class="toctree-l2"><a class="reference internal" href="index.html#indices-and-tables">Indices and tables</a></li>
 </ul>
 </li>
@@ -119,8 +117,8 @@
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       <li><a href="../index.html" class="icon icon-home" aria-label="Home"></a></li>
-          <li class="breadcrumb-item"><a href="index.html">Case Control System Part 1: Basic Usage</a></li>
-      <li class="breadcrumb-item active"><span class="section-number">9. </span>Fortran Unit Testing</li>
+          <li class="breadcrumb-item"><a href="index.html">Using the Case Control System</a></li>
+      <li class="breadcrumb-item active"><span class="section-number">7. </span>Fortran Unit Testing</li>
       <li class="wy-breadcrumbs-aside">
             <a href="../_sources/users_guide/unit_testing.rst.txt" rel="nofollow"> View page source</a>
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@@ -131,11 +129,11 @@
            <div itemprop="articleBody">
              
   <section id="fortran-unit-testing">
-<span id="unit-testing"></span><h1><span class="section-number">9. </span>Fortran Unit Testing<a class="headerlink" href="#fortran-unit-testing" title="Link to this heading"></a></h1>
+<span id="unit-testing"></span><h1><span class="section-number">7. </span>Fortran Unit Testing<a class="headerlink" href="#fortran-unit-testing" title="Link to this heading"></a></h1>
 <section id="introduction">
-<h2><span class="section-number">9.1. </span>Introduction<a class="headerlink" href="#introduction" title="Link to this heading"></a></h2>
+<h2><span class="section-number">7.1. </span>Introduction<a class="headerlink" href="#introduction" title="Link to this heading"></a></h2>
 <section id="what-is-a-unit-test">
-<h3><span class="section-number">9.1.1. </span>What is a unit test?<a class="headerlink" href="#what-is-a-unit-test" title="Link to this heading"></a></h3>
+<h3><span class="section-number">7.1.1. </span>What is a unit test?<a class="headerlink" href="#what-is-a-unit-test" title="Link to this heading"></a></h3>
 <p>A unit test is a fast, self-verifying test of a small piece of code.
 A single unit test typically covers 10s to 100s of lines of code; a single function or small module, for example.
 It typically runs in milliseconds and produces a simple pass/fail result.</p>
@@ -149,7 +147,7 @@ <h3><span class="section-number">9.1.1. </span>What is a unit test?<a class="hea
 </ul>
 </section>
 <section id="overview-of-unit-test-support-in-cime">
-<h3><span class="section-number">9.1.2. </span>Overview of unit test support in CIME<a class="headerlink" href="#overview-of-unit-test-support-in-cime" title="Link to this heading"></a></h3>
+<h3><span class="section-number">7.1.2. </span>Overview of unit test support in CIME<a class="headerlink" href="#overview-of-unit-test-support-in-cime" title="Link to this heading"></a></h3>
 <p>CIME comes with a set of tools to support building and running unit tests.
 These consist of:</p>
 <ol class="arabic simple">
@@ -160,7 +158,7 @@ <h3><span class="section-number">9.1.2. </span>Overview of unit test support in
 </section>
 </section>
 <section id="running-cime-s-fortran-unit-tests">
-<span id="running-unit-tests"></span><h2><span class="section-number">9.2. </span>Running CIME’s Fortran unit tests<a class="headerlink" href="#running-cime-s-fortran-unit-tests" title="Link to this heading"></a></h2>
+<span id="running-unit-tests"></span><h2><span class="section-number">7.2. </span>Running CIME’s Fortran unit tests<a class="headerlink" href="#running-cime-s-fortran-unit-tests" title="Link to this heading"></a></h2>
 <p>These instructions assume that you are using a machine that already has pFUnit installed, along with the necessary support in CIME.
 If that is not the case, see <a class="reference internal" href="#adding-machine-support"><span class="std std-ref">How to add unit testing support on your machine</span></a>.</p>
 <p>From the top-level CIME directory, you can run all of CIME’s Fortran unit tests by running:</p>
@@ -200,7 +198,7 @@ <h3><span class="section-number">9.1.2. </span>Overview of unit test support in
 <p>These unit tests are run automatically as part of <strong>scripts_regression_tests</strong> on machines that have a serial build of pFUnit available for the default compiler.</p>
 </section>
 <section id="how-to-add-unit-testing-support-on-your-machine">
-<span id="adding-machine-support"></span><h2><span class="section-number">9.3. </span>How to add unit testing support on your machine<a class="headerlink" href="#how-to-add-unit-testing-support-on-your-machine" title="Link to this heading"></a></h2>
+<span id="adding-machine-support"></span><h2><span class="section-number">7.3. </span>How to add unit testing support on your machine<a class="headerlink" href="#how-to-add-unit-testing-support-on-your-machine" title="Link to this heading"></a></h2>
 <p>The following instructions assume that you have ported CIME to your
 machine by following the instructions in
 <a class="reference internal" href="porting-cime.html"><span class="doc">Porting and validating CIME on a new platform</span></a>.  If you have done that, you can add
@@ -208,7 +206,7 @@ <h3><span class="section-number">9.1.2. </span>Overview of unit test support in
 pointing to the build in your ** <em>MACH*_*COMPILER</em>.cmake** file. Those
 processes are described in the following sections.</p>
 <section id="building-pfunit">
-<h3><span class="section-number">9.3.1. </span>Building pFUnit<a class="headerlink" href="#building-pfunit" title="Link to this heading"></a></h3>
+<h3><span class="section-number">7.3.1. </span>Building pFUnit<a class="headerlink" href="#building-pfunit" title="Link to this heading"></a></h3>
 <p>Follow the instructions below to build pFUnit using the default compiler on your machine.
 That is the default for <strong>run_tests.py</strong> and that is required for <strong>scripts_regression_tests.py</strong> to run the unit tests on your machine.
 For the CMake step, we typically build with <code class="docutils literal notranslate"><span class="pre">-DSKIP_MPI=YES</span></code>, <code class="docutils literal notranslate"><span class="pre">-DSKIP_OPENMP=YES</span></code> and <code class="docutils literal notranslate"><span class="pre">-DCMAKE_INSTALL_PREFIX</span></code> set to the directory where you want pFUnit to be installed.
@@ -263,7 +261,7 @@ <h3><span class="section-number">9.3.1. </span>Building pFUnit<a class="headerli
 Make sure to choose a different installation directory for each build by setting the <code class="docutils literal notranslate"><span class="pre">PFUNIT</span></code> variable differently.</p>
 </section>
 <section id="adding-to-the-appropriate-cmake-file">
-<h3><span class="section-number">9.3.2. </span>Adding to the appropriate cmake file<a class="headerlink" href="#adding-to-the-appropriate-cmake-file" title="Link to this heading"></a></h3>
+<h3><span class="section-number">7.3.2. </span>Adding to the appropriate cmake file<a class="headerlink" href="#adding-to-the-appropriate-cmake-file" title="Link to this heading"></a></h3>
 <p>After you build pFUnit, tell CIME about your build or builds.
 To do this, specify the appropriate path using the <code class="docutils literal notranslate"><span class="pre">PFUNIT_PATH</span></code> CMake variable in the ** <em>MACH*_*COMPILER</em>.cmake** file.
 For a build with no MPI or openMP support (as recommended above), the block should look like this (with the actual path replaced with the PFUNIT path you specified when doing the build):</p>
@@ -278,7 +276,7 @@ <h3><span class="section-number">9.3.2. </span>Adding to the appropriate cmake f
 </section>
 </section>
 <section id="how-to-write-a-new-unit-test">
-<h2><span class="section-number">9.4. </span>How to write a new unit test<a class="headerlink" href="#how-to-write-a-new-unit-test" title="Link to this heading"></a></h2>
+<h2><span class="section-number">7.4. </span>How to write a new unit test<a class="headerlink" href="#how-to-write-a-new-unit-test" title="Link to this heading"></a></h2>
 <div class="admonition-todo admonition" id="id1">
 <p class="admonition-title">Todo</p>
 <p>Need to write this section. This will draw on some of the information in sections 3 and 4 of <a class="reference external" href="https://github.com/NCAR/cesm_unit_test_tutorial">https://github.com/NCAR/cesm_unit_test_tutorial</a> (though without the clm and cam stuff).</p>
@@ -286,7 +284,7 @@ <h2><span class="section-number">9.4. </span>How to write a new unit test<a clas
 <p>It should also introduce the role of .pf files, which are referenced several paragraphs later as if already explained.</p>
 </section>
 <section id="general-guidelines-for-writing-unit-tests">
-<h2><span class="section-number">9.5. </span>General guidelines for writing unit tests<a class="headerlink" href="#general-guidelines-for-writing-unit-tests" title="Link to this heading"></a></h2>
+<h2><span class="section-number">7.5. </span>General guidelines for writing unit tests<a class="headerlink" href="#general-guidelines-for-writing-unit-tests" title="Link to this heading"></a></h2>
 <p>Unit tests typically test a small piece of code, on the order of 10-100 lines, as in a single function or small class.</p>
 <p>Good unit tests are <strong>“FIRST”</strong>:
 (<a class="reference external" href="https://pragprog.com/magazines/2012-01/unit-tests-are-first">https://pragprog.com/magazines/2012-01/unit-tests-are-first</a>):</p>
@@ -319,9 +317,9 @@ <h2><span class="section-number">9.5. </span>General guidelines for writing unit
 for your tests, not for your helper routines.</p>
 </section>
 <section id="more-details-on-writing-pfunit-based-unit-tests">
-<h2><span class="section-number">9.6. </span>More details on writing pFUnit-based unit tests<a class="headerlink" href="#more-details-on-writing-pfunit-based-unit-tests" title="Link to this heading"></a></h2>
+<h2><span class="section-number">7.6. </span>More details on writing pFUnit-based unit tests<a class="headerlink" href="#more-details-on-writing-pfunit-based-unit-tests" title="Link to this heading"></a></h2>
 <section id="assertion-methods">
-<h3><span class="section-number">9.6.1. </span>Assertion methods<a class="headerlink" href="#assertion-methods" title="Link to this heading"></a></h3>
+<h3><span class="section-number">7.6.1. </span>Assertion methods<a class="headerlink" href="#assertion-methods" title="Link to this heading"></a></h3>
 <p>pFUnit provides many assertion methods that you can use in the Verify step.
 Here are some of the most useful:</p>
 <table class="docutils align-default">
@@ -366,7 +364,7 @@ <h3><span class="section-number">9.6.1. </span>Assertion methods<a class="header
 file and line number of the failed assertion.</p>
 </section>
 <section id="defining-a-test-class-in-order-to-define-setup-and-teardown-methods">
-<h3><span class="section-number">9.6.2. </span>Defining a test class in order to define setUp and tearDown methods<a class="headerlink" href="#defining-a-test-class-in-order-to-define-setup-and-teardown-methods" title="Link to this heading"></a></h3>
+<h3><span class="section-number">7.6.2. </span>Defining a test class in order to define setUp and tearDown methods<a class="headerlink" href="#defining-a-test-class-in-order-to-define-setup-and-teardown-methods" title="Link to this heading"></a></h3>
 <p>As noted in the comments in <strong>test_circle.pf</strong>, defining a test class is optional.
 However, defining a minimal test class as shown here with <code class="docutils literal notranslate"><span class="pre">TestCircle</span></code> allows you
 use some pFUnit features such as the setUp and tearDown methods.</p>
@@ -425,7 +423,7 @@ <h3><span class="section-number">9.6.2. </span>Defining a test class in order to
 </div>
 </section>
 <section id="more-on-test-teardown">
-<h3><span class="section-number">9.6.3. </span>More on test teardown<a class="headerlink" href="#more-on-test-teardown" title="Link to this heading"></a></h3>
+<h3><span class="section-number">7.6.3. </span>More on test teardown<a class="headerlink" href="#more-on-test-teardown" title="Link to this heading"></a></h3>
 <p>As stated in <a class="reference internal" href="#defining-a-test-class-in-order-to-define-setup-and-teardown-methods">Defining a test class in order to define setUp and tearDown methods</a>,
 code in the tearDown method is executed after each test, often to do cleanup operations.</p>
 <p>Using the tearDown method is recommended because tests abort if an assertion fails.
@@ -458,9 +456,9 @@ <h3><span class="section-number">9.6.3. </span>More on test teardown<a class="he
 </section>
 </section>
 <section id="finding-more-documentation-and-examples">
-<h2><span class="section-number">9.7. </span>Finding more documentation and examples<a class="headerlink" href="#finding-more-documentation-and-examples" title="Link to this heading"></a></h2>
+<h2><span class="section-number">7.7. </span>Finding more documentation and examples<a class="headerlink" href="#finding-more-documentation-and-examples" title="Link to this heading"></a></h2>
 <section id="more-detailed-examples-in-cime">
-<h3><span class="section-number">9.7.1. </span>More detailed examples in CIME<a class="headerlink" href="#more-detailed-examples-in-cime" title="Link to this heading"></a></h3>
+<h3><span class="section-number">7.7.1. </span>More detailed examples in CIME<a class="headerlink" href="#more-detailed-examples-in-cime" title="Link to this heading"></a></h3>
 <p>There are many examples of unit tests in CIME, some simple and some quite complex.
 You can find them by looking for files with the “.pf” extension:</p>
 <div class="highlight-shell notranslate"><div class="highlight"><pre><span></span>&gt;<span class="w"> </span>find<span class="w"> </span>.<span class="w"> </span>--name<span class="w"> </span><span class="s1">&#39;*.pf&#39;</span>
@@ -470,11 +468,11 @@ <h3><span class="section-number">9.7.1. </span>More detailed examples in CIME<a
 <strong>CMakeLists.txt</strong> files throughout the source tree.</p>
 </section>
 <section id="other-pfunit-documentation-sources">
-<h3><span class="section-number">9.7.2. </span>Other pFUnit documentation sources<a class="headerlink" href="#other-pfunit-documentation-sources" title="Link to this heading"></a></h3>
+<h3><span class="section-number">7.7.2. </span>Other pFUnit documentation sources<a class="headerlink" href="#other-pfunit-documentation-sources" title="Link to this heading"></a></h3>
 <p>Unfortunately, the documentation inside the pFUnit repository (in the documentation and Examples directories) is out-of-date (at least as of April, 2023): much of this documentation refers to version 3 of pFUnit, which differs in some ways from version 4. However, some working examples are provided in <a class="reference external" href="https://github.com/Goddard-Fortran-Ecosystem/pFUnit_demos">https://github.com/Goddard-Fortran-Ecosystem/pFUnit_demos</a>.</p>
 </section>
 <section id="documentation-of-the-unit-test-build-system">
-<h3><span class="section-number">9.7.3. </span>Documentation of the unit test build system<a class="headerlink" href="#documentation-of-the-unit-test-build-system" title="Link to this heading"></a></h3>
+<h3><span class="section-number">7.7.3. </span>Documentation of the unit test build system<a class="headerlink" href="#documentation-of-the-unit-test-build-system" title="Link to this heading"></a></h3>
 <p>The CMake build infrastructure is in <strong>$CIMEROOT/CIME/non_py/src/CMake</strong>.</p>
 <p>The infrastructure for building and running tests with <strong>run_tests.py</strong> is in
 <strong>$CIMEROOT/scripts/fortran_unit_testing</strong>. That directory also contains general
@@ -488,8 +486,8 @@ <h3><span class="section-number">9.7.3. </span>Documentation of the unit test bu
            </div>
           </div>
           <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
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+        <a href="porting-cime.html" class="btn btn-neutral float-left" title="6. Porting and validating CIME on a new platform" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
+        <a href="multi-instance.html" class="btn btn-neutral float-right" title="8. Multi-instance component functionality" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
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diff --git a/versions/master/html/users_guide/workflows.html b/versions/master/html/users_guide/workflows.html
index 0ac65a18a13..1fbf7ad4ae9 100644
--- a/versions/master/html/users_guide/workflows.html
+++ b/versions/master/html/users_guide/workflows.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>11. Workflows &mdash; CIME master documentation</title>
+  <title>9. Workflows &mdash; CIME master documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../_static/custom.css" />
@@ -22,8 +22,8 @@
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
-    <link rel="next" title="12. Directory content" href="cime-dir.html" />
-    <link rel="prev" title="10. Multi-instance component functionality" href="multi-instance.html" /> 
+    <link rel="next" title="10. Directory content" href="cime-dir.html" />
+    <link rel="prev" title="8. Multi-instance component functionality" href="multi-instance.html" /> 
 </head>
 
 <body class="wy-body-for-nav"> 
@@ -50,20 +50,18 @@
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
               <ul class="current">
 <li class="toctree-l1"><a class="reference internal" href="../what_cime/index.html">What is CIME?</a></li>
-<li class="toctree-l1"><a class="reference internal" href="index.html">Case Control System Part 1: Basic Usage</a></li>
-<li class="toctree-l1 current"><a class="reference internal" href="index.html#case-control-system-part-2-configuration-porting-testing-and-use-cases">Case Control System Part 2: Configuration, Porting, Testing and Use Cases</a><ul class="current">
+<li class="toctree-l1"><a class="reference internal" href="index.html">Using the Case Control System</a></li>
+<li class="toctree-l1 current"><a class="reference internal" href="index.html#configuring-the-case-control-system">Configuring the Case Control System</a><ul class="current">
 <li class="toctree-l2"><a class="reference internal" href="cime-internals.html">1. Main Configuration File</a></li>
 <li class="toctree-l2"><a class="reference internal" href="compsets.html">2. Component sets</a></li>
 <li class="toctree-l2"><a class="reference internal" href="grids.html">3. Model grids</a></li>
 <li class="toctree-l2"><a class="reference internal" href="machine.html">4. Defining the machine</a></li>
 <li class="toctree-l2"><a class="reference internal" href="pes-threads.html">5. Controlling processors and threads</a></li>
 <li class="toctree-l2"><a class="reference internal" href="porting-cime.html">6. Porting and validating CIME on a new platform</a></li>
-<li class="toctree-l2"><a class="reference internal" href="timers.html">7. Timers and timing</a></li>
-<li class="toctree-l2"><a class="reference internal" href="testing.html">8. Testing</a></li>
-<li class="toctree-l2"><a class="reference internal" href="unit_testing.html">9. Fortran Unit Testing</a></li>
-<li class="toctree-l2"><a class="reference internal" href="multi-instance.html">10. Multi-instance component functionality</a></li>
-<li class="toctree-l2 current"><a class="current reference internal" href="#">11. Workflows</a></li>
-<li class="toctree-l2"><a class="reference internal" href="cime-dir.html">12. Directory content</a></li>
+<li class="toctree-l2"><a class="reference internal" href="unit_testing.html">7. Fortran Unit Testing</a></li>
+<li class="toctree-l2"><a class="reference internal" href="multi-instance.html">8. Multi-instance component functionality</a></li>
+<li class="toctree-l2 current"><a class="current reference internal" href="#">9. Workflows</a></li>
+<li class="toctree-l2"><a class="reference internal" href="cime-dir.html">10. Directory content</a></li>
 <li class="toctree-l2"><a class="reference internal" href="index.html#indices-and-tables">Indices and tables</a></li>
 </ul>
 </li>
@@ -92,8 +90,8 @@
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
       <li><a href="../index.html" class="icon icon-home" aria-label="Home"></a></li>
-          <li class="breadcrumb-item"><a href="index.html">Case Control System Part 1: Basic Usage</a></li>
-      <li class="breadcrumb-item active"><span class="section-number">11. </span>Workflows</li>
+          <li class="breadcrumb-item"><a href="index.html">Using the Case Control System</a></li>
+      <li class="breadcrumb-item active"><span class="section-number">9. </span>Workflows</li>
       <li class="wy-breadcrumbs-aside">
             <a href="../_sources/users_guide/workflows.rst.txt" rel="nofollow"> View page source</a>
       </li>
@@ -104,7 +102,7 @@
            <div itemprop="articleBody">
              
   <section id="workflows">
-<span id="id1"></span><h1><span class="section-number">11. </span>Workflows<a class="headerlink" href="#workflows" title="Link to this heading"></a></h1>
+<span id="id1"></span><h1><span class="section-number">9. </span>Workflows<a class="headerlink" href="#workflows" title="Link to this heading"></a></h1>
 <p>Currently, there are three kinds of workflow controls available in CIME.</p>
 <ol class="arabic">
 <li><p>Multiple jobs workflow</p>
@@ -200,8 +198,8 @@
            </div>
           </div>
           <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
-        <a href="multi-instance.html" class="btn btn-neutral float-left" title="10. Multi-instance component functionality" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
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+        <a href="multi-instance.html" class="btn btn-neutral float-left" title="8. Multi-instance component functionality" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
+        <a href="cime-dir.html" class="btn btn-neutral float-right" title="10. Directory content" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
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diff --git a/versions/master/html/what_cime/index.html b/versions/master/html/what_cime/index.html
index ff64f3286dd..859afcd90ae 100644
--- a/versions/master/html/what_cime/index.html
+++ b/versions/master/html/what_cime/index.html
@@ -22,7 +22,7 @@
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
-    <link rel="next" title="Case Control System Part 1: Basic Usage" href="../users_guide/index.html" />
+    <link rel="next" title="Using the Case Control System" href="../users_guide/index.html" />
     <link rel="prev" title="CIME documentation" href="../index.html" /> 
 </head>
 
@@ -54,8 +54,8 @@
 <li class="toctree-l2"><a class="reference internal" href="#development">Development</a></li>
 </ul>
 </li>
-<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html">Case Control System Part 1: Basic Usage</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html#case-control-system-part-2-configuration-porting-testing-and-use-cases">Case Control System Part 2: Configuration, Porting, Testing and Use Cases</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html">Using the Case Control System</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html#configuring-the-case-control-system">Configuring the Case Control System</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../build_cpl/index.html">Building a Coupled Model with CIME</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../misc_tools/index.html">Miscellaneous Tools</a></li>
 </ul>
@@ -97,12 +97,15 @@ <h1>What is CIME?<a class="headerlink" href="#what-is-cime" title="Link to this
 </div>
 <section id="overview">
 <h2>Overview<a class="headerlink" href="#overview" title="Link to this heading"></a></h2>
-<p>CIME, pronounced “SEAM”, primarily consists of a Case Control System that supports the configuration, compilation, execution, system testing and unit testing of an Earth System Model. The two main components of the Case Control System are:</p>
+<p>CIME (Common Infrastructure for Modeling the Earth, pronounced “SEAM”) primarily consists of a Case Control System that supports the configuration, compilation, execution, system testing and unit testing of an Earth System Model. The three main components of the Case Control System are:</p>
 <ol class="arabic simple">
-<li><p>Scripts to enable simple generation of model executables and associated input files for different scientific cases, component resolutions and combinations of full, data and stub components with a handful of commands.</p></li>
+<li><p>XML files that  describe the available machines, models and model configurations.</p></li>
+<li><p>Python scripts that take user commands and parse the XML files to configure a set of models with their
+build and runtime options for a specified machine and the provide additional commands to build executables and
+submit jobs.</p></li>
 <li><p>Testing utilities to run defined system tests and report results for different configurations of the coupled system.</p></li>
 </ol>
-<p>CIME also contains additional stand-alone tools, including:</p>
+<p>CIME also contains additional stand-alone tools useful for Earth system modeling including:</p>
 <ol class="arabic simple">
 <li><p>Parallel regridding weight generation program</p></li>
 <li><p>Scripts to automate off-line load-balancing.</p></li>
@@ -124,7 +127,7 @@ <h2>Development<a class="headerlink" href="#development" title="Link to this hea
           </div>
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diff --git a/versions/master/html/xml_files/atmosphere.html b/versions/master/html/xml_files/atmosphere.html
index 25328af2054..cce732756ee 100644
--- a/versions/master/html/xml_files/atmosphere.html
+++ b/versions/master/html/xml_files/atmosphere.html
@@ -48,8 +48,8 @@
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 <li class="toctree-l1"><a class="reference internal" href="../what_cime/index.html">What is CIME?</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html">Case Control System Part 1: Basic Usage</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html#case-control-system-part-2-configuration-porting-testing-and-use-cases">Case Control System Part 2: Configuration, Porting, Testing and Use Cases</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html">Using the Case Control System</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html#configuring-the-case-control-system">Configuring the Case Control System</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../build_cpl/index.html">Building a Coupled Model with CIME</a></li>
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diff --git a/versions/master/html/xml_files/cesm.html b/versions/master/html/xml_files/cesm.html
index ec8756f0452..bffff59f529 100644
--- a/versions/master/html/xml_files/cesm.html
+++ b/versions/master/html/xml_files/cesm.html
@@ -50,8 +50,8 @@
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-<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html">Case Control System Part 1: Basic Usage</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html#case-control-system-part-2-configuration-porting-testing-and-use-cases">Case Control System Part 2: Configuration, Porting, Testing and Use Cases</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html">Using the Case Control System</a></li>
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+<li class="toctree-l1"><a class="reference internal" href="../users_guide/index.html#configuring-the-case-control-system">Configuring the Case Control System</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../build_cpl/index.html">Building a Coupled Model with CIME</a></li>
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