Merge doc_overview_section from jrscott

Author: jahn

doc/Makefile

@@ -17,4 +17,4 @@ help:
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

doc/conf.py

@@ -92,7 +92,7 @@
 # number figures within section
 numfig_secnum_depth = 1
 
-math_number_all = True
+#math_number_all = True
 
 numfig_format = {'figure': 'Figure %s', 'table': 'Table %s', 'code-block': 'Listing %s', 'section': 'Section %s'}
 
@@ -141,6 +141,7 @@
     # Additional stuff for the LaTeX preamble.
     #
     # 'preamble': '',
+    'preamble': '\setcounter{secnumdepth}{3}',
 
     # Latex figure (float) alignment
     #

doc/index.rst

@@ -12,8 +12,8 @@ Welcome to MITgcm's user manual
    :numbered: 4
 
    overview/overview
-   phys_pkgs/phys_pkgs
    getting_started/getting_started
-   examples/examples
    contributing
+   examples/examples
+   phys_pkgs/phys_pkgs
    zreferences