Since we're autodocumenting from a sphinx ext, we can scrap it in Makefile.

doc/Makefile

@@ -38,40 +38,33 @@ clean:
         rm .autogenerated ; \
     fi
 
-module_autodoc: generate_autodoc_index.sh
-	@echo "Generating module autodocs."
-	./generate_autodoc_index.sh
-
-source/code.rst: module_autodoc
-	@# pass
-
-html: source/code.rst
+html:
 	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
 	@echo
 	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
 
-dirhtml: source/code.rst
+dirhtml:
 	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
 	@echo
 	@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
 
-pickle: source/code.rst
+pickle:
 	$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
 	@echo
 	@echo "Build finished; now you can process the pickle files."
 
-json: source/code.rst
+json:
 	$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
 	@echo
 	@echo "Build finished; now you can process the JSON files."
 
-htmlhelp: source/code.rst
+htmlhelp:
 	$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
 	@echo
 	@echo "Build finished; now you can run HTML Help Workshop with the" \
 	      ".hhp project file in $(BUILDDIR)/htmlhelp."
 
-qthelp: source/code.rst
+qthelp:
 	$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
 	@echo
 	@echo "Build finished; now you can run "qcollectiongenerator" with the" \
@@ -80,25 +73,25 @@ qthelp: source/code.rst
 	@echo "To view the help file:"
 	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/nova.qhc"
 
-latex: source/code.rst
+latex:
 	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
 	@echo
 	@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
 	@echo "Run \`make all-pdf' or \`make all-ps' in that directory to" \
 	      "run these through (pdf)latex."
 
-changes: source/code.rst
+changes:
 	$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
 	@echo
 	@echo "The overview file is in $(BUILDDIR)/changes."
 
-linkcheck: source/code.rst
+linkcheck:
 	$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
 	@echo
 	@echo "Link check complete; look for any errors in the above output " \
 	      "or in $(BUILDDIR)/linkcheck/output.txt."
 
-doctest: source/code.rst
+doctest:
 	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
 	@echo "Testing of doctests in the sources finished, look at the " \
 	      "results in $(BUILDDIR)/doctest/output.txt."