CommonMark is now an extra and processing should go through without it.

Author: dpryan79

docs/extend.rst

@@ -20,7 +20,7 @@ You can add extra content or even replace some parts of the documentation genera
             any directives you usually use.
 
 
-Also, there is an option to insert custom content into a specific argument/option/subcommand/argument-group description. Just create a name:definition pair, where the name is an argument/option/subcommand/argument-group name and the definition is any reStructured markup. Changes to options/arguments appearing in multiple action groups can either be targetted (i.e., only one instance of the argument is changed) or general (i.e., all instances are modified).::
+Also, there is an option to insert custom content into a specific argument/option/subcommand/argument-group description. Just create a name:definition pair, where the name is an argument/option/subcommand/argument-group name and the definition is any reStructured markup. Changes to options/arguments appearing in multiple action groups can either be targeted (i.e., only one instance of the argument is changed) or general (i.e., all instances are modified).::
 
    .. argparse::
        :module: my.module

setup.py

@@ -37,10 +37,10 @@ def getVersion():
         'Topic :: Software Development :: Documentation'
     ],
     install_requires=[
-        'sphinx>=1.2.0',
-        'CommonMark'
+        'sphinx>=1.2.0'
     ],
     extras_require={
-        'dev': ['pytest', 'sphinx_rtd_theme']
+        'dev': ['pytest', 'sphinx_rtd_theme'],
+        'markdown': ['CommonMark>=0.5.6']
     }
 )