diff --git a/hdmf_docutils/init_sphinx_extension_doc.py b/hdmf_docutils/init_sphinx_extension_doc.py
index befda0f..7091d05 100644
--- a/hdmf_docutils/init_sphinx_extension_doc.py
+++ b/hdmf_docutils/init_sphinx_extension_doc.py
@@ -263,8 +263,8 @@ def get_format_rst(spec_output_dir, output_master, project):
 def get_index_rst(project, format_master, custom_description=None, custom_release_notes=None):
     index_rst = \
 """Specification for the %s extension
-==================================
-""" % project
+%s
+""" % (project, '=' * (len(project) + 32))
 
     if custom_description is not None:
         index_rst += \
@@ -346,7 +346,9 @@ def get_custom_settings(utils_dir,
     """
     # Define the base html and latex settings
     custom_sphinx_settings = \
-"""############################################################################
+"""
+
+############################################################################
 #  CUSTOM CONFIGURATIONS ADDED BY THE NWB TOOL FOR GENERATING FORMAT DOCS
 ###########################################################################
 
@@ -354,7 +356,10 @@ def get_custom_settings(utils_dir,
 import textwrap  # noqa: E402
 
 # -- Options for intersphinx  ---------------------------------------------
-intersphinx_mapping = {'core': ('https://nwb-schema.readthedocs.io/en/latest/', None)}
+intersphinx_mapping.update({
+    'core': ('https://nwb-schema.readthedocs.io/en/latest/', None),
+    'hdmf-common': ('https://hdmf-common-schema.readthedocs.io/en/latest/', None),
+})
 
 # -- Generate sources from YAML---------------------------------------------------
 # Always rebuild the source docs from YAML even if the folder with the source files already exists
@@ -758,7 +763,7 @@ def define_cl_args():
     parser.add_argument('--release', dest='release', action='store', type=str, required=True,
                         help='Release of the project/docs')
     parser.add_argument('--language', dest='language', action='store', type=str, required=False,
-                        help='Document language', default='English')
+                        help='Document language', default='en')
     parser.add_argument('--master', dest='master', action='store', type=str, required=False,
                         help='Master document name', default='index.rst')
     parser.add_argument('--credits_master', dest='credits_master', action='store', type=str, required=False,
@@ -920,26 +925,10 @@ def init_sphinx(project, author, version, release, language, sphinx_master, outp
 
         print("Cleaning file %s" % conf_py)
 
-        # Remove example of intersphinx configuration
-        _remove_lines(
-            conf_py,
-            ['# Example configuration for intersphinx: refer to the Python standard library.',
-             'intersphinx_mapping = {\'https://docs.python.org/\': None}']
-        )
-
-        # Fix indent of intersphinx extension list
-        _replace_line_text(conf_py, '    \'sphinx.ext.', '              \'sphinx.ext.')
-
-        # Remove timestamp info added by sphinx-quickstart
-        _remove_lines_after(conf_py, '# simulation_output documentation build configuration file, created by', 5)
-        _remove_lines(conf_py, ['# simulation_output documentation build configuration file, created by'])
-
         # Remove empty directories
         os.rmdir(os.path.join(output, "build"))
         os.rmdir(os.path.join(output, "source", "_templates"))
 
-        # Remove empty lines from the end of files
-        _write_lines(conf_py, _read_lines(conf_py)[:-2])
     except CalledProcessError:
         exit(0)