diff --git a/doc/CMakeLists.txt b/doc/CMakeLists.txt
index bdbb0e7b69..427d2b86b6 100644
--- a/doc/CMakeLists.txt
+++ b/doc/CMakeLists.txt
@@ -21,13 +21,13 @@ add_subdirectory(scripts)
 add_custom_target(broxygen
                   # copy the template documentation to the build directory
                   # to give as input for sphinx
-                  COMMAND "${CMAKE_COMMAND}" -E copy_directory
-                          ${DOC_SOURCE_DIR}
+                  COMMAND rsync -r --copy-links --times
+                          ${DOC_SOURCE_DIR}/
                           ${DOC_SOURCE_WORKDIR}
                   # copy generated policy script documentation into the
                   # working copy of the template documentation
-                  COMMAND "${CMAKE_COMMAND}" -E copy_directory
-                          ${RST_OUTPUT_DIR}
+                  COMMAND rsync -r --copy-links --times
+                          ${RST_OUTPUT_DIR}/
                           ${DOC_SOURCE_WORKDIR}/scripts
                   # append to the master index of all policy scripts
                   COMMAND cat ${MASTER_POLICY_INDEX} >>
@@ -58,7 +58,7 @@ add_custom_target(broxygen
                   # SOURCES just adds stuff to IDE projects as a convenience
                   SOURCES ${DOC_SOURCES})
 
-# The "sphinxclean" target removes just the Sphinx input/output directories
+# The "broxygenclean" target removes just the Sphinx input/output directories
 # from the build directory.
 add_custom_target(broxygenclean
                   COMMAND "${CMAKE_COMMAND}" -E remove_directory
@@ -67,7 +67,7 @@ add_custom_target(broxygenclean
                           ${DOC_OUTPUT_DIR}
                   VERBATIM)
 
-add_dependencies(broxygen broxygenclean restdoc)
+add_dependencies(broxygen restdoc)
 
 add_custom_target(doc)
 add_custom_target(docclean)
diff --git a/doc/bin/group_index_generator.py b/doc/bin/group_index_generator.py
index 720081e8b5..b41dcb379c 100755
--- a/doc/bin/group_index_generator.py
+++ b/doc/bin/group_index_generator.py
@@ -8,9 +8,11 @@
 # 2nd argument is the directory containing ${group}_files lists of
 #   scripts that belong to the group and ${group}_doc_names lists of
 #   document names that can be supplied to a reST :doc: role
-# 3rd argument is a directory in which write a ${group}.rst file (will
-#   append to existing file) that contains reST style references to
-#   script docs along with summary text contained in original script
+# 3rd argument is a directory in which write a ${group}.rst file that contains
+#   reST style references to script docs along with summary text contained
+#   in original script.  If ${group} ends with "index", then the file
+#   is always clobbered by this script, but for other unique group names,
+#   this script will append to existing files.
 
 import sys
 import os
@@ -20,9 +22,28 @@ group_list = sys.argv[1]
 file_manifest_dir = sys.argv[2]
 output_dir = sys.argv[3]
 
+def make_group_file_index(dir_name, group_name):
+    group_file = os.path.join(dir_name, group_name + ".rst")
+
+    if not os.path.exists(group_file):
+        if not os.path.exists(os.path.dirname(group_file)):
+            os.makedirs(os.path.dirname(group_file))
+
+    if group_name.endswith("index"):
+        with open(group_file, 'w') as f_group_file:
+            f_group_file.write(":orphan:\n\n")
+            title = "Package Index: %s\n" % os.path.dirname(group_name)
+            f_group_file.write(title);
+            for n in range(len(title)):
+                f_group_file.write("=")
+            f_group_file.write("\n");
+
+    return group_file
+
 with open(group_list, 'r') as f_group_list:
     for group in f_group_list.read().splitlines():
         #print group
+        group_file = make_group_file_index(output_dir, group)
         file_manifest = os.path.join(file_manifest_dir, group + "_files")
         doc_manifest = os.path.join(file_manifest_dir, group + "_doc_names")
         src_files = []
@@ -44,17 +65,6 @@ with open(group_list, 'r') as f_group_list:
                     if sum_pos != -1:
                         summary_comments.append(line[(sum_pos+3):])
             #print summary_comments
-            group_file = os.path.join(output_dir, group + ".rst")
-            if not os.path.exists(group_file):
-                if not os.path.exists(os.path.dirname(group_file)):
-                    os.makedirs(os.path.dirname(group_file))
-                with open(group_file, 'w') as f_group_file:
-                    f_group_file.write(":orphan:\n\n")
-                    title = "Package Index: %s\n" % os.path.dirname(group)
-                    f_group_file.write(title);
-                    for n in range(len(title)):
-                        f_group_file.write("=")
-                    f_group_file.write("\n");
 
             with open(group_file, 'a') as f_group_file:
                 f_group_file.write("\n:doc:`/scripts/%s`\n" % doc_names[i])