diff --git a/calibre-plugin/plugin-defaults.ini b/calibre-plugin/plugin-defaults.ini
index fd48a29e..14fee2a2 100644
--- a/calibre-plugin/plugin-defaults.ini
+++ b/calibre-plugin/plugin-defaults.ini
@@ -400,16 +400,18 @@ chapter_title_strip_pattern:^[0-9]+[\.: -]+(?=[^0-9]|$)
 mark_new_chapters:false
 
 ## chapter title patterns use python template substitution.  The
-## ${index} is the 'chapter' number and ${title} is the chapter title,
-## after applying chapter_title_strip_pattern.  Those are the only
-## variables available.
+## ${number} is the 'chapter' number and ${title} is the chapter
+## title, after applying chapter_title_strip_pattern.  ${index04} is
+## chapter number padded with leading zeros (mostly for internal use)
+## such as 0001.  ${index} == ${number} for backward compatibility.  A
+## few site adapters add additional chapter metadata.
 
 ## The basic pattern used when not using add_chapter_numbers or
 ## mark_new_chapters
 chapter_title_def_pattern:${title}
 
 ## Pattern used with add_chapter_numbers, but not mark_new_chapters
-chapter_title_add_pattern:${index}. ${title}
+chapter_title_add_pattern:${number}. ${title}
 
 ## Pattern used with mark_new_chapters, but not add_chapter_numbers
 ## (new) is just text and can be changed.
@@ -417,7 +419,7 @@ chapter_title_new_pattern:(new) ${title}
 
 ## Pattern used with add_chapter_numbers and mark_new_chapters
 ## (new) is just text and can be changed.
-chapter_title_addnew_pattern:${index}. (new) ${title}
+chapter_title_addnew_pattern:${number}. (new) ${title}
 
 ## Uses a python template substitution.  The ${title} is the default
 ## title of a new anthology, <series name> in the case of a series, or
@@ -684,7 +686,7 @@ use_threadmark_wordcounts:true
 ## chapter_title_*_pattern settings.
 ## Example:
 #tocpage_entry:
-# <a href="#section${index}">${chapter}</a> ${date} ${kwords}<br />
+# <a href="#section${index04}">${chapter}</a> ${date} ${kwords}<br />
 
 ## The 'date' value for chapters mentioned above can be formated with
 ## datethreadmark_format.  Otherwise it will default to
diff --git a/fanficfare/adapters/base_adapter.py b/fanficfare/adapters/base_adapter.py
index 913b4bc0..329eda94 100644
--- a/fanficfare/adapters/base_adapter.py
+++ b/fanficfare/adapters/base_adapter.py
@@ -75,7 +75,7 @@ class BaseSiteAdapter(Configurable):
         self.story = Story(configuration)
         self.story.setMetadata('site',self.getConfigSection())
         self.story.setMetadata('dateCreated',datetime.now())
-        self.chapterUrls = [] # tuples of (chapter title,chapter url)
+        self.chapterUrls = [] # dicts of (chapter title,chapter url)
         self.chapterFirst = None
         self.chapterLast = None
         self.oldchapters = None
@@ -150,7 +150,7 @@ class BaseSiteAdapter(Configurable):
         if self.ignore_chapter_url_list == None:
             self.ignore_chapter_url_list = [ self.normalize_chapterurl(u) for u in self.getConfig('ignore_chapter_url_list').splitlines() ]
         if self.normalize_chapterurl(url) not in self.ignore_chapter_url_list:
-            meta = dict(othermeta) # copy
+            meta = defaultdict(unicode,othermeta) # copy othermeta
             meta.update({'title':stripHTML(title),'url':url}) # after other to make sure they are set
             self.chapterUrls.append(meta)
             self.story.setMetadata('numChapters', self.num_chapters())
@@ -166,7 +166,7 @@ class BaseSiteAdapter(Configurable):
         return self.chapterUrls[i].get(attr,None)
 
     def get_chapters(self):
-        return copy.copy(self.chapterUrls)
+        return copy.deepcopy(self.chapterUrls)
 
     def del_chapter(self,i):
         del self.chapterUrls[i]
diff --git a/fanficfare/defaults.ini b/fanficfare/defaults.ini
index ad2f7479..9b955794 100644
--- a/fanficfare/defaults.ini
+++ b/fanficfare/defaults.ini
@@ -403,16 +403,18 @@ chapter_title_strip_pattern:^[0-9]+[\.: -]+(?=[^0-9]|$)
 mark_new_chapters:false
 
 ## chapter title patterns use python template substitution.  The
-## ${index} is the 'chapter' number and ${title} is the chapter title,
-## after applying chapter_title_strip_pattern.  Those are the only
-## variables available.
+## ${number} is the 'chapter' number and ${title} is the chapter
+## title, after applying chapter_title_strip_pattern.  ${index04} is
+## chapter number padded with leading zeros (mostly for internal use)
+## such as 0001.  ${index} == ${number} for backward compatibility.  A
+## few site adapters add additional chapter metadata.
 
 ## The basic pattern used when not using add_chapter_numbers or
 ## mark_new_chapters
 chapter_title_def_pattern:${title}
 
 ## Pattern used with add_chapter_numbers, but not mark_new_chapters
-chapter_title_add_pattern:${index}. ${title}
+chapter_title_add_pattern:${number}. ${title}
 
 ## Pattern used with mark_new_chapters, but not add_chapter_numbers
 ## (new) is just text and can be changed.
@@ -420,7 +422,7 @@ chapter_title_new_pattern:(new) ${title}
 
 ## Pattern used with add_chapter_numbers and mark_new_chapters
 ## (new) is just text and can be changed.
-chapter_title_addnew_pattern:${index}. (new) ${title}
+chapter_title_addnew_pattern:${number}. (new) ${title}
 
 ## Reorder ships so b/a and c/b/a become a/b and a/b/c. '/' is no
 ## longer hard coded and can be changed and added to with
@@ -711,7 +713,7 @@ use_threadmark_wordcounts:true
 ## chapter_title_*_pattern settings.
 ## Example:
 #tocpage_entry:
-# <a href="#section${index}">${chapter}</a> ${date} ${kwords}<br />
+# <a href="#section${index04}">${chapter}</a> ${date} ${kwords}<br />
 
 ## The 'date' value for chapters mentioned above can be formated with
 ## datethreadmark_format.  Otherwise it will default to
diff --git a/fanficfare/story.py b/fanficfare/story.py
index 77758398..97f658ce 100644
--- a/fanficfare/story.py
+++ b/fanficfare/story.py
@@ -1020,8 +1020,12 @@ class Story(Configurable):
                         'toctitle':chapter['title'],
                         'new':newchap,
                         'number':len(self.chapters)+1,
-                        'index':len(self.chapters)+1,
-                        '0index':"%04d"%(len(self.chapters)+1)})
+                        'index04':"%04d"%(len(self.chapters)+1)})
+        ## Due to poor planning on my part, chapter_title_*_pattern
+        ## expect index==1 while output settings expected index=0001.
+        ## index04 is to disambiguate, but index is kept for users'
+        ## pre-existing settings.
+        chapter['index']=chapter['index04']
         self.chapters.append(chapter)
 
     def getChapters(self,fortoc=False):
@@ -1065,22 +1069,17 @@ class Story(Configurable):
                 else:
                     usetempl = templ
                 # logger.debug("chap(%s)"%chap)
-            # Chapter = namedtuple('Chapter', 'url title html origtitle toctitle new')
                 chapter = defaultdict(unicode,chap)
-                chapter['chapter'] = chapter['title'] = usetempl.substitute(chap)
-                chapter['origtitle'] = templ.substitute(chap)
-                chapter['toctitle'] = toctempl.substitute(chap)
-                chapter['index'] = chap['number']  ## Due to poor planning on my part, chapter_title_*_pattern
-                retval.append(chapter)             ## expect index==1 not index=0001 like output settings.
-                    # Chapter(chap.url,
-                    #                    # 'new'
-                    #                    usetempl.substitute({'index':index+1,'title':chap.title}),
-                    #                    chap.html,
-                    #                    # 'orig'
-                    #                    templ.substitute({'index':index+1,'title':chap.title}),
-                    #                    # 'toc'
-                    #                    toctempl.substitute({'index':index+1,'title':chap.title}),
-                    #                    chap.new) )
+                ## Due to poor planning on my part,
+                ## chapter_title_*_pattern expect index==1 not
+                ## index=0001 like output settings.  index04 is now
+                ## used, but index is still included for backward
+                ## compatibility.
+                chapter['index'] = chapter['number']
+                chapter['chapter'] = chapter['title'] = usetempl.substitute(chapter)
+                chapter['origtitle'] = templ.substitute(chapter)
+                chapter['toctitle'] = toctempl.substitute(chapter)
+                retval.append(chapter)
         else:
             retval = self.chapters
 
diff --git a/fanficfare/writers/writer_epub.py b/fanficfare/writers/writer_epub.py
index d51babe7..049126d0 100644
--- a/fanficfare/writers/writer_epub.py
+++ b/fanficfare/writers/writer_epub.py
@@ -118,7 +118,7 @@ ${value}<br />
 ''')
 
         self.EPUB_TOC_ENTRY = string.Template('''
-<a href="file${index}.xhtml">${chapter}</a><br />
+<a href="file${index04}.xhtml">${chapter}</a><br />
 ''')
 
         self.EPUB_TOC_PAGE_END = string.Template('''
@@ -540,12 +540,12 @@ div { margin: 0pt; padding: 0pt; }
         for index, chap in enumerate(self.story.getChapters(fortoc=True)):
             if chap['html']:
                 i=index+1
-                items.append(("file%04d"%i,
-                              "OEBPS/file%04d.xhtml"%i,
+                items.append(("file%s"%chap['index04'],
+                              "OEBPS/file%s.xhtml"%chap['index04'],
                               "application/xhtml+xml",
                               chap['title']))
-                itemrefs.append("file%04d"%i)
-                chapurlmap[chap['url']]="file%04d.xhtml"%i # url -> relative epub file name.
+                itemrefs.append("file%s"%chap['index04'])
+                chapurlmap[chap['url']]="file%s.xhtml"%chap['index04'] # url -> relative epub file name.
 
         if dologpage:
             if self.getConfig("logpage_at_end") == "true":
@@ -715,12 +715,6 @@ div { margin: 0pt; padding: 0pt; }
                 chap['title']=removeEntities(chap['title'])
                 chap['origchapter']=removeEntities(chap['origtitle'])
                 chap['tocchapter']=removeEntities(chap['toctitle'])
-                # vals={'url':removeEntities(chap.url),
-                #       'chapter':removeEntities(chap.title),
-                #       'origchapter':removeEntities(chap.origtitle),
-                #       'tocchapter':removeEntities(chap.toctitle),
-                #       'index':"%04d"%(index+1),
-                #       'number':index+1}
                 # escape double quotes in all vals.
                 for k,v in chap.items():
                     if isinstance(v,basestring): chap[k]=v.replace('"','&quot;')
@@ -734,7 +728,7 @@ div { margin: 0pt; padding: 0pt; }
                 # (200k+)
                 fullhtml = re.sub(r'(</p>|<br ?/>)\n*',r'\1\n',fullhtml)
 
-                outputepub.writestr("OEBPS/file%04d.xhtml"%(index+1),fullhtml.encode('utf-8'))
+                outputepub.writestr("OEBPS/file%s.xhtml"%chap['index04'],fullhtml.encode('utf-8'))
                 del fullhtml
 
         if self.story.calibrebookmark:
diff --git a/fanficfare/writers/writer_html.py b/fanficfare/writers/writer_html.py
index 79f2c0a7..9dbd254e 100644
--- a/fanficfare/writers/writer_html.py
+++ b/fanficfare/writers/writer_html.py
@@ -137,7 +137,7 @@ ${output_css}
                 ## anchor to work.  Which it does by default.  This
                 ## could also be made configurable if some user
                 ## changed it.
-                chapurlmap[chap['url']]="#section%04d"%(index+1) # url -> index
+                chapurlmap[chap['url']]="#section"%chap['index04'] # url -> index
 
         for index, chap in enumerate(self.story.getChapters()):
             if chap['html']:
@@ -157,7 +157,6 @@ ${output_css}
 
 
                 logging.debug('Writing chapter text for: %s' % chap['title'])
-                # vals={'url':chap.url, 'chapter':chap.title, 'index':"%04d"%(index+1), 'number':index+1}
                 self._write(out,CHAPTER_START.substitute(chap))
                 self._write(out,chap_data)
                 self._write(out,CHAPTER_END.substitute(chap))
diff --git a/fanficfare/writers/writer_mobi.py b/fanficfare/writers/writer_mobi.py
index 9b039cc1..f37ee2fe 100644
--- a/fanficfare/writers/writer_mobi.py
+++ b/fanficfare/writers/writer_mobi.py
@@ -164,7 +164,6 @@ ${value}<br />
         for index, chap in enumerate(self.story.getChapters()):
             if chap['html']:
                 logger.debug('Writing chapter text for: %s' % chap['title'])
-                # vals={'url':chap.url, 'chapter':chap.title, 'index':"%04d"%(index+1), 'number':index+1}
                 fullhtml = CHAPTER_START.substitute(chap) + chap['html'] + CHAPTER_END.substitute(chap)
                 # ffnet(& maybe others) gives the whole chapter text
                 # as one line.  This causes problems for nook(at
diff --git a/fanficfare/writers/writer_txt.py b/fanficfare/writers/writer_txt.py
index 46182cb8..b5c10647 100644
--- a/fanficfare/writers/writer_txt.py
+++ b/fanficfare/writers/writer_txt.py
@@ -157,7 +157,6 @@ End file.
         for index, chap in enumerate(self.story.getChapters()):
             if chap['html']:
                 logging.debug('Writing chapter text for: %s' % chap['title'])
-                # vals={'url':chap.url, 'chapter':chap.title, 'index':"%04d"%(index+1), 'number':index+1}
                 self._write(out,self.lineends(self.wraplines(removeAllEntities(CHAPTER_START.substitute(chap)))))
                 self._write(out,self.lineends(html2text(chap['html'],bodywidth=self.wrap_width)))
                 self._write(out,self.lineends(self.wraplines(removeAllEntities(CHAPTER_END.substitute(chap)))))