Check Book: When reporting unmanifested file warnings, allow auto fixing by adding the file to the manifest if it is referenced elsewhere or removing the file if it is not. Fixes #1323362 [Automatic fix does not work for "file is not listed in the book manifest."](https://bugs.launchpad.net/calibre/+bug/1323362)

src/calibre/ebooks/oeb/polish/check/links.py

@@ -95,10 +95,21 @@ class Unmanifested(BadLink):
              ' it is good practice to list all files in the manifest. Either list this'
              ' file in the manifest or remove it from the book if it is an unnecessary file.')
 
-    def __init__(self, name):
+    def __init__(self, name, unreferenced=None):
         BadLink.__init__(self, _(
             'The file %s is not listed in the manifest') % name, name)
+        self.file_action = None
+        if unreferenced is not None:
+            self.INDIVIDUAL_FIX = _(
+                'Remove %s from the book') % name if unreferenced else _(
+                    'Add %s to the manifest') % name
+            self.file_action = 'remove' if unreferenced else 'add'
 
+    def __call__(self, container):
+        if self.file_action == 'remove':
+            container.remove_item(self.name)
+        else:
+            container.add_name_to_manifest(self.name)
 
 class Bookmarks(BadLink):
 
@@ -251,7 +262,7 @@ def check_links(container):
     manifest_names = set(container.manifest_id_map.itervalues())
     for name in container.mime_map:
         if name not in manifest_names and not container.ok_to_be_unmanifested(name):
-            a(Unmanifested(name))
+            a(Unmanifested(name, unreferenced=name in unreferenced))
         if name == 'META-INF/calibre_bookmarks.txt':
             a(Bookmarks(name))
 

src/calibre/ebooks/oeb/polish/container.py

@@ -171,6 +171,22 @@ class Container(object):  # {{{
             ans = 'application/xhtml+xml'
         return ans
 
+    def add_name_to_manifest(self, name):
+        all_ids = {x.get('id') for x in self.opf_xpath('//*[@id]')}
+        c = 0
+        item_id = 'id'
+        while item_id in all_ids:
+            c += 1
+            item_id = 'id' + '%d'%c
+        manifest = self.opf_xpath('//opf:manifest')[0]
+        href = self.name_to_href(name, self.opf_name)
+        item = manifest.makeelement(OPF('item'),
+                                    id=item_id, href=href)
+        item.set('media-type', self.mime_map[name])
+        self.insert_into_xml(manifest, item)
+        self.dirty(self.opf_name)
+        return item_id
+
     def add_file(self, name, data, media_type=None, spine_index=None):
         ''' Add a file to this container. Entries for the file are
         automatically created in the OPF manifest and spine
@@ -194,19 +210,9 @@ class Container(object):  # {{{
         self.mime_map[name] = mt
         if self.ok_to_be_unmanifested(name):
             return
-        all_ids = {x.get('id') for x in self.opf_xpath('//*[@id]')}
+        item_id = self.add_name_to_manifest(name)
-        c = 0
-        item_id = 'id'
-        while item_id in all_ids:
-            c += 1
-            item_id = 'id' + '%d'%c
-        manifest = self.opf_xpath('//opf:manifest')[0]
-        item = manifest.makeelement(OPF('item'),
-                                    id=item_id, href=href)
-        item.set('media-type', mt)
-        self.insert_into_xml(manifest, item)
-        self.dirty(self.opf_name)
         if mt in OEB_DOCS:
+            manifest = self.opf_xpath('//opf:manifest')[0]
             spine = self.opf_xpath('//opf:spine')[0]
             si = manifest.makeelement(OPF('itemref'), idref=item_id)
             self.insert_into_xml(spine, si, index=spine_index)