diff --git a/src/calibre/ebooks/oeb/polish/container.py b/src/calibre/ebooks/oeb/polish/container.py
index e82bffe5dd..0591117a44 100644
--- a/src/calibre/ebooks/oeb/polish/container.py
+++ b/src/calibre/ebooks/oeb/polish/container.py
@@ -205,17 +205,20 @@ class Container(object):
                 if id_ is not None:
                     removed.add(id_)
                 elem.getparent().remove(elem)
+                self.dirty(self.opf_name)
         if removed:
             for item in self.opf.xpath('//opf:spine/opf:itemref[@idref]',
                                     namespaces={'opf':OPF2_NS}):
                 idref = item.get('idref')
                 if idref in removed:
                     item.getparent().remove(item)
+                    self.dirty(self.opf_name)
 
         for item in self.opf.xpath('//opf:guide/opf:reference[@href]',
                                     namespaces={'opf':OPF2_NS}):
             if self.href_to_name(item.get('href')) == name:
                 item.getparent().remove(item)
+                self.dirty(self.opf_name)
 
         path = self.name_path_map.pop(name)
         if os.path.exists(path):
@@ -228,10 +231,10 @@ class Container(object):
         self.dirtied.add(name)
 
     def commit(self, outpath=None):
-        for name in self.dirtied:
+        for name in tuple(self.dirtied):
             self.dirtied.remove(name)
             data = self.parsed_cache.pop(name)
-            data = serialize(data)
+            data = serialize(data, self.mime_map[name])
             with open(self.name_path_map[name], 'wb') as f:
                 f.write(data)
 
@@ -365,6 +368,8 @@ class EpubContainer(Container):
         if outpath is None:
             outpath = self.pathtoepub
         from calibre.ebooks.tweak import zip_rebuilder
+        with open(join(self.root, 'mimetype'), 'wb') as f:
+            f.write(guess_type('a.epub')[0])
         zip_rebuilder(self.root, outpath)
 
 # }}}
diff --git a/src/calibre/ebooks/oeb/polish/subset.py b/src/calibre/ebooks/oeb/polish/subset.py
index 76906ed3ca..c13bdb860f 100644
--- a/src/calibre/ebooks/oeb/polish/subset.py
+++ b/src/calibre/ebooks/oeb/polish/subset.py
@@ -7,10 +7,11 @@ __license__   = 'GPL v3'
 __copyright__ = '2013, Kovid Goyal <kovid at kovidgoyal.net>'
 __docformat__ = 'restructuredtext en'
 
-import os
+import os, sys
 
+from calibre import prints
 from calibre.ebooks.oeb.base import OEB_STYLES, OEB_DOCS, XPath
-from calibre.ebooks.oeb.polish import OEB_FONTS
+from calibre.ebooks.oeb.polish.container import OEB_FONTS
 from calibre.utils.fonts.sfnt.subset import subset
 
 def remove_font_face_rules(container, sheet, remove_names):
@@ -74,3 +75,22 @@ def subset_all_fonts(container, font_stats, report):
     report('Reduced total font size to %.1f%% of original'%(
         total_new/total_old*100))
 
+if __name__ == '__main__':
+    from calibre.ebooks.oeb.polish.container import get_container
+    from calibre.ebooks.oeb.polish.stats import StatsCollector
+    from calibre.utils.logging import default_log
+    default_log.filter_level = default_log.DEBUG
+    inbook = sys.argv[-1]
+    ebook = get_container(inbook, default_log)
+    report = []
+    stats = StatsCollector(ebook).font_stats
+    subset_all_fonts(ebook, stats, report.append)
+    outbook, ext = inbook.rpartition('.')[0::2]
+    outbook += '_subset.'+ext
+    ebook.commit(outbook)
+    prints('\nReport:')
+    for msg in report:
+        prints(msg)
+    print()
+    prints('Output written to:', outbook)
+