The script removes duplicate message files.  It takes no options.

Files are assumed duplicates if their content is the same except for
ignored headers.  Currently, the only ignored header is Received:.
---
 contrib/notmuch-remove-duplicates.py |   95 ++++++++++++++++++++++++++++++++++
 1 file changed, 95 insertions(+)
 create mode 100755 contrib/notmuch-remove-duplicates.py

diff --git a/contrib/notmuch-remove-duplicates.py b/contrib/notmuch-remove-duplicates.py
new file mode 100755
index 0000000..dbe2e25
--- /dev/null
+++ b/contrib/notmuch-remove-duplicates.py
@@ -0,0 +1,95 @@
+#!/usr/bin/env python
+
+import sys
+
+IGNORED_HEADERS = [ "Received:" ]
+
+if len(sys.argv) != 1:
+    print "Usage: %s" % sys.argv[0]
+    print
+    print "The script removes duplicate message files.  Takes no options."
+    print "Requires notmuch python module."
+    print
+    print "Files are assumed duplicates if their content is the same"
+    print "except for the following headers: %s." % ", ".join(IGNORED_HEADERS)
+    exit(1)
+
+import notmuch
+import os
+import time
+
+class MailComparator:
+    """Checks if mail files are duplicates."""
+    def __init__(self, filename):
+        self.filename = filename
+        self.mail = self.readFile(self.filename)
+
+    def isDuplicate(self, filename):
+        return self.mail == self.readFile(filename)
+
+    @staticmethod
+    def readFile(filename):
+        with open(filename) as f:
+            data = ""
+            while True:
+                line = f.readline()
+                for header in IGNORED_HEADERS:
+                    if line.startswith(header):
+                        # skip header continuation lines
+                        while True:
+                            line = f.readline()
+                            if len(line) == 0 or line[0] not in [" ", "\t"]:
+                                break
+                        break
+                else:
+                    data += line
+                    if line == "\n":
+                        break
+            data += f.read()
+            return data
+
+db = notmuch.Database()
+query = db.create_query('*')
+print "Number of messages: %s" % query.count_messages()
+
+files_count = 0
+for root, dirs, files in os.walk(db.get_path()):
+    if not root.startswith(os.path.join(db.get_path(), ".notmuch/")):
+        files_count += len(files)
+print "Number of files: %s" % files_count
+print "Estimated number of duplicates: %s" % (files_count - query.count_messages())
+
+msgs = query.search_messages()
+msg_count = 0
+suspected_duplicates_count = 0
+duplicates_count = 0
+timestamp = time.time()
+for msg in msgs:
+    msg_count += 1
+    if len(msg.get_filenames()) > 1:
+        filenames = msg.get_filenames()
+        comparator = MailComparator(filenames.next())
+        for filename in filenames:
+            if os.path.realpath(comparator.filename) == os.path.realpath(filename):
+                print "Message '%s' has filenames pointing to the same file: '%s' '%s'" % (msg.get_message_id(), comparator.filename, filename)
+            elif comparator.isDuplicate(filename):
+                os.remove(filename)
+                duplicates_count += 1
+            else:
+                #print "Potential duplicates: %s" % msg.get_message_id()
+                suspected_duplicates_count += 1
+
+    new_timestamp = time.time()
+    if new_timestamp - timestamp > 1:
+        timestamp = new_timestamp
+        sys.stdout.write("\rProcessed %s messages, removed %s duplicates..." % (msg_count, duplicates_count))
+        sys.stdout.flush()
+
+print "\rFinished. Processed %s messages, removed %s duplicates." % (msg_count, duplicates_count)
+if duplicates_count > 0:
+    print "You might want to run 'notmuch new' now."
+
+if suspected_duplicates_count > 0:
+    print
+    print "Found %s messages with duplicate IDs but different content." % suspected_duplicates_count
+    print "Perhaps we should ignore more headers."
-- 
1.7.10.4