Assistant, repair: Filter out git fsck lines about duplicate file entries in tree objects.

CHANGELOG

@@ -9,6 +9,8 @@ git-annex (6.20160809) UNRELEASED; urgency=medium
   * Make --json and --quiet suppress automatic init messages, and any
     other messages that might be output before a command starts.
     Fixes a reversion introduced in version 5.20150727.
+  * Assistant, repair: Filter out git fsck lines about duplicate file
+    entries in tree objects.
 
  -- Joey Hess <id@joeyh.name>  Mon, 05 Sep 2016 11:51:49 -0400
 

Git/Fsck.hs

@@ -104,6 +104,8 @@ findShas :: Bool -> String -> [Sha]
 findShas supportsNoDangling = catMaybes . map extractSha . concat . map words . filter wanted . lines
   where
 	wanted l
+		-- Skip lines like "error in tree <sha>: duplicateEntries: contains duplicate file entries"
+		| "duplicateEntries" `isPrefixOf` l = False
 		| supportsNoDangling = True
 		| otherwise = not ("dangling " `isPrefixOf` l)
 

doc/forum/how_to_disaster_recovery/comment_5_9b9403a80c5b0a1a441dfb94feece37d._comment

@@ -0,0 +1,20 @@
+[[!comment format=mdwn
+ username="joey"
+ subject="""comment 5"""
+ date="2016-09-05T20:02:39Z"
+ content="""
+Very interesting git fsck output!
+
+It seems like your git repository has somehow gotten a tree object in it
+which contains two files with the same name.
+
+While git's data structures allow this, it's pretty nonsensical, and it's
+not something that would normally ever happen. It would be interesting to
+take a look and see what commits use those tree objects, and where those
+strange trees came from.
+
+git-annex in turn is seeing that tree object's sha in the fsck output and
+assumes fsck means that the data for that object is broken or missing.
+So, I suppose what I'll do is make it skip over lines containing
+`duplicateEntries`, and then it won't try to repair this repository.
+"""]]