6 files changed, 69 insertions, 16 deletions
diff --git a/Git/RecoverRepository.hs b/Git/RecoverRepository.hs
index 8dce04f1e..c2cad53f2 100644
--- a/Git/RecoverRepository.hs
+++ b/Git/RecoverRepository.hs
@@ -10,6 +10,7 @@ module Git.RecoverRepository (
 	retrieveMissingObjects,
 	resetLocalBranches,
 	removeTrackingBranches,
+	rewriteIndex,
 	emptyGoodCommits,
 ) where
 
@@ -19,17 +20,21 @@ import Git.Command
 import Git.Fsck
 import Git.Objects
 import Git.Sha
+import Git.Types
 import qualified Git.Config
 import qualified Git.Construct
 import qualified Git.LsTree as LsTree
+import qualified Git.LsFiles as LsFiles
 import qualified Git.Ref as Ref
 import qualified Git.RefLog as RefLog
+import qualified Git.UpdateIndex as UpdateIndex
 import Utility.Tmp
 import Utility.Rsync
 
 import qualified Data.Set as S
 import qualified Data.ByteString.Lazy as L
 import System.Log.Logger
+import Data.Tuple.Utils
 
 {- Finds and removes corrupt objects from the repository, returning a list
  - of all such objects, which need to be found elsewhere to finish
@@ -349,6 +354,30 @@ verifyTree missing treesha r
 			-- as long as ls-tree succeeded, we're good
 			else cleanup
 
+{- Rewrites the index file, removing from it any files whose blobs are
+ - missing. Returns the list of affected files. -}
+rewriteIndex :: MissingObjects -> Repo -> IO [FilePath]
+rewriteIndex missing r
+	| repoIsLocalBare r = return []
+	| otherwise = do
+		(indexcontents, cleanup) <- LsFiles.stagedDetails [Git.repoPath r] r
+		let (missing, present) = partition ismissing indexcontents
+		unless (null missing) $ do
+			nukeFile (localGitDir r </> "index")
+			UpdateIndex.streamUpdateIndex r
+				=<< (catMaybes <$> mapM reinject present)
+		void cleanup
+		return $ map fst3 missing
+  where
+	getblob (_file, Just sha, Just _mode) = Just sha
+	getblob _ = Nothing
+	ismissing = maybe False (`S.member` missing) . getblob
+	reinject (file, Just sha, Just mode) = case toBlobType mode of
+		Nothing -> return Nothing
+		Just blobtype -> Just <$>
+			UpdateIndex.stageFile sha blobtype file r
+	reinject _ = return Nothing
+
 newtype GoodCommits = GoodCommits (S.Set Sha)
 
 emptyGoodCommits :: GoodCommits
diff --git a/Git/Types.hs b/Git/Types.hs
index 4765aad6c..abfb99f9f 100644
--- a/Git/Types.hs
+++ b/Git/Types.hs
@@ -9,6 +9,7 @@ module Git.Types where
 
 import Network.URI
 import qualified Data.Map as M
+import System.Posix.Types
 
 {- Support repositories on local disk, and repositories accessed via an URL.
  -
@@ -81,3 +82,9 @@ readBlobType "100644" = Just FileBlob
 readBlobType "100755" = Just ExecutableBlob
 readBlobType "120000" = Just SymlinkBlob
 readBlobType _ = Nothing
+
+toBlobType :: FileMode -> Maybe BlobType
+toBlobType 0o100644 = Just FileBlob
+toBlobType 0o100755 = Just ExecutableBlob
+toBlobType 0o120000 = Just SymlinkBlob
+toBlobType _ = Nothing
diff --git a/Git/UpdateIndex.hs b/Git/UpdateIndex.hs
index 5d07e2011..3b33ac846 100644
--- a/Git/UpdateIndex.hs
+++ b/Git/UpdateIndex.hs
@@ -13,6 +13,7 @@ module Git.UpdateIndex (
 	streamUpdateIndex,
 	lsTree,
 	updateIndexLine,
+	stageFile,
 	unstageFile,
 	stageSymlink
 ) where
@@ -61,6 +62,11 @@ updateIndexLine :: Sha -> BlobType -> TopFilePath -> String
 updateIndexLine sha filetype file =
 	show filetype ++ " blob " ++ show sha ++ "\t" ++ indexPath file
 
+stageFile :: Sha -> BlobType -> FilePath -> Repo -> IO Streamer
+stageFile sha filetype file repo = do
+	p <- toTopFilePath file repo
+	return $ pureStreamer $ updateIndexLine sha filetype p
+
 {- A streamer that removes a file from the index. -}
 unstageFile :: FilePath -> Repo -> IO Streamer
 unstageFile file repo = do
diff --git a/doc/design/assistant/disaster_recovery.mdwn b/doc/design/assistant/disaster_recovery.mdwn
index 4b3d2a290..c630a72b4 100644
--- a/doc/design/assistant/disaster_recovery.mdwn
+++ b/doc/design/assistant/disaster_recovery.mdwn
@@ -148,8 +148,5 @@ that was found for it.
   if none was found. **done**
 * (Decided not to touch tags.)
 
-TODO: The index file can still refer to objects that were missing.
-This prevents git commit from working. And simply re-staging things doesn't
-seem to help; git sees the sha is "known" and does not re-add it,
-apparently. So, need to do something to clean up the index, while ideally
-not losing any staged changes.
+The index file can still refer to objects that were missing.
+Rewrite to remove them. **done**
diff --git a/doc/git-recover-repository.mdwn b/doc/git-recover-repository.mdwn
index f437e5688..dac4a310b 100644
--- a/doc/git-recover-repository.mdwn
+++ b/doc/git-recover-repository.mdwn
@@ -15,11 +15,12 @@ It does by deleting all corrupt objects, and retreiving all missing
 objects that it can from the remotes of the repository.
 
 If that is not sufficient to fully recover the repository, it can also
-reset branches back to commits before the corruption happened, and delete
-branches that are no longer available due to the lost data. It will only
-do this if run with the `--force` option, since that rewrites history
-and throws out missing data. Note that the `--force` option never touches
-tags, even if they are no longer usable due to missing data.
+reset branches back to commits before the corruption happened, delete
+branches that are no longer available due to the lost data, and remove any
+missing files from the index. It will only do this if run with the
+`--force` option, since that rewrites history and throws out missing data.
+Note that the `--force` option never touches tags, even if they are no
+longer usable due to missing data.
 
 After running this command, you will probably want to run `git fsck` to
 verify it fixed the repository. Note that fsck may still complain about
diff --git a/git-recover-repository.hs b/git-recover-repository.hs
index 21852e376..998ab802c 100644
--- a/git-recover-repository.hs
+++ b/git-recover-repository.hs
@@ -68,12 +68,13 @@ main = do
 							, "remote tracking branches that referred to missing objects"
 							]
 					(resetbranches, deletedbranches, _) <- Git.RecoverRepository.resetLocalBranches stillmissing goodcommits g
-					unless (null resetbranches) $ do
-						putStrLn "Reset these local branches to old versions before the missing objects were committed:"
-						putStr $ unlines $ map show resetbranches
-					unless (null deletedbranches) $ do
-						putStrLn "Deleted these local branches, which could not be recovered due to missing objects:"
-						putStr $ unlines $ map show deletedbranches
+					printList (map show resetbranches)
+						"Reset these local branches to old versions before the missing objects were committed:"
+					printList (map show deletedbranches)
+						"Deleted these local branches, which could not be recovered due to missing objects:"
+					deindexedfiles <- Git.RecoverRepository.rewriteIndex stillmissing g
+					printList deindexedfiles
+						"Removed these missing files from the index. You should look at what files are present in your working tree and git add them back to the index when appropriate."
 					mcurr <- Git.Branch.currentUnsafe g
 					case mcurr of
 						Nothing -> return ()
@@ -84,3 +85,15 @@ main = do
 								, "checked out. You may have staged changes in the index that can be committed to recover the lost state of this branch!"
 								]
 				else putStrLn "To force a recovery to a usable state, run this command again with the --force parameter."
+
+printList :: [String] -> String -> IO ()
+printList items header
+	| null items = return ()
+	| otherwise = do
+		putStrLn header
+		putStr $ unlines $ map (\i -> "\t" ++ i) truncateditems
+  where
+  	numitems = length items
+	truncateditems
+		| numitems > 10 = take 10 items ++ ["(and " ++ show (numitems - 10) ++ " more)"]
+		| otherwise = items