fixed reconcileStaged crash when index is locked or in conflict

Eg, when git commit runs the smudge filter.

Commit 428c91606b introduced the crash,
as write-tree fails in those situations. Now it will work, and git-annex
always gets up-to-date information even in those situations. It does
need to do a bit more work, each time git-annex is run with the index
locked. Although if the index is unmodified from the last time
write-tree succeeded, that work is avoided.

Git/Branch.hs

@@ -185,8 +185,18 @@ commitAlways :: CommitMode -> String -> Branch -> [Ref] -> Repo -> IO Sha
 commitAlways commitmode message branch parentrefs repo = fromJust
 	<$> commit commitmode True message branch parentrefs repo
 
+-- Throws exception if the index is locked, with an error message output by
+-- git on stderr.
 writeTree :: Repo -> IO Sha
-writeTree repo = getSha "write-tree" $ pipeReadStrict [Param "write-tree"] repo
+writeTree repo = getSha "write-tree" $
+	pipeReadStrict [Param "write-tree"] repo
+
+-- Avoids error output if the command fails due to eg, the index being locked.
+writeTreeQuiet :: Repo -> IO (Maybe Sha)
+writeTreeQuiet repo = extractSha <$> withNullHandle go
+  where
+	go nullh = pipeReadStrict' (\p -> p { std_err = UseHandle nullh }) 
+		[Param "write-tree"] repo
 
 commitTree :: CommitMode -> String -> [Ref] -> Ref -> Repo -> IO Sha
 commitTree commitmode message parentrefs tree repo =

Git/Command.hs

@@ -70,17 +70,15 @@ pipeReadLazy params repo = assertLocal repo $ do
  - Nonzero exit status is ignored.
  -}
 pipeReadStrict :: [CommandParam] -> Repo -> IO S.ByteString
-pipeReadStrict = pipeReadStrict' S.hGetContents
+pipeReadStrict = pipeReadStrict' id
 
-{- The reader action must be strict. -}
-pipeReadStrict' :: (Handle -> IO a) -> [CommandParam] -> Repo -> IO a
-pipeReadStrict' reader params repo = assertLocal repo $ withCreateProcess p go
+pipeReadStrict' :: (CreateProcess -> CreateProcess) -> [CommandParam] -> Repo -> IO S.ByteString
+pipeReadStrict' fp params repo = assertLocal repo $ withCreateProcess p go
   where
-	p  = (gitCreateProcess params repo)
-		{ std_out = CreatePipe }
+	p = fp (gitCreateProcess params repo) { std_out = CreatePipe }
 
 	go _ (Just outh) _ pid = do
-		output <- reader outh
+		output <- S.hGetContents outh
 		hClose outh
 		void $ waitForProcess pid
 		return output