Fix a long-standing bug that could cause the wrong index file to be used when committing to the git-annex branch, if GIT_INDEX_FILE is set in the environment. This typically resulted in git-annex branch log files being committed to the master branch and later showing up in the work tree. (These log files can be safely removed.)

Remote/Git.hs

@@ -54,6 +54,7 @@ import Control.Concurrent
 import Control.Concurrent.MSampleVar
 import System.Process (std_in, std_err)
 import qualified Data.Map as M
+import qualified Data.AssocList as A
 import Control.Exception.Extensible
 
 remote :: RemoteType
@@ -414,13 +415,13 @@ fsckOnRemote r params
 			Just (c, ps) -> batchCommand c ps
 	| otherwise = return $ do
 		program <- readProgramFile
-		env <- getEnvironment
 		r' <- Git.Config.read r
-		let env' =
+		env <- getEnvironment
+		let env' = A.addEntries 
 			[ ("GIT_WORK_TREE", Git.repoPath r')
 			, ("GIT_DIR", Git.localGitDir r')
-			] ++ env
-		batchCommandEnv program (Param "fsck" : params) (Just env')
+			] env
+		batchCommandEnv program (Param "fsck" : params) $ Just env'
 
 {- The passed repair action is run in the Annex monad of the remote. -}
 repairRemote :: Git.Repo -> Annex Bool -> Annex (IO Bool)

Remote/Glacier.hs

@@ -9,6 +9,7 @@ module Remote.Glacier (remote, jobList) where
 
 import qualified Data.Map as M
 import qualified Data.Text as T
+import Data.AssocList as A
 import System.Environment
 
 import Common.Annex
@@ -232,7 +233,7 @@ glacierEnv c u = go =<< getRemoteCredPairFor "glacier" c creds
 	go Nothing = return Nothing
 	go (Just (user, pass)) = do
 		e <- liftIO getEnvironment
-		return $ Just $ (uk, user):(pk, pass):e
+		return $ Just $ A.addEntries [(uk, user), (pk, pass)] e
 
 	creds = AWS.creds u
 	(uk, pk) = credPairEnvironment creds

Remote/Hook.hs

@@ -9,6 +9,7 @@ module Remote.Hook (remote) where
 
 import qualified Data.ByteString.Lazy as L
 import qualified Data.Map as M
+import qualified Data.AssocList as A
 import System.Environment
 
 import Common.Annex
@@ -77,8 +78,7 @@ hookSetup mu c = do
 hookEnv :: Action -> Key -> Maybe FilePath -> IO (Maybe [(String, String)])
 hookEnv action k f = Just <$> mergeenv (fileenv f ++ keyenv)
   where
-	mergeenv l = M.toList . M.union (M.fromList l) 
-		<$> M.fromList <$> getEnvironment
+	mergeenv l = A.addEntries l <$> getEnvironment
 	env s v = ("ANNEX_" ++ s, v)
 	keyenv = catMaybes
 		[ Just $ env "KEY" (key2file k)