diff --git a/Annex/AdjustedBranch.hs b/Annex/AdjustedBranch.hs
--- a/Annex/AdjustedBranch.hs
+++ b/Annex/AdjustedBranch.hs
@@ -20,6 +20,7 @@
 	adjustToCrippledFileSystem,
 	updateAdjustedBranch,
 	propigateAdjustedCommits,
+	AdjustedClone(..),
 	checkAdjustedClone,
 	isGitVersionSupported,
 	checkVersionSupported,
@@ -51,6 +52,7 @@
 import Annex.GitOverlay
 import Utility.Tmp
 import qualified Database.Keys
+import Config
 
 import qualified Data.Map as M
 
@@ -298,9 +300,20 @@
 	mkcommit = Git.Branch.commitTree Git.Branch.AutomaticCommit
 		adjustedBranchCommitMessage parents treesha
 
+{- This message should never be changed. -}
 adjustedBranchCommitMessage :: String
 adjustedBranchCommitMessage = "git-annex adjusted branch"
 
+findAdjustingCommit :: AdjBranch -> Annex (Maybe Commit)
+findAdjustingCommit (AdjBranch b) = go =<< catCommit b
+  where
+	go Nothing = return Nothing
+	go (Just c)
+		| commitMessage c == adjustedBranchCommitMessage = return (Just c)
+		| otherwise = case commitParent c of
+			[p] -> go =<< catCommit p
+			_ -> return Nothing
+
 {- Update the currently checked out adjusted branch, merging the provided
  - branch into it. Note that the provided branch should be a non-adjusted
  - branch. -}
@@ -345,10 +358,16 @@
 		withTmpDirIn misctmpdir "git" $ \tmpgit -> withWorkTreeRelated tmpgit $
 			withemptydir tmpwt $ withWorkTree tmpwt $ do
 				liftIO $ writeFile (tmpgit </> "HEAD") (fromRef updatedorig)
+				-- This reset makes git merge not care
+				-- that the work tree is empty; otherwise
+				-- it will think that all the files have
+				-- been staged for deletion, and sometimes
+				-- the merge includes these deletions
+				-- (for an unknown reason).
+				-- http://thread.gmane.org/gmane.comp.version-control.git/297237
+				inRepo $ Git.Command.run [Param "reset", Param "HEAD", Param "--quiet"]
 				showAction $ "Merging into " ++ fromRef (Git.Ref.base origbranch)
-				-- The --no-ff is important; it makes git
-				-- merge not care that the work tree is empty.
-				merged <- inRepo (Git.Merge.merge' [Param "--no-ff"] tomerge mergeconfig commitmode)
+				merged <- inRepo (Git.Merge.merge' [] tomerge mergeconfig commitmode)
 					<||> (resolveMerge (Just updatedorig) tomerge True <&&> commitResolvedMerge commitmode)
 				if merged
 					then do
@@ -539,23 +558,49 @@
 	(Git.DiffTree.dstmode dti)
 	(Git.DiffTree.dstsha dti)
 
+data AdjustedClone = InAdjustedClone | NotInAdjustedClone | NeedUpgradeForAdjustedClone
+
 {- Cloning a repository that has an adjusted branch checked out will
  - result in the clone having the same adjusted branch checked out -- but
- - the origbranch won't exist in the clone, nor will the basis.
- - Create them. -}
-checkAdjustedClone :: Annex ()
-checkAdjustedClone = go =<< inRepo Git.Branch.current
+ - the origbranch won't exist in the clone, nor will the basis. So
+ - to properly set up the adjusted branch, the origbranch and basis need
+ - to be set.
+ - 
+ - We can't trust that the origin's origbranch matches up with the currently
+ - checked out adjusted branch; the origin could have the two branches
+ - out of sync (eg, due to another branch having been pushed to the origin's
+ - origbranch), or due to a commit on its adjusted branch not having been
+ - propigated back to origbranch.
+ -
+ - So, find the adjusting commit on the currently checked out adjusted
+ - branch, and use the parent of that commit as the basis, and set the
+ - origbranch to it.
+ -
+ - The repository may also need to be upgraded to a new version, if the
+ - current version is too old to support adjusted branches. -}
+checkAdjustedClone :: Annex AdjustedClone
+checkAdjustedClone = ifM isBareRepo
+	( return NotInAdjustedClone
+	, go =<< inRepo Git.Branch.current
+	)
   where
-	go Nothing = return ()
+	go Nothing = return NotInAdjustedClone
 	go (Just currbranch) = case adjustedToOriginal currbranch of
-		Nothing -> return ()
+		Nothing -> return NotInAdjustedClone
 		Just (adj, origbranch) -> do
-			let remotebranch = Git.Ref.underBase "refs/remotes/origin" origbranch
 			let basis@(BasisBranch bb) = basisBranch (originalToAdjusted origbranch adj)
-			unlessM (inRepo $ Git.Ref.exists bb) $
-				setBasisBranch basis remotebranch
-			unlessM (inRepo $ Git.Ref.exists origbranch) $
-				inRepo $ Git.Branch.update' origbranch remotebranch
+			unlessM (inRepo $ Git.Ref.exists bb) $ do
+				unlessM (inRepo $ Git.Ref.exists origbranch) $ do
+					let remotebranch = Git.Ref.underBase "refs/remotes/origin" origbranch
+					inRepo $ Git.Branch.update' origbranch remotebranch
+				aps <- fmap commitParent <$> findAdjustingCommit (AdjBranch currbranch)
+				case aps of
+					Just [p] -> setBasisBranch basis p
+					_ -> error $ "Unable to clean up from clone of adjusted branch; perhaps you should check out " ++ Git.Ref.describe origbranch
+			ifM versionSupportsUnlockedPointers
+				( return InAdjustedClone
+				, return NeedUpgradeForAdjustedClone
+				)
 
 -- git 2.2.0 needed for GIT_COMMON_DIR which is needed
 -- by updateAdjustedBranch to use withWorkTreeRelated.
diff --git a/Annex/AutoMerge.hs b/Annex/AutoMerge.hs
--- a/Annex/AutoMerge.hs
+++ b/Annex/AutoMerge.hs
@@ -121,7 +121,7 @@
 	let merged = not (null mergedfs')
 	void $ liftIO cleanup
 
-	unlessM isDirect $ do
+	unlessM (pure inoverlay <||> isDirect) $ do
 		(deleted, cleanup2) <- inRepo (LsFiles.deleted [top])
 		unless (null deleted) $
 			Annex.Queue.addCommand "rm"
diff --git a/Annex/Environment.hs b/Annex/Environment.hs
--- a/Annex/Environment.hs
+++ b/Annex/Environment.hs
@@ -33,7 +33,7 @@
 
 checkEnvironmentIO :: IO ()
 checkEnvironmentIO = whenM (isNothing <$> myUserGecos) $ do
-	username <- myUserName
+	username <- either (const "unknown") id <$> myUserName
 	ensureEnv "GIT_AUTHOR_NAME" username
 	ensureEnv "GIT_COMMITTER_NAME" username
   where
@@ -52,7 +52,7 @@
 ensureCommit a = either retry return =<< tryNonAsync a 
   where
 	retry _ = do
-		name <- liftIO myUserName
+		name <- liftIO $ either (const "unknown") id <$> myUserName
 		setConfig (ConfigKey "user.name") name
 		setConfig (ConfigKey "user.email") name
 		a
diff --git a/Annex/GitOverlay.hs b/Annex/GitOverlay.hs
--- a/Annex/GitOverlay.hs
+++ b/Annex/GitOverlay.hs
@@ -15,6 +15,7 @@
 import Git.Index
 import Git.Env
 import qualified Annex
+import qualified Annex.Queue
 
 {- Runs an action using a different git index file. -}
 withIndexFile :: FilePath -> Annex a -> Annex a
@@ -71,8 +72,18 @@
 withAltRepo modrepo unmodrepo a = do
 	g <- gitRepo
 	g' <- liftIO $ modrepo g
-	r <- tryNonAsync $ do
-		Annex.changeState $ \s -> s { Annex.repo = g' }
+	q <- Annex.Queue.get
+	v <- tryNonAsync $ do
+		Annex.changeState $ \s -> s
+			{ Annex.repo = g'
+			-- Start a separate queue for any changes made
+			-- with the modified repo.
+			, Annex.repoqueue = Nothing
+			}
 		a
-	Annex.changeState $ \s -> s { Annex.repo = unmodrepo g (Annex.repo s) }
-	either E.throw return r
+	void $ tryNonAsync Annex.Queue.flush
+	Annex.changeState $ \s -> s
+		{ Annex.repo = unmodrepo g (Annex.repo s)
+		, Annex.repoqueue = Just q
+		}
+	either E.throw return v
diff --git a/Annex/Ingest.hs b/Annex/Ingest.hs
--- a/Annex/Ingest.hs
+++ b/Annex/Ingest.hs
@@ -11,6 +11,7 @@
 	lockDown,
 	ingestAdd,
 	ingest,
+	ingest',
 	finishIngestDirect,
 	finishIngestUnlocked,
 	cleanOldKeys,
@@ -140,9 +141,12 @@
  - tree or the index.
  -}
 ingest :: Maybe LockedDown -> Annex (Maybe Key, Maybe InodeCache)
-ingest Nothing = return (Nothing, Nothing)
-ingest (Just (LockedDown cfg source)) = withTSDelta $ \delta -> do
-	backend <- chooseBackend $ keyFilename source
+ingest = ingest' Nothing
+
+ingest' :: Maybe Backend -> Maybe LockedDown -> Annex (Maybe Key, Maybe InodeCache)
+ingest' _ Nothing = return (Nothing, Nothing)
+ingest' preferredbackend (Just (LockedDown cfg source)) = withTSDelta $ \delta -> do
+	backend <- maybe (chooseBackend $ keyFilename source) (return . Just) preferredbackend
 	k <- genKey source backend
 	let src = contentLocation source
 	ms <- liftIO $ catchMaybeIO $ getFileStatus src
diff --git a/Annex/Init.hs b/Annex/Init.hs
--- a/Annex/Init.hs
+++ b/Annex/Init.hs
@@ -40,8 +40,8 @@
 import Upgrade
 import Annex.Perms
 import qualified Database.Keys
-#ifndef mingw32_HOST_OS
 import Utility.UserInfo
+#ifndef mingw32_HOST_OS
 import Utility.FileMode
 import System.Posix.User
 import qualified Utility.LockFile.Posix as Posix
@@ -52,13 +52,11 @@
 genDescription Nothing = do
 	reldir <- liftIO . relHome =<< liftIO . absPath =<< fromRepo Git.repoPath
 	hostname <- fromMaybe "" <$> liftIO getHostname
-#ifndef mingw32_HOST_OS
 	let at = if null hostname then "" else "@"
-	username <- liftIO myUserName
-	return $ concat [username, at, hostname, ":", reldir]
-#else
-	return $ concat [hostname, ":", reldir]
-#endif
+	v <- liftIO myUserName
+	return $ concat $ case v of
+		Right username -> [username, at, hostname, ":", reldir]
+		Left _ -> [hostname, ":", reldir]
 
 initialize :: Maybe String -> Maybe Version -> Annex ()
 initialize mdescription mversion = do
@@ -85,7 +83,7 @@
 	checkLockSupport
 	checkFifoSupport
 	checkCrippledFileSystem
-	unlessM isBare $
+	unlessM isBareRepo $
 		hookWrite preCommitHook
 	setDifferences
 	unlessM (isJust <$> getVersion) $
@@ -93,19 +91,23 @@
 	whenM versionSupportsUnlockedPointers $ do
 		configureSmudgeFilter
 		Database.Keys.scanAssociatedFiles
-	ifM (crippledFileSystem <&&> (not <$> isBare))
-		( ifM versionSupportsUnlockedPointers
-			( adjustToCrippledFileSystem
-			, do
-				enableDirectMode
-				setDirect True
-			)
-		-- Handle case where this repo was cloned from a
-		-- direct mode repo
-		, unlessM isBare
-			switchHEADBack
-		)
-	checkAdjustedClone
+	v <- checkAdjustedClone
+	case v of
+		NeedUpgradeForAdjustedClone -> void $ upgrade True
+		InAdjustedClone -> return ()
+		NotInAdjustedClone ->
+			ifM (crippledFileSystem <&&> (not <$> isBareRepo))
+				( ifM versionSupportsUnlockedPointers
+					( adjustToCrippledFileSystem
+					, do
+						enableDirectMode
+						setDirect True
+					)
+				-- Handle case where this repo was cloned from a
+				-- direct mode repo
+				, unlessM isBareRepo
+					switchHEADBack
+				)
 	createInodeSentinalFile False
 
 uninitialize :: Annex ()
@@ -132,9 +134,6 @@
 {- Checks if a repository is initialized. Does not check version for ugrade. -}
 isInitialized :: Annex Bool
 isInitialized = maybe Annex.Branch.hasSibling (const $ return True) =<< getVersion
-
-isBare :: Annex Bool
-isBare = fromRepo Git.repoIsLocalBare
 
 {- A crippled filesystem is one that does not allow making symlinks,
  - or removing write access from files. -}
diff --git a/Annex/Locations.hs b/Annex/Locations.hs
--- a/Annex/Locations.hs
+++ b/Annex/Locations.hs
@@ -411,7 +411,7 @@
  -
  - This is used when a new Key is initially being generated, eg by getKey.
  - Unlike keyFile and fileKey, it does not need to be a reversable
- - escaping. Also, it's ok to change this to add more problimatic
+ - escaping. Also, it's ok to change this to add more problematic
  - characters later. Unlike changing keyFile, which could result in the
  - filenames used for existing keys changing and contents getting lost.
  -
diff --git a/Annex/Queue.hs b/Annex/Queue.hs
--- a/Annex/Queue.hs
+++ b/Annex/Queue.hs
@@ -13,6 +13,7 @@
 	flush,
 	flushWhenFull,
 	size,
+	get,
 	mergeFrom,
 ) where
 
diff --git a/Annex/Transfer.hs b/Annex/Transfer.hs
--- a/Annex/Transfer.hs
+++ b/Annex/Transfer.hs
@@ -46,10 +46,17 @@
 noObserver _ _ _ = noop
 
 upload :: Observable v => UUID -> Key -> AssociatedFile -> RetryDecider -> TransferObserver -> (MeterUpdate -> Annex v) -> NotifyWitness -> Annex v
-upload u key f d o a _witness = runTransfer (Transfer Upload u key) f d o a
+upload u key f d o a _witness = guardHaveUUID u $ 
+	runTransfer (Transfer Upload u key) f d o a
 
 download :: Observable v => UUID -> Key -> AssociatedFile -> RetryDecider -> TransferObserver -> (MeterUpdate -> Annex v) -> NotifyWitness -> Annex v
-download u key f d o a _witness = runTransfer (Transfer Download u key) f d o a
+download u key f d o a _witness = guardHaveUUID u $
+	runTransfer (Transfer Download u key) f d o a
+
+guardHaveUUID :: Observable v => UUID -> Annex v -> Annex v
+guardHaveUUID u a
+	| u == NoUUID = return observeFailure
+	| otherwise = a
 
 {- Runs a transfer action. Creates and locks the lock file while the
  - action is running, and stores info in the transfer information
diff --git a/Assistant/DaemonStatus.hs b/Assistant/DaemonStatus.hs
--- a/Assistant/DaemonStatus.hs
+++ b/Assistant/DaemonStatus.hs
@@ -55,6 +55,7 @@
 	let good r = Remote.uuid r `elem` alive
 	let syncable = filter good rs
 	let syncdata = filter (not . remoteAnnexIgnore . Remote.gitconfig) $
+		filter (\r -> Remote.uuid r /= NoUUID) $
 		filter (not . Remote.isXMPPRemote) syncable
 
 	return $ \dstatus -> dstatus
diff --git a/Assistant/Gpg.hs b/Assistant/Gpg.hs
--- a/Assistant/Gpg.hs
+++ b/Assistant/Gpg.hs
@@ -12,12 +12,14 @@
 import Types.Remote (RemoteConfigKey)
 
 import qualified Data.Map as M
+import Control.Applicative
+import Prelude
 
 {- Generates a gpg user id that is not used by any existing secret key -}
 newUserId :: GpgCmd -> IO UserId
 newUserId cmd = do
 	oldkeys <- secretKeys cmd
-	username <- myUserName
+	username <- either (const "unknown") id <$> myUserName
 	let basekeyname = username ++ "'s git-annex encryption key"
 	return $ Prelude.head $ filter (\n -> M.null $ M.filter (== n) oldkeys)
 		( basekeyname
diff --git a/Assistant/Restart.hs b/Assistant/Restart.hs
--- a/Assistant/Restart.hs
+++ b/Assistant/Restart.hs
@@ -91,7 +91,7 @@
 
 {- Checks if the assistant is listening on an url.
  -
- - Always checks http, because https with self-signed cert is problimatic.
+ - Always checks http, because https with self-signed cert is problematic.
  - warp-tls listens to http, in order to show an error page, so this works.
  -}
 assistantListening :: URLString -> IO Bool
diff --git a/Assistant/WebApp/Configurators/Pairing.hs b/Assistant/WebApp/Configurators/Pairing.hs
--- a/Assistant/WebApp/Configurators/Pairing.hs
+++ b/Assistant/WebApp/Configurators/Pairing.hs
@@ -226,7 +226,7 @@
 		let pubkey = either error id $ validateSshPubKey $ sshPubKey keypair
 		pairdata <- liftIO $ PairData
 			<$> getHostname
-			<*> myUserName
+			<*> (either error id <$> myUserName)
 			<*> pure reldir
 			<*> pure pubkey
 			<*> (maybe genUUID return muuid)
@@ -291,8 +291,8 @@
 		let (username, hostname) = maybe ("", "")
 			(\(_, v, a) -> (T.pack $ remoteUserName v, T.pack $ fromMaybe (showAddr a) (remoteHostName v)))
 			(verifiableVal . fromPairMsg <$> msg)
-		u <- T.pack <$> liftIO myUserName
-		let sameusername = username == u
+		u <- liftIO myUserName
+		let sameusername = Right username == (T.pack <$> u)
 		$(widgetFile "configurators/pairing/local/prompt")
 
 {- This counts unicode characters as more than one character,
diff --git a/Assistant/WebApp/Configurators/Ssh.hs b/Assistant/WebApp/Configurators/Ssh.hs
--- a/Assistant/WebApp/Configurators/Ssh.hs
+++ b/Assistant/WebApp/Configurators/Ssh.hs
@@ -156,10 +156,10 @@
 getAddSshR = postAddSshR
 postAddSshR :: Handler Html
 postAddSshR = sshConfigurator $ do
-	username <- liftIO $ T.pack <$> myUserName
+	username <- liftIO $ either (const Nothing) (Just . T.pack) <$> myUserName
 	((result, form), enctype) <- liftH $
 		runFormPostNoToken $ renderBootstrap3 bootstrapFormLayout $ sshInputAForm textField $
-			SshInput Nothing (Just username) Password Nothing Nothing 22
+			SshInput Nothing username Password Nothing Nothing 22
 	case result of
 		FormSuccess sshinput -> do
 			s <- liftAssistant $ testServer sshinput
diff --git a/Backend/Hash.hs b/Backend/Hash.hs
--- a/Backend/Hash.hs
+++ b/Backend/Hash.hs
@@ -101,8 +101,9 @@
 	| otherwise = intercalate "." ("":es)
   where
 	es = filter (not . null) $ reverse $
-		take 2 $ takeWhile shortenough $
-		reverse $ split "." $ filter validExtension $ takeExtensions f
+		take 2 $ map (filter validInExtension) $
+		takeWhile shortenough $
+		reverse $ split "." $ takeExtensions f
 	shortenough e = length e <= 4 -- long enough for "jpeg"
 
 {- A key's checksum is checked during fsck. -}
@@ -133,8 +134,8 @@
 keyHash :: Key -> String
 keyHash key = dropExtensions (keyName key)
 
-validExtension :: Char -> Bool
-validExtension c
+validInExtension :: Char -> Bool
+validInExtension c
 	| isAlphaNum c = True
 	| c == '.' = True
 	| otherwise = False
@@ -143,7 +144,7 @@
  - that contain non-alphanumeric characters in their extension. -}
 needsUpgrade :: Key -> Bool
 needsUpgrade key = "\\" `isPrefixOf` keyHash key ||
-	any (not . validExtension) (takeExtensions $ keyName key)
+	any (not . validInExtension) (takeExtensions $ keyName key)
 
 trivialMigrate :: Key -> Backend -> AssociatedFile -> Maybe Key
 trivialMigrate oldkey newbackend afile
diff --git a/Build/BundledPrograms.hs b/Build/BundledPrograms.hs
--- a/Build/BundledPrograms.hs
+++ b/Build/BundledPrograms.hs
@@ -70,7 +70,7 @@
 	, Just "sh"
 #endif
 #ifndef darwin_HOST_OS
-	-- wget on OSX has been problimatic, looking for certs in the wrong
+	-- wget on OSX has been problematic, looking for certs in the wrong
 	-- places. Don't ship it, use curl or the OSX's own wget if it has
 	-- one.
 	, ifset SysConfig.wget "wget"
diff --git a/Build/EvilSplicer.hs b/Build/EvilSplicer.hs
--- a/Build/EvilSplicer.hs
+++ b/Build/EvilSplicer.hs
@@ -620,7 +620,7 @@
 		void $ string "= "
 		return $ "= do { " ++ x ++ " <- return $ "
 
-{- Embedded files use unsafe packing, which is problimatic
+{- Embedded files use unsafe packing, which is problematic
  - for several reasons, including that GHC sometimes omits trailing
  - newlines in the file content, which leads to the wrong byte
  - count. Also, GHC sometimes outputs unicode characters, which 
diff --git a/Build/MakeMans.hs b/Build/MakeMans.hs
new file mode 100644
--- /dev/null
+++ b/Build/MakeMans.hs
@@ -0,0 +1,15 @@
+{- Build man pages, for use by Makefile
+ -
+ - Copyright 2016 Joey Hess <id@joeyh.name>
+ -
+ - Licensed under the GNU GPL version 3 or higher.
+ -}
+
+{-# OPTIONS_GHC -fno-warn-tabs #-}
+
+module Main where
+
+import Build.Mans
+
+main :: IO ()
+main = buildMansOrWarn
diff --git a/Build/Mans.hs b/Build/Mans.hs
new file mode 100644
--- /dev/null
+++ b/Build/Mans.hs
@@ -0,0 +1,60 @@
+{- Build man pages.
+ -
+ - Copyright 2016 Joey Hess <id@joeyh.name>
+ -
+ - Licensed under the GNU GPL version 3 or higher.
+ -}
+
+{-# OPTIONS_GHC -fno-warn-tabs #-}
+
+module Build.Mans where
+
+import System.Directory
+import System.FilePath
+import Data.List
+import Control.Monad
+import System.Process
+import System.Exit
+import Data.Maybe
+import Utility.Exception
+import Control.Applicative
+import Prelude
+
+buildMansOrWarn :: IO ()
+buildMansOrWarn = do
+	mans <- buildMans
+	when (any isNothing mans) $
+		error "mdwn2man failed"
+
+buildMans :: IO [Maybe FilePath]
+buildMans = do
+	mansrc <- filter isManSrc <$> getDirectoryContents "doc"
+	createDirectoryIfMissing False "man"
+	forM mansrc $ \f -> do
+		let src = "doc" </> f
+		let dest = srcToDest src
+		srcm <- getModificationTime src
+		destm <- catchMaybeIO $ getModificationTime dest
+		if (Just srcm > destm)
+			then do
+				r <- system $ unwords
+					[ "./Build/mdwn2man"
+					, progName src
+					, "1"
+					, src
+					, "> " ++ dest
+					]
+				if r == ExitSuccess
+					then return (Just dest)
+					else return Nothing
+			else return (Just dest)
+
+isManSrc :: FilePath -> Bool
+isManSrc s = "git-annex" `isPrefixOf` (takeFileName s)
+	&& takeExtension s == ".mdwn"
+
+srcToDest :: FilePath -> FilePath
+srcToDest s = "man" </> progName s ++ ".1"
+
+progName :: FilePath -> FilePath
+progName = dropExtension . takeFileName
diff --git a/Build/mdwn2man b/Build/mdwn2man
--- a/Build/mdwn2man
+++ b/Build/mdwn2man
@@ -2,8 +2,6 @@
 # Warning: hack
 
 my $prog=shift;
-$prog=~s/\.\d+$//;
-$prog=~s/man\///;
 my $section=shift;
 
 print ".TH $prog $section\n";
diff --git a/CHANGELOG b/CHANGELOG
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -1,3 +1,40 @@
+git-annex (6.20160613) unstable; urgency=medium
+
+  * Improve SHA*E extension extraction code.
+  * Windows: Avoid terminating git-annex branch lines with \r\n when
+    union merging and performing transitions.
+  * Remove Makefile from cabal tarball; man page building is now handled by
+    a small haskell program.
+  * sync --content: Fix bug that caused transfers of files to be made 
+    to a git remote that does not have a UUID. This particularly impacted
+    clones from gcrypt repositories.
+  * Pass -S to git commit-tree when commit.gpgsign is set and when
+    making a non-automatic commit, in order to preserve current behavior
+    when used with git 2.9, which has stopped doing this itself.
+  * remotedaemon: Fixed support for notifications of changes to gcrypt
+    remotes, which was never tested and didn't quite work before.
+  * list: Do not include dead repositories.
+  * move --to: Better behavior when system is completely out of disk space;
+    drop content from disk before writing location log.
+  * Avoid a crash if getpwuid does not work, when querying the user's full
+    name.
+  * Automatically enable v6 mode when initializing in a clone from a repo
+    that has an adjusted branch checked out.
+  * v6: Fix initialization of a bare clone of a repo that has an adjusted
+    branch checked out.
+  * v6: Fix bad automatic merge conflict resolution between an annexed file
+    and a directory with the same name when in an adjusted branch.
+  * v6: Fix bad merge in an adjusted branch that resulted in an empty tree.
+  * v6: Fix bug in initialization of clone from a repo with an adjusted branch
+    that had not been synced back to master. 
+    (This bug caused broken tree objects to get built by a later git annex
+    sync.)
+  * v6: Make lock and unlock work on files whose content is not present.
+  * v6: Fix update of associated files db when unlocking a file.
+  * v6: Make git clean filter preserve the backend that was used for a file.
+
+ -- Joey Hess <id@joeyh.name>  Mon, 13 Jun 2016 14:57:38 -0400
+
 git-annex (6.20160527) unstable; urgency=medium
 
   * Split lines in the git-annex branch on \r as well as \n, to deal
@@ -3524,7 +3561,7 @@
     (Requested by the Internet Archive)
   * uninit: Clear annex.uuid from .git/config. Closes: #670639
   * Added shared cipher mode to encryptable special remotes. This option
-    avoids gpg key distribution, at the expense of flexability, and with
+    avoids gpg key distribution, at the expense of flexibility, and with
     the requirement that all clones of the git repository be equally trusted.
 
  -- Joey Hess <joeyh@debian.org>  Mon, 30 Apr 2012 13:16:10 -0400
diff --git a/Command.hs b/Command.hs
--- a/Command.hs
+++ b/Command.hs
@@ -91,9 +91,6 @@
 stopUnless :: Annex Bool -> Annex (Maybe a) -> Annex (Maybe a)
 stopUnless c a = ifM c ( a , stop )
 
-isBareRepo :: Annex Bool
-isBareRepo = fromRepo Git.repoIsLocalBare
-
 commonChecks :: [CommandCheck]
 commonChecks = [repoExists]
 
diff --git a/Command/List.hs b/Command/List.hs
--- a/Command/List.hs
+++ b/Command/List.hs
@@ -56,7 +56,8 @@
 		ts <- mapM (lookupTrust . uuid) rs
 		hereu <- getUUID
 		heretrust <- lookupTrust hereu
-		return $ (hereu, "here", heretrust) : zip3 (map uuid rs) (map name rs) ts
+		let l = (hereu, "here", heretrust) : zip3 (map uuid rs) (map name rs) ts
+		return $ filter (\(_, _, t) -> t /= DeadTrusted) l 
 	getAllUUIDs = do
 		rs <- M.toList <$> uuidMap
 		rs3 <- forM rs $ \(u, n) -> (,,)
diff --git a/Command/Lock.hs b/Command/Lock.hs
--- a/Command/Lock.hs
+++ b/Command/Lock.hs
@@ -45,7 +45,7 @@
 	)
   where
 	go (Just key')
-		| key' == key = error "content not present; cannot lock"
+		| key' == key = cont True
 		| otherwise = errorModified
 	go Nothing = 
 		ifM (isUnmodified key file) 
diff --git a/Command/Move.hs b/Command/Move.hs
--- a/Command/Move.hs
+++ b/Command/Move.hs
@@ -113,23 +113,29 @@
 				upload (Remote.uuid dest) key afile noRetry noObserver $
 					Remote.storeKey dest key afile
 			if ok
-				then do
+				then finish $
 					Remote.logStatus dest key InfoPresent
-					finish
 				else do
 					when fastcheck $
 						warning "This could have failed because --fast is enabled."
 					stop
-		Right True -> do
+		Right True -> finish $
 			unlessM (expectedPresent dest key) $
 				Remote.logStatus dest key InfoPresent
-			finish
   where
-	finish
+	finish :: Annex () -> CommandPerform
+	finish setpresentremote
 		| move = lockContentForRemoval key $ \contentlock -> do
+			-- Drop content before updating location logs,
+			-- in case disk space is very low this frees up
+			-- space before writing data to disk.
 			removeAnnex contentlock
-			next $ Command.Drop.cleanupLocal key
-		| otherwise = next $ return True
+			next $ do
+				setpresentremote
+				Command.Drop.cleanupLocal key
+		| otherwise = next $ do
+			setpresentremote
+			return True
 
 {- Moves (or copies) the content of an annexed file from a remote
  - to the current repository.
diff --git a/Command/Smudge.hs b/Command/Smudge.hs
--- a/Command/Smudge.hs
+++ b/Command/Smudge.hs
@@ -13,9 +13,11 @@
 import Annex.Link
 import Annex.FileMatcher
 import Annex.Ingest
+import Annex.CatFile
 import Logs.Location
 import qualified Database.Keys
 import Git.FilePath
+import Backend
 
 import qualified Data.ByteString.Lazy as B
 
@@ -78,8 +80,16 @@
 				-- and not stdin, we need to consume all
 				-- stdin, or git will get annoyed.
 				B.length b `seq` return ()
+				-- Look up the backend that was used
+				-- for this file before, so that when
+				-- git re-cleans a file its backend does
+				-- not change.
+				currbackend <- maybe Nothing (maybeLookupBackendName . keyBackendName)
+					<$> catKeyFile file
 				liftIO . emitPointer
-					=<< go =<< ingest =<< lockDown cfg file
+					=<< go
+					=<< ingest' currbackend
+					=<< lockDown cfg file
 			, liftIO $ B.hPut stdout b
 			)
 	stop
diff --git a/Command/Sync.hs b/Command/Sync.hs
--- a/Command/Sync.hs
+++ b/Command/Sync.hs
@@ -106,7 +106,8 @@
 
 	remotes <- syncRemotes (syncWith o)
 	let gitremotes = filter Remote.gitSyncableRemote remotes
-	let dataremotes = filter (not . remoteAnnexIgnore . Remote.gitconfig) remotes
+	let dataremotes = filter (\r -> Remote.uuid r /= NoUUID) $ 
+		filter (not . remoteAnnexIgnore . Remote.gitconfig) remotes
 
 	-- Syncing involves many actions, any of which can independently
 	-- fail, without preventing the others from running.
diff --git a/Command/Unlock.hs b/Command/Unlock.hs
--- a/Command/Unlock.hs
+++ b/Command/Unlock.hs
@@ -1,6 +1,6 @@
 {- git-annex command
  -
- - Copyright 2010,2015 Joey Hess <id@joeyh.name>
+ - Copyright 2010-2016 Joey Hess <id@joeyh.name>
  -
  - Licensed under the GNU GPL version 3 or higher.
  -}
@@ -16,6 +16,8 @@
 import Annex.ReplaceFile
 import Utility.CopyFile
 import Utility.FileMode
+import Git.FilePath
+import qualified Database.Keys
 
 cmd :: Command
 cmd = mkcmd "unlock" "unlock files for modification"
@@ -37,14 +39,9 @@
 start file key = ifM (isJust <$> isAnnexLink file)
 	( do
 		showStart "unlock" file
-		ifM (inAnnex key)
-			( ifM versionSupportsUnlockedPointers
-				( next $ performNew file key
-				, startOld file key 
-				)
-			, do
-				warning "content not present; cannot unlock"
-				next $ next $ return False
+		ifM versionSupportsUnlockedPointers
+			( next $ performNew file key
+			, startOld file key
 			)
 	, stop
 	)
@@ -52,16 +49,22 @@
 performNew :: FilePath -> Key -> CommandPerform
 performNew dest key = do
 	destmode <- liftIO $ catchMaybeIO $ fileMode <$> getFileStatus dest
-	replaceFile dest $ \tmp -> do
-		r <- linkFromAnnex key tmp destmode
-		case r of
-			LinkAnnexOk -> return ()
-			_ -> error "unlock failed"
+	replaceFile dest $ \tmp ->
+		ifM (inAnnex key)
+			( do
+				r <- linkFromAnnex key tmp destmode
+				case r of
+					LinkAnnexOk -> return ()
+					LinkAnnexNoop -> return ()
+					_ -> error "unlock failed"
+			, liftIO $ writePointerFile tmp key destmode
+			)
 	next $ cleanupNew dest key destmode
 
 cleanupNew ::  FilePath -> Key -> Maybe FileMode -> CommandCleanup
 cleanupNew dest key destmode = do
 	stagePointerFile dest destmode =<< hashPointerFile key
+	Database.Keys.addAssociatedFile key =<< inRepo (toTopFilePath dest)
 	return True
 
 startOld :: FilePath -> Key -> CommandStart
diff --git a/Command/Unused.hs b/Command/Unused.hs
--- a/Command/Unused.hs
+++ b/Command/Unused.hs
@@ -32,6 +32,7 @@
 import Git.Types
 import Git.Sha
 import Git.FilePath
+import Config
 import Logs.View (is_branchView)
 import Annex.BloomFilter
 import qualified Database.Keys
diff --git a/Config.hs b/Config.hs
--- a/Config.hs
+++ b/Config.hs
@@ -86,6 +86,9 @@
 setRemoteBare :: Git.Repo -> Bool -> Annex ()
 setRemoteBare r b = setConfig (remoteConfig r "bare") (Git.Config.boolConfig b)
 
+isBareRepo :: Annex Bool
+isBareRepo = fromRepo Git.repoIsLocalBare
+
 isDirect :: Annex Bool
 isDirect = annexDirect <$> Annex.getGitConfig
 
diff --git a/Git/Branch.hs b/Git/Branch.hs
--- a/Git/Branch.hs
+++ b/Git/Branch.hs
@@ -13,6 +13,7 @@
 import Git
 import Git.Sha
 import Git.Command
+import qualified Git.Config
 import qualified Git.Ref
 import qualified Git.BuildVersion
 
@@ -114,19 +115,33 @@
 			(False, True) -> findbest c rs -- worse
 			(False, False) -> findbest c rs -- same
 
-{- The user may have set commit.gpgsign, indending all their manual
+{- The user may have set commit.gpgsign, intending all their manual
  - commits to be signed. But signing automatic/background commits could
  - easily lead to unwanted gpg prompts or failures.
  -}
 data CommitMode = ManualCommit | AutomaticCommit
 	deriving (Eq)
 
+{- Prevent signing automatic commits. -}
 applyCommitMode :: CommitMode -> [CommandParam] -> [CommandParam]
 applyCommitMode commitmode ps
 	| commitmode == AutomaticCommit && not (Git.BuildVersion.older "2.0.0") =
 		Param "--no-gpg-sign" : ps
 	| otherwise = ps
 
+{- Some versions of git commit-tree honor commit.gpgsign themselves,
+ - but others need -S to be passed to enable gpg signing of manual commits. -}
+applyCommitModeForCommitTree :: CommitMode -> [CommandParam] -> Repo -> [CommandParam]
+applyCommitModeForCommitTree commitmode ps r
+	| commitmode == ManualCommit =
+		case (Git.Config.getMaybe "commit.gpgsign" r) of
+			Just s | Git.Config.isTrue s == Just True ->
+				Param "-S":ps
+			_ -> ps'
+	| otherwise = ps'
+  where
+	ps' = applyCommitMode commitmode ps
+
 {- Commit via the usual git command. -}
 commitCommand :: CommitMode -> [CommandParam] -> Repo -> IO Bool
 commitCommand = commitCommand' runBool
@@ -172,9 +187,9 @@
 		pipeWriteRead ([Param "commit-tree", Param (fromRef tree)] ++ ps)
 			sendmsg repo
   where
-	ps = applyCommitMode commitmode $
-		map Param $ concatMap (\r -> ["-p", fromRef r]) parentrefs
 	sendmsg = Just $ flip hPutStr message
+	ps = applyCommitModeForCommitTree commitmode parentparams repo
+	parentparams = map Param $ concatMap (\r -> ["-p", fromRef r]) parentrefs
 
 {- A leading + makes git-push force pushing a branch. -}
 forcePush :: String -> String
diff --git a/Git/HashObject.hs b/Git/HashObject.hs
--- a/Git/HashObject.hs
+++ b/Git/HashObject.hs
@@ -5,6 +5,8 @@
  - Licensed under the GNU GPL version 3 or higher.
  -}
 
+{-# LANGUAGE CPP #-}
+
 module Git.HashObject where
 
 import Common
@@ -39,6 +41,10 @@
  - interface does not allow batch hashing without using temp files. -}
 hashBlob :: HashObjectHandle -> String -> IO Sha
 hashBlob h s = withTmpFile "hash" $ \tmp tmph -> do
+	fileEncoding tmph
+#ifdef mingw32_HOST_OS
+	hSetNewlineMode tmph noNewlineTranslation
+#endif
 	hPutStr tmph s
 	hClose tmph
 	hashFile h tmp
diff --git a/Git/Queue.hs b/Git/Queue.hs
--- a/Git/Queue.hs
+++ b/Git/Queue.hs
@@ -163,7 +163,7 @@
 		hPutStr h $ intercalate "\0" $ toCommand $ getFiles action
 		hClose h
 #else
-	-- Using xargs on Windows is problimatic, so just run the command
+	-- Using xargs on Windows is problematic, so just run the command
 	-- once per file (not as efficient.)
 	if null (getFiles action)
 		then void $ boolSystemEnv "git" gitparams (gitEnv repo)
diff --git a/Makefile b/Makefile
deleted file mode 100644
--- a/Makefile
+++ /dev/null
@@ -1,292 +0,0 @@
-mans=$(shell find doc -maxdepth 1 -name git-annex*.mdwn | sed -e 's/^doc/man/' -e 's/\.mdwn/\.1/')
-all=git-annex mans docs
-
-# set to "./Setup" if you lack a cabal program. Or can be set to "stack"
-BUILDER?=cabal
-GHC?=ghc
-
-PREFIX?=/usr
-SHAREDIR?=share
-
-# Am I typing :make in vim? Do a fast build.
-ifdef VIM
-all=fast
-endif
-
-build: $(all)
-
-Build/SysConfig.hs: Build/TestConfig.hs Build/Configure.hs
-	if [ "$(BUILDER)" = ./Setup ]; then ghc --make Setup; fi
-	if [ "$(BUILDER)" = stack ]; then \
-		$(BUILDER) build $(BUILDEROPTIONS); \
-	else \
-		$(BUILDER) configure --ghc-options="$(shell Build/collect-ghc-options.sh)"; \
-	fi
-
-git-annex: Build/SysConfig.hs
-	$(BUILDER) build $(BUILDEROPTIONS)
-	if [ "$(BUILDER)" = stack ]; then \
-		ln -sf $$(find .stack-work/ -name git-annex -type f | grep build/git-annex/git-annex | tail -n 1) git-annex; \
-	else \
-		ln -sf dist/build/git-annex/git-annex git-annex; \
-	fi
-
-man/%.1: doc/%.mdwn
-	./Build/mdwn2man $@ 1 $< > $@
-
-# These are not built normally.
-git-union-merge.1: doc/git-union-merge.mdwn
-	./Build/mdwn2man git-union-merge 1 doc/git-union-merge.mdwn > git-union-merge.1
-git-union-merge:
-	$(GHC) --make -threaded $@
-
-install-mans: mans
-	install -d $(DESTDIR)$(PREFIX)/$(SHAREDIR)/man/man1
-	install -m 0644 $(mans) $(DESTDIR)$(PREFIX)/$(SHAREDIR)/man/man1
-
-install-docs: docs install-mans
-	install -d $(DESTDIR)$(PREFIX)/$(SHAREDIR)/doc/git-annex
-	if [ -d html ]; then \
-		rsync -a --delete html/ $(DESTDIR)$(PREFIX)/$(SHAREDIR)/doc/git-annex/html/; \
-	fi
-
-install-bins: build
-	install -d $(DESTDIR)$(PREFIX)/bin
-	install git-annex $(DESTDIR)$(PREFIX)/bin
-	ln -sf git-annex $(DESTDIR)$(PREFIX)/bin/git-annex-shell
-
-install-misc: Build/InstallDesktopFile
-	./Build/InstallDesktopFile $(PREFIX)/bin/git-annex || true
-	install -d $(DESTDIR)$(PREFIX)/share/bash-completion/completions
-	install -m 0644 bash-completion.bash $(DESTDIR)$(PREFIX)/share/bash-completion/completions/git-annex
-
-install: install-bins install-docs install-misc
-
-test: git-annex
-	./git-annex test
-
-retest: git-annex
-	./git-annex test --rerun-update --rerun-filter failures
-
-# hothasktags chokes on some template haskell etc, so ignore errors
-tags:
-	(for f in $$(find . | grep -v /.git/ | grep -v /tmp/ | grep -v /dist/ | grep -v /doc/ | egrep '\.hs$$'); do hothasktags -c --cpp -c -traditional -c --include=dist/build/autogen/cabal_macros.h $$f; done) 2>/dev/null | sort > tags
-
-# If ikiwiki is available, build static html docs suitable for being
-# shipped in the software package.
-ifeq ($(shell which ikiwiki),)
-IKIWIKI=echo "** ikiwiki not found, skipping building docs" >&2; true
-else
-IKIWIKI=ikiwiki
-endif
-
-mans: man $(mans)
-
-man:
-	mkdir -p man
-
-docs: mans
-	@if [ ! -e doc/index.mdwn ]; then \
-		echo "** doc/index.mdwn does not exist, skipping building docs (clone git-annex source to enable full docs build)" >&2; \
-	else \
-		LC_ALL=C TZ=UTC $(IKIWIKI) doc html -v --wikiname git-annex \
-			--plugin=goodstuff \
-			--no-usedirs --disable-plugin=openid --plugin=sidebar \
-			--underlaydir=/dev/null --set deterministic=1 \
-			--disable-plugin=shortcut --disable-plugin=smiley \
-			--plugin=comments --set comments_pagespec="*" \
-			--exclude='news/.*' --exclude='design/assistant/blog/*' \
-			--exclude='bugs/*' --exclude='todo/*' --exclude='forum/*' \
-			--exclude='users/*' --exclude='devblog/*' --exclude='thanks'; \
-	fi
-
-clean:
-	if [ "$(BUILDER)" != ./Setup ] && [ "$(BUILDER)" != cabal ]; then $(BUILDER) clean; fi
-	rm -rf tmp dist git-annex $(mans) configure  *.tix .hpc \
-		doc/.ikiwiki html dist tags Build/SysConfig.hs \
-		Setup Build/InstallDesktopFile Build/EvilSplicer \
-		Build/Standalone Build/OSXMkLibs Build/LinuxMkLibs \
-		Build/DistributionUpdate Build/BuildVersion \
-		git-union-merge .tasty-rerun-log
-	find . -name \*.o -exec rm {} \;
-	find . -name \*.hi -exec rm {} \;
-
-Build/InstallDesktopFile: Build/InstallDesktopFile.hs
-	$(GHC) --make $@ -Wall -fno-warn-tabs
-Build/EvilSplicer: Build/EvilSplicer.hs
-	$(GHC) --make $@ -Wall -fno-warn-tabs
-Build/Standalone: Build/Standalone.hs Build/SysConfig.hs
-	$(GHC) --make $@ -Wall -fno-warn-tabs
-Build/OSXMkLibs: Build/OSXMkLibs.hs
-	$(GHC) --make $@ -Wall -fno-warn-tabs
-Build/LinuxMkLibs: Build/LinuxMkLibs.hs
-	$(GHC) --make $@ -Wall -fno-warn-tabs
-
-# Upload to hackage.
-hackage:
-	@cabal sdist
-	@cabal upload dist/*.tar.gz
-
-LINUXSTANDALONE_DEST=tmp/git-annex.linux
-linuxstandalone:
-	$(MAKE) git-annex linuxstandalone-nobuild
-linuxstandalone-nobuild: Build/Standalone Build/LinuxMkLibs
-	rm -rf "$(LINUXSTANDALONE_DEST)"
-	mkdir -p tmp
-	cp -R standalone/linux/skel "$(LINUXSTANDALONE_DEST)"
-	sed -i -e 's/^GIT_ANNEX_PACKAGE_INSTALL=/GIT_ANNEX_PACKAGE_INSTALL=$(GIT_ANNEX_PACKAGE_INSTALL)/' "$(LINUXSTANDALONE_DEST)/runshell"
-	
-	install -d "$(LINUXSTANDALONE_DEST)/bin"
-	cp git-annex "$(LINUXSTANDALONE_DEST)/bin/"
-	strip "$(LINUXSTANDALONE_DEST)/bin/git-annex"
-	ln -sf git-annex "$(LINUXSTANDALONE_DEST)/bin/git-annex-shell"
-	zcat standalone/licences.gz > $(LINUXSTANDALONE_DEST)/LICENSE
-	cp doc/logo_16x16.png doc/logo.svg $(LINUXSTANDALONE_DEST)
-	cp standalone/trustedkeys.gpg $(LINUXSTANDALONE_DEST)
-
-	./Build/Standalone "$(LINUXSTANDALONE_DEST)"
-	
-	install -d "$(LINUXSTANDALONE_DEST)/git-core"
-	(cd "$(shell git --exec-path)" && tar c .) | (cd "$(LINUXSTANDALONE_DEST)"/git-core && tar x)
-	install -d "$(LINUXSTANDALONE_DEST)/templates"
-	install -d "$(LINUXSTANDALONE_DEST)/magic"
-	cp /usr/share/file/magic.mgc "$(LINUXSTANDALONE_DEST)/magic"
-	
-	./Build/LinuxMkLibs "$(LINUXSTANDALONE_DEST)"
-	
-	$(MAKE) install-mans DESTDIR="$(LINUXSTANDALONE_DEST)"
-
-	cd tmp/git-annex.linux && find . -type f > git-annex.MANIFEST
-	cd tmp/git-annex.linux && find . -type l >> git-annex.MANIFEST
-	cd tmp && tar c git-annex.linux | gzip -9 --rsyncable > git-annex-standalone-$(shell dpkg --print-architecture).tar.gz
-
-# Run this target to build git-annex-standalone*.deb
-debianstandalone: dpkg-buildpackage-F
-# Run this target to build git-annex-standalone*.dsc
-debianstandalone-dsc: dpkg-buildpackage-S
-
-prep-standalone:
-	$(MAKE) undo-standalone
-	QUILT_PATCHES=debian/patches QUILT_SERIES=series.standalone-build quilt push -a
-	debian/create-standalone-changelog
-
-undo-standalone:
-	test -e .git
-	git checkout debian/changelog CHANGELOG
-	quilt pop -a || true
-
-commit-standalone:
-	QUILT_PATCHES=debian/patches QUILT_SERIES=series.standalone-build  quilt refresh
-
-dpkg-buildpackage%: prep-standalone
-	umask 022; dpkg-buildpackage -rfakeroot $*
-	$(MAKE) undo-standalone
-
-OSXAPP_DEST=tmp/build-dmg/git-annex.app
-OSXAPP_BASE=$(OSXAPP_DEST)/Contents/MacOS/bundle
-osxapp: Build/Standalone Build/OSXMkLibs
-	$(MAKE) git-annex
-
-	rm -rf "$(OSXAPP_DEST)" "$(OSXAPP_BASE)"
-	install -d tmp/build-dmg
-	cp -R standalone/osx/git-annex.app "$(OSXAPP_DEST)"
-
-	install -d "$(OSXAPP_BASE)"
-	cp git-annex "$(OSXAPP_BASE)"
-	strip "$(OSXAPP_BASE)/git-annex"
-	ln -sf git-annex "$(OSXAPP_BASE)/git-annex-shell"
-	gzcat standalone/licences.gz > $(OSXAPP_BASE)/LICENSE
-	cp $(OSXAPP_BASE)/LICENSE tmp/build-dmg/LICENSE.txt
-	cp standalone/trustedkeys.gpg $(OSXAPP_DEST)/Contents/MacOS
-
-	./Build/Standalone $(OSXAPP_BASE)
-
-	(cd "$(shell git --exec-path)" && tar c .) | (cd "$(OSXAPP_BASE)" && tar x)
-	install -d "$(OSXAPP_BASE)/templates"
-	install -d "$(OSXAPP_BASE)/magic"
-	if [ -e "$(OSX_MAGIC_FILE)" ]; then \
-		cp "$(OSX_MAGIC_FILE)" "$(OSXAPP_BASE)/magic/magic.mgc"; \
-	else \
-		echo "** OSX_MAGIC_FILE not set; not including it" >&2; \
-	fi
-
-	# OSX looks in man dir nearby the bin
-	$(MAKE) install-mans DESTDIR="$(OSXAPP_BASE)/.." SHAREDIR="" PREFIX=""
-
-	./Build/OSXMkLibs $(OSXAPP_BASE)
-	cd $(OSXAPP_DEST) && find . -type f > Contents/MacOS/git-annex.MANIFEST
-	cd $(OSXAPP_DEST) && find . -type l >> Contents/MacOS/git-annex.MANIFEST
-	rm -f tmp/git-annex.dmg
-	hdiutil create -format UDBZ -size 640m -srcfolder tmp/build-dmg \
-		-volname git-annex -o tmp/git-annex.dmg
-
-ANDROID_FLAGS?=
-# Cross compile for Android.
-# Uses https://github.com/neurocyte/ghc-android
-android: Build/EvilSplicer
-	echo "Running native build, to get TH splices.."
-	if [ ! -e dist/setup/setup ]; then $(BUILDER) configure -O0 $(ANDROID_FLAGS) -fAndroidSplice;  fi
-	mkdir -p tmp
-	if ! $(BUILDER) build --ghc-options=-ddump-splices 2> tmp/dump-splices; then tail tmp/dump-splices >&2; exit 1; fi
-	echo "Setting up Android build tree.."
-	./Build/EvilSplicer tmp/splices tmp/dump-splices standalone/no-th/evilsplicer-headers.hs
-	rsync -az --exclude tmp --exclude dist . tmp/androidtree
-# Copy the files with expanded splices to the source tree, but
-# only if the existing source file is not newer. (So, if a file
-# used to have TH splices but they were removed, it will be newer,
-# and not overwritten.)
-	cp -uR tmp/splices/* tmp/androidtree || true
-# Some additional dependencies needed by the expanded splices.
-	sed -i 's/^  Build-Depends: */  Build-Depends: yesod-core, yesod-routes, shakespeare, blaze-markup, file-embed, wai-app-static, wai, unordered-containers, /' tmp/androidtree/git-annex.cabal
-# Avoid warnings due to sometimes unused imports added for the splices.
-	sed -i 's/GHC-Options: \(.*\)-Wall/GHC-Options: \1-Wall -fno-warn-unused-imports /i' tmp/androidtree/git-annex.cabal
-	sed -i 's/Extensions: /Extensions: MagicHash /i' tmp/androidtree/git-annex.cabal
-# Cabal cannot cross compile with custom build type, so workaround.
-	sed -i 's/Build-type: Custom/Build-type: Simple/' tmp/androidtree/git-annex.cabal
-# Build just once, but link repeatedly, for different versions of Android.
-	mkdir -p tmp/androidtree/dist/build/git-annex/4.0 tmp/androidtree/dist/build/git-annex/4.3 tmp/androidtree/dist/build/git-annex/5.0
-	if [ ! -e tmp/androidtree/dist/setup-config ]; then \
-		cd tmp/androidtree && $$HOME/.ghc/$(shell cat standalone/android/abiversion)/arm-linux-androideabi/bin/cabal configure -fAndroid $(ANDROID_FLAGS); \
-	fi
-	cd tmp/androidtree && $$HOME/.ghc/$(shell cat standalone/android/abiversion)/arm-linux-androideabi/bin/cabal build \
-		&& mv dist/build/git-annex/git-annex dist/build/git-annex/4.0/git-annex
-	cd tmp/androidtree && $$HOME/.ghc/$(shell cat standalone/android/abiversion)/arm-linux-androideabi/bin/cabal build \
-		--ghc-options=-optl-z --ghc-options=-optlnocopyreloc \
-		&& mv dist/build/git-annex/git-annex dist/build/git-annex/4.3/git-annex
-	cd tmp/androidtree && $$HOME/.ghc/$(shell cat standalone/android/abiversion)/arm-linux-androideabi/bin/cabal build \
-		--ghc-options=-optl-z --ghc-options=-optlnocopyreloc --ghc-options=-optl-fPIE --ghc-options=-optl-pie --ghc-options=-optc-fPIE --ghc-options=-optc-pie \
-		&& mv dist/build/git-annex/git-annex dist/build/git-annex/5.0/git-annex
-
-androidapp:
-	$(MAKE) android
-	$(MAKE) -C standalone/android
-
-# Bypass cabal, and only run the main ghc --make command for a
-# faster development build.
-fast: dist/cabalbuild
-	@sh dist/cabalbuild
-	@ln -sf dist/build/git-annex/git-annex git-annex
-	@$(MAKE) tags >/dev/null 2>&1 &
-
-dist/cabalbuild: dist/caballog
-	grep 'ghc --make' dist/caballog | tail -n 1 > dist/cabalbuild
-	
-dist/caballog: git-annex.cabal
-	$(BUILDER) configure -f"-Production" -O0 --enable-executable-dynamic
-	$(BUILDER) build -v2 --ghc-options="-O0 -j" | tee dist/caballog
-
-# Hardcoded command line to make hdevtools start up and work.
-# You will need some memory. It's worth it.
-# Note: Don't include WebDAV or Webapp. TH use bloats memory > 500 mb!
-# TODO should be possible to derive this from caballog.
-hdevtools:
-	hdevtools --stop-server || true
-	hdevtools check git-annex.hs -g -cpp -g -i -g -idist/build/git-annex/git-annex-tmp -g -i. -g -idist/build/autogen -g -Idist/build/autogen -g -Idist/build/git-annex/git-annex-tmp -g -IUtility -g -DWITH_TESTSUITE -g -DWITH_S3 -g -DWITH_ASSISTANT -g -DWITH_INOTIFY -g -DWITH_DBUS -g -DWITH_PAIRING -g -DWITH_XMPP -g -optP-include -g -optPdist/build/autogen/cabal_macros.h -g -odir -g dist/build/git-annex/git-annex-tmp -g -hidir -g dist/build/git-annex/git-annex-tmp -g -stubdir -g dist/build/git-annex/git-annex-tmp -g -threaded -g -Wall -g -XHaskell98 -g -XPackageImports
-
-distributionupdate:
-	git pull
-	cabal configure
-	ghc -Wall -fno-warn-tabs --make Build/DistributionUpdate -XPackageImports -optP-include -optPdist/build/autogen/cabal_macros.h
-	./Build/DistributionUpdate
-
-.PHONY: git-annex git-union-merge tags
diff --git a/RemoteDaemon/Common.hs b/RemoteDaemon/Common.hs
--- a/RemoteDaemon/Common.hs
+++ b/RemoteDaemon/Common.hs
@@ -30,7 +30,7 @@
 	return r
 
 inLocalRepo :: TransportHandle -> (Git.Repo -> IO a) -> IO a
-inLocalRepo (TransportHandle g _) a = a g
+inLocalRepo (TransportHandle (LocalRepo g) _) a = a g
 
 -- Check if any of the shas are actally new in the local git repo,
 -- to avoid unnecessary fetching.
diff --git a/RemoteDaemon/Core.hs b/RemoteDaemon/Core.hs
--- a/RemoteDaemon/Core.hs
+++ b/RemoteDaemon/Core.hs
@@ -111,7 +111,7 @@
 -- Generates a map with a transport for each supported remote in the git repo,
 -- except those that have annex.sync = false
 genRemoteMap :: TransportHandle -> TChan Emitted -> IO RemoteMap
-genRemoteMap h@(TransportHandle g _) ochan = 
+genRemoteMap h@(TransportHandle (LocalRepo g) _) ochan = 
 	M.fromList . catMaybes <$> mapM gen (Git.remotes g)
   where
 	gen r = case Git.location r of
@@ -126,17 +126,17 @@
 			_ -> return Nothing
 		_ -> return Nothing
 	  where
-		gc = extractRemoteGitConfig r (Git.repoDescribe r)
+		gc = extractRemoteGitConfig g (Git.repoDescribe r)
 
 genTransportHandle :: IO TransportHandle
 genTransportHandle = do
 	annexstate <- newMVar =<< Annex.new =<< Git.CurrentRepo.get
 	g <- Annex.repo <$> readMVar annexstate
-	return $ TransportHandle g annexstate
+	return $ TransportHandle (LocalRepo g) annexstate
 
 updateTransportHandle :: TransportHandle -> IO TransportHandle
 updateTransportHandle h@(TransportHandle _g annexstate) = do
 	g' <- liftAnnex h $ do
 		reloadConfig
 		Annex.fromRepo id
-	return (TransportHandle g' annexstate)
+	return (TransportHandle (LocalRepo g') annexstate)
diff --git a/RemoteDaemon/Transport/GCrypt.hs b/RemoteDaemon/Transport/GCrypt.hs
--- a/RemoteDaemon/Transport/GCrypt.hs
+++ b/RemoteDaemon/Transport/GCrypt.hs
@@ -16,7 +16,7 @@
 import Remote.GCrypt (accessShellConfig)
 
 transport :: Transport
-transport rr@(RemoteRepo r gc) url h@(TransportHandle g _) ichan ochan
+transport rr@(RemoteRepo r gc) url h@(TransportHandle (LocalRepo g) _) ichan ochan
 	| accessShellConfig gc = do
 		r' <- encryptedRemote g r
 		v <- liftAnnex h $ git_annex_shell r' "notifychanges" [] []
diff --git a/RemoteDaemon/Transport/Ssh.hs b/RemoteDaemon/Transport/Ssh.hs
--- a/RemoteDaemon/Transport/Ssh.hs
+++ b/RemoteDaemon/Transport/Ssh.hs
@@ -29,10 +29,10 @@
 		Just (cmd, params) -> transportUsingCmd cmd params rr url h ichan ochan
 
 transportUsingCmd :: FilePath -> [CommandParam] -> Transport
-transportUsingCmd cmd params rr@(RemoteRepo r gc) url h@(TransportHandle g s) ichan ochan = do
+transportUsingCmd cmd params rr@(RemoteRepo r gc) url h@(TransportHandle (LocalRepo g) s) ichan ochan = do
 	-- enable ssh connection caching wherever inLocalRepo is called
 	g' <- liftAnnex h $ sshOptionsTo r gc g
-	let transporthandle = TransportHandle g' s
+	let transporthandle = TransportHandle (LocalRepo g') s
 	transportUsingCmd' cmd params rr url transporthandle ichan ochan
 
 transportUsingCmd' :: FilePath -> [CommandParam] -> Transport
diff --git a/RemoteDaemon/Types.hs b/RemoteDaemon/Types.hs
--- a/RemoteDaemon/Types.hs
+++ b/RemoteDaemon/Types.hs
@@ -29,7 +29,7 @@
 type Transport = RemoteRepo -> RemoteURI -> TransportHandle -> TChan Consumed -> TChan Emitted -> IO ()
 
 data RemoteRepo = RemoteRepo Git.Repo RemoteGitConfig
-type LocalRepo = Git.Repo
+newtype LocalRepo = LocalRepo Git.Repo
 
 -- All Transports share a single AnnexState MVar
 --
diff --git a/Setup.hs b/Setup.hs
--- a/Setup.hs
+++ b/Setup.hs
@@ -14,11 +14,13 @@
 import Control.Monad
 import System.Directory
 import Data.List
+import Data.Maybe
 import Control.Exception
 import qualified System.Info
 
 import qualified Build.DesktopFile as DesktopFile
 import qualified Build.Configure as Configure
+import Build.Mans (buildMans)
 import Utility.SafeCommand
 
 main :: IO ()
@@ -51,13 +53,10 @@
 	installOrdinaryFiles verbosity dstManDir =<< srcManpages
   where
 	dstManDir   = mandir (absoluteInstallDirs pkg lbi copyDest) </> "man1"
-	srcManpages = do
-		havemans <- boolSystem "make" [Param "mans"]
-		if havemans
-			then zip (repeat "man")
-				. filter (".1" `isSuffixOf`)
-				<$> getDirectoryContents "man"
-			else return []
+	-- If mdwn2man fails, perhaps because perl is not available,
+	-- we just skip installing man pages.
+	srcManpages = zip (repeat "man") . map takeFileName . catMaybes
+		<$> buildMans
 
 installDesktopFile :: CopyDest -> Verbosity -> PackageDescription -> LocalBuildInfo -> IO ()
 installDesktopFile copyDest _verbosity pkg lbi
diff --git a/Test.hs b/Test.hs
--- a/Test.hs
+++ b/Test.hs
@@ -232,6 +232,7 @@
 	, testCase "version" test_version
 	, testCase "sync" test_sync
 	, testCase "union merge regression" test_union_merge_regression
+	, testCase "adjusted branch merge regression" test_adjusted_branch_merge_regression
 	, testCase "conflict resolution" test_conflict_resolution
 	, testCase "conflict resolution (adjusted branch)" test_conflict_resolution_adjusted_branch
 	, testCase "conflict resolution movein regression" test_conflict_resolution_movein_regression
@@ -564,10 +565,11 @@
 test_lock :: Assertion
 test_lock = intmpclonerepoInDirect $ do
 	annexed_notpresent annexedfile
-	ifM (unlockedFiles <$> getTestMode)
-		( not <$> git_annex "lock" [annexedfile] @? "lock failed to fail with not present file"
-		, not <$> git_annex "unlock" [annexedfile] @? "unlock failed to fail with not present file"
-		)
+	unlessM (annexeval Annex.Version.versionSupportsUnlockedPointers) $
+		ifM (unlockedFiles <$> getTestMode)
+			( not <$> git_annex "lock" [annexedfile] @? "lock failed to fail with not present file"
+			, not <$> git_annex "unlock" [annexedfile] @? "unlock failed to fail with not present file"
+			)
 	annexed_notpresent annexedfile
 
 	-- regression test: unlock of newly added, not committed file
@@ -969,9 +971,9 @@
 					git_annex "get" [annexedfile] @? "get failed"
 					boolSystem "git" [Param "remote", Param "rm", Param "origin"] @? "remote rm"
 				forM_ [r3, r2, r1] $ \r -> indir r $
-					git_annex "sync" [] @? "sync failed"
+					git_annex "sync" [] @? ("sync failed in " ++ r)
 				forM_ [r3, r2] $ \r -> indir r $
-					git_annex "drop" ["--force", annexedfile] @? "drop failed"
+					git_annex "drop" ["--force", annexedfile] @? ("drop failed in " ++ r)
 				indir r1 $ do
 					git_annex "sync" [] @? "sync failed in r1"
 					git_annex_expectoutput "find" ["--in", "r3"] []
@@ -1394,6 +1396,33 @@
 		git_annex_expectoutput "find" [conflictor] [conflictor]
 		-- regular file because it's unlocked
 		checkregularfile conflictor
+
+{- Regression test for a bad merge between two adjusted branch repos,
+ - where the same file is added to both independently. The bad merge
+ - emptied the whole tree. -}
+test_adjusted_branch_merge_regression :: Assertion
+test_adjusted_branch_merge_regression = whenM Annex.AdjustedBranch.isGitVersionSupported $
+	withtmpclonerepo $ \r1 ->
+		withtmpclonerepo $ \r2 -> do
+			pair r1 r2
+			setup r1
+			setup r2
+			checkmerge "r1" r1
+			checkmerge "r2" r2
+  where
+	conflictor = "conflictor"
+	setup r = indir r $ do
+		disconnectOrigin
+		git_annex "upgrade" [] @? "upgrade failed"
+		git_annex "adjust" ["--unlock", "--force"] @? "adjust failed"
+		writeFile conflictor "conflictor"
+		git_annex "add" [conflictor] @? "add conflicter failed"
+		git_annex "sync" [] @? "sync failed"
+	checkmerge what d = indir d $ do
+		git_annex "sync" [] @? ("sync failed in " ++ what)
+		l <- getDirectoryContents "."
+		conflictor `elem` l
+			@? ("conflictor not present after merge in " ++ what)
 
 {- Set up repos as remotes of each other. -}
 pair :: FilePath -> FilePath -> Assertion
diff --git a/Types/MetaData.hs b/Types/MetaData.hs
--- a/Types/MetaData.hs
+++ b/Types/MetaData.hs
@@ -95,7 +95,7 @@
 	serialize (MetaField f) = CI.original f
 	deserialize = Just . mkMetaFieldUnchecked
 
-{- Base64 problimatic values. -}
+{- Base64 problematic values. -}
 instance MetaSerializable MetaValue where
 	serialize (MetaValue isset v) =
 		serialize isset ++
diff --git a/Utility/QuickCheck.hs b/Utility/QuickCheck.hs
--- a/Utility/QuickCheck.hs
+++ b/Utility/QuickCheck.hs
@@ -16,8 +16,10 @@
 import Test.QuickCheck as X
 import Data.Time.Clock.POSIX
 import System.Posix.Types
+#if ! MIN_VERSION_QuickCheck(2,8,2)
 import qualified Data.Map as M
 import qualified Data.Set as S
+#endif
 import Control.Applicative
 import Prelude
 
diff --git a/Utility/UserInfo.hs b/Utility/UserInfo.hs
--- a/Utility/UserInfo.hs
+++ b/Utility/UserInfo.hs
@@ -15,6 +15,7 @@
 ) where
 
 import Utility.Env
+import Utility.Data
 
 import System.PosixCompat
 import Control.Applicative
@@ -24,7 +25,7 @@
  -
  - getpwent will fail on LDAP or NIS, so use HOME if set. -}
 myHomeDir :: IO FilePath
-myHomeDir = myVal env homeDirectory
+myHomeDir = either error return =<< myVal env homeDirectory
   where
 #ifndef mingw32_HOST_OS
 	env = ["HOME"]
@@ -33,7 +34,7 @@
 #endif
 
 {- Current user's user name. -}
-myUserName :: IO String
+myUserName :: IO (Either String String)
 myUserName = myVal env userName
   where
 #ifndef mingw32_HOST_OS
@@ -47,15 +48,15 @@
 #if defined(__ANDROID__) || defined(mingw32_HOST_OS)
 myUserGecos = return Nothing
 #else
-myUserGecos = Just <$> myVal [] userGecos
+myUserGecos = eitherToMaybe <$> myVal [] userGecos
 #endif
 
-myVal :: [String] -> (UserEntry -> String) -> IO String
+myVal :: [String] -> (UserEntry -> String) -> IO (Either String String)
 myVal envvars extract = go envvars
   where
 #ifndef mingw32_HOST_OS
-	go [] = extract <$> (getUserEntryForID =<< getEffectiveUserID)
+	go [] = Right . extract <$> (getUserEntryForID =<< getEffectiveUserID)
 #else
-	go [] = extract <$> error ("environment not set: " ++ show envvars)
+	go [] = return $ Left ("environment not set: " ++ show envvars)
 #endif
-	go (v:vs) = maybe (go vs) return =<< getEnv v
+	go (v:vs) = maybe (go vs) (return . Right) =<< getEnv v
diff --git a/git-annex.cabal b/git-annex.cabal
--- a/git-annex.cabal
+++ b/git-annex.cabal
@@ -1,5 +1,5 @@
 Name: git-annex
-Version: 6.20160527
+Version: 6.20160613
 Cabal-Version: >= 1.8
 License: GPL-3
 Maintainer: Joey Hess <id@joeyh.name>
@@ -139,7 +139,6 @@
   doc/git-annex-xmppgit.mdwn
   doc/logo.svg
   doc/logo_16x16.png
-  Makefile
   Build/mdwn2man
   Assistant/WebApp/routes
   static/activityicon.gif
@@ -663,6 +662,8 @@
     Build.EvilSplicer
     Build.InstallDesktopFile
     Build.LinuxMkLibs
+    Build.MakeMans
+    Build.Mans
     Build.NullSoftInstaller
     Build.OSXMkLibs
     Build.Standalone