diff --git a/Annex.hs b/Annex.hs
--- a/Annex.hs
+++ b/Annex.hs
@@ -65,6 +65,7 @@
 import Types.LockCache
 import Types.DesktopNotify
 import Types.CleanupActions
+import Types.AdjustedBranch
 import qualified Database.Keys.Handle as Keys
 import Utility.InodeCache
 import Utility.Url
@@ -144,7 +145,7 @@
 	, activekeys :: TVar (M.Map Key ThreadId)
 	, activeremotes :: MVar (M.Map (Types.Remote.RemoteA Annex) Integer)
 	, keysdbhandle :: Maybe Keys.DbHandle
-	, cachedcurrentbranch :: Maybe Git.Branch
+	, cachedcurrentbranch :: (Maybe (Maybe Git.Branch, Maybe Adjustment))
 	, cachedgitenv :: Maybe [(String, String)]
 	, urloptions :: Maybe UrlOptions
 	}
diff --git a/Annex/AdjustedBranch.hs b/Annex/AdjustedBranch.hs
--- a/Annex/AdjustedBranch.hs
+++ b/Annex/AdjustedBranch.hs
@@ -1,14 +1,17 @@
 {- adjusted branch
  -
- - Copyright 2016 Joey Hess <id@joeyh.name>
+ - Copyright 2016-2018 Joey Hess <id@joeyh.name>
  -
- - Licensed under the GNU GPL version 3 or higher.
+ - Licensed under the GNU AGPL version 3 or higher.
  -}
 
 {-# LANGUAGE BangPatterns #-}
 
 module Annex.AdjustedBranch (
 	Adjustment(..),
+	LinkAdjustment(..),
+	PresenceAdjustment(..),
+	adjustmentHidesFiles,
 	OrigBranch,
 	AdjBranch(..),
 	originalToAdjusted,
@@ -16,17 +19,20 @@
 	fromAdjustedBranch,
 	getAdjustment,
 	enterAdjustedBranch,
+	updateAdjustedBranch,
 	adjustBranch,
 	adjustToCrippledFileSystem,
-	updateAdjustedBranch,
+	mergeToAdjustedBranch,
 	propigateAdjustedCommits,
 	AdjustedClone(..),
 	checkAdjustedClone,
-	isGitVersionSupported,
+	isSupported,
 	checkVersionSupported,
 ) where
 
 import Annex.Common
+import Types.AdjustedBranch
+import Annex.AdjustedBranch.Name
 import qualified Annex
 import Git
 import Git.Types
@@ -57,38 +63,34 @@
 
 import qualified Data.Map as M
 
-data Adjustment
-	= UnlockAdjustment
-	| LockAdjustment
-	| FixAdjustment
-	| UnFixAdjustment
-	| HideMissingAdjustment
-	| ShowMissingAdjustment
-	deriving (Show, Eq)
+-- How to perform various adjustments to a TreeItem.
+class AdjustTreeItem t where
+	adjustTreeItem :: t -> TreeItem -> Annex (Maybe TreeItem)
 
-reverseAdjustment :: Adjustment -> Adjustment
-reverseAdjustment UnlockAdjustment = LockAdjustment
-reverseAdjustment LockAdjustment = UnlockAdjustment
-reverseAdjustment HideMissingAdjustment = ShowMissingAdjustment
-reverseAdjustment ShowMissingAdjustment = HideMissingAdjustment
-reverseAdjustment FixAdjustment = UnFixAdjustment
-reverseAdjustment UnFixAdjustment = FixAdjustment
+instance AdjustTreeItem Adjustment where
+	adjustTreeItem (LinkAdjustment l) t = adjustTreeItem l t
+	adjustTreeItem (PresenceAdjustment p Nothing) t = adjustTreeItem p t
+	adjustTreeItem (PresenceAdjustment p (Just l)) t =
+		adjustTreeItem p t >>= \case
+			Nothing -> return Nothing
+			Just t' -> adjustTreeItem l t'
 
-{- How to perform various adjustments to a TreeItem. -}
-adjustTreeItem :: Adjustment -> TreeItem -> Annex (Maybe TreeItem)
-adjustTreeItem UnlockAdjustment = ifSymlink adjustToPointer noAdjust
-adjustTreeItem LockAdjustment = ifSymlink noAdjust adjustToSymlink
-adjustTreeItem FixAdjustment = ifSymlink adjustToSymlink noAdjust
-adjustTreeItem UnFixAdjustment = ifSymlink (adjustToSymlink' gitAnnexLinkCanonical) noAdjust
-adjustTreeItem HideMissingAdjustment = \ti@(TreeItem _ _ s) ->
-	catKey s >>= \case
-		Just k -> ifM (inAnnex k)
-			( return (Just ti)
-			, return Nothing
-			)
-		Nothing -> return (Just ti)
-adjustTreeItem ShowMissingAdjustment = noAdjust
+instance AdjustTreeItem LinkAdjustment where
+	adjustTreeItem UnlockAdjustment = ifSymlink adjustToPointer noAdjust
+	adjustTreeItem LockAdjustment = ifSymlink noAdjust adjustToSymlink
+	adjustTreeItem FixAdjustment = ifSymlink adjustToSymlink noAdjust
+	adjustTreeItem UnFixAdjustment = ifSymlink (adjustToSymlink' gitAnnexLinkCanonical) noAdjust
 
+instance AdjustTreeItem PresenceAdjustment where
+	adjustTreeItem HideMissingAdjustment = \ti@(TreeItem _ _ s) ->
+		catKey s >>= \case
+			Just k -> ifM (inAnnex k)
+				( return (Just ti)
+				, return Nothing
+				)
+			Nothing -> return (Just ti)
+	adjustTreeItem ShowMissingAdjustment = noAdjust
+
 ifSymlink :: (TreeItem -> Annex a) -> (TreeItem -> Annex a) -> TreeItem -> Annex a
 ifSymlink issymlink notsymlink ti@(TreeItem _f m _s)
 	| toTreeItemType m == Just TreeSymlink = issymlink ti
@@ -118,9 +120,6 @@
 			<$> hashSymlink linktarget
 	Nothing -> return (Just ti)
 
-type OrigBranch = Branch
-newtype AdjBranch = AdjBranch { adjBranch :: Branch }
-
 -- This is a hidden branch ref, that's used as the basis for the AdjBranch,
 -- since pushes can overwrite the OrigBranch at any time. So, changes
 -- are propigated from the AdjBranch to the head of the BasisBranch.
@@ -132,42 +131,6 @@
 basisBranch (AdjBranch adjbranch) = BasisBranch $
 	Ref ("refs/basis/" ++ fromRef (Git.Ref.base adjbranch))
 
-adjustedBranchPrefix :: String
-adjustedBranchPrefix = "refs/heads/adjusted/"
-
-serialize :: Adjustment -> String
-serialize UnlockAdjustment = "unlocked"
-serialize LockAdjustment = "locked"
-serialize HideMissingAdjustment = "present"
-serialize ShowMissingAdjustment = "showmissing"
-serialize FixAdjustment = "fixed"
-serialize UnFixAdjustment = "unfixed"
-
-deserialize :: String -> Maybe Adjustment
-deserialize "unlocked" = Just UnlockAdjustment
-deserialize "locked" = Just UnlockAdjustment
-deserialize "present" = Just HideMissingAdjustment
-deserialize "fixed" = Just FixAdjustment
-deserialize "unfixed" = Just UnFixAdjustment
-deserialize _ = Nothing
-
-originalToAdjusted :: OrigBranch -> Adjustment -> AdjBranch
-originalToAdjusted orig adj = AdjBranch $ Ref $
-	adjustedBranchPrefix ++ base ++ '(' : serialize adj ++ ")"
-  where
-	base = fromRef (Git.Ref.base orig)
-
-adjustedToOriginal :: Branch -> Maybe (Adjustment, OrigBranch)
-adjustedToOriginal b
-	| adjustedBranchPrefix `isPrefixOf` bs = do
-		let (base, as) = separate (== '(') (drop prefixlen bs)
-		adj <- deserialize (takeWhile (/= ')') as)
-		Just (adj, Git.Ref.branchRef (Ref base))
-	| otherwise = Nothing
-  where
-	bs = fromRef b
-	prefixlen = length adjustedBranchPrefix
-
 getAdjustment :: Branch -> Maybe Adjustment
 getAdjustment = fmap fst . adjustedToOriginal
 
@@ -182,12 +145,21 @@
  - branch).
  -
  - Can fail, if no branch is checked out, or if the adjusted branch already
- - exists, or perhaps if staged changes conflict with the adjusted branch.
+ - exists, or if staged changes prevent a checkout.
  -}
 enterAdjustedBranch :: Adjustment -> Annex Bool
-enterAdjustedBranch adj = go =<< originalBranch
+enterAdjustedBranch adj = inRepo Git.Branch.current >>= \case
+	Just currbranch -> case getAdjustment currbranch of
+		Just curradj | curradj == adj ->
+			updateAdjustedBranch adj (AdjBranch currbranch)
+				(fromAdjustedBranch currbranch)
+		_ -> go currbranch
+	Nothing -> do
+		warning "not on any branch!"
+		return False
   where
-	go (Just origbranch) = do
+	go currbranch = do
+		let origbranch = fromAdjustedBranch currbranch
 		let adjbranch = adjBranch $ originalToAdjusted origbranch adj
 		ifM (inRepo (Git.Ref.exists adjbranch) <&&> (not <$> Annex.getState Annex.force))
 			( do
@@ -200,23 +172,58 @@
 					  , Git.Ref.describe origbranch
 					  ]
 					, [ "You can check out the adjusted branch manually to enter it,"
-					  , "or delete the adjusted branch and re-run this command."
+					  , "or add the --force option to overwrite the old branch."
 					  ]
 					]
 				return False
 			, do
-				AdjBranch b <- preventCommits $ const $ 
+				b <- preventCommits $ const $ 
 					adjustBranch adj origbranch
-				showOutput -- checkout can have output in large repos
-				inRepo $ Git.Command.runBool
-					[ Param "checkout"
-					, Param $ fromRef $ Git.Ref.base b
-					]
+				checkoutAdjustedBranch b []
 			)
-	go Nothing = do
-		warning "not on any branch!"
-		return False
 
+checkoutAdjustedBranch :: AdjBranch -> [CommandParam] -> Annex Bool
+checkoutAdjustedBranch (AdjBranch b) checkoutparams = do
+	showOutput -- checkout can have output in large repos
+	inRepo $ Git.Command.runBool $
+		[ Param "checkout"
+		, Param $ fromRef $ Git.Ref.base b
+		-- always show checkout progress, even if --quiet is used
+		-- to suppress other messages
+		, Param "--progress"
+		] ++ checkoutparams
+
+{- Already in a branch with this adjustment, but the user asked to enter it
+ - again. This should have the same result as checking out the original branch,
+ - deleting and rebuilding the adjusted branch, and then checking it out.
+ - But, it can be implemented more efficiently than that.
+ -}
+updateAdjustedBranch :: Adjustment -> AdjBranch -> OrigBranch -> Annex Bool
+updateAdjustedBranch adj@(PresenceAdjustment _ _) (AdjBranch currbranch) origbranch = do
+	b <- preventCommits $ \commitlck -> do
+		-- Avoid losing any commits that the adjusted branch has that
+		-- have not yet been propigated back to the origbranch.
+		_ <- propigateAdjustedCommits' origbranch adj commitlck
+
+		-- Git normally won't do anything when asked to check out the
+		-- currently checked out branch, even when its ref has
+		-- changed. Work around this by writing a raw sha to .git/HEAD.
+		inRepo (Git.Ref.sha currbranch) >>= \case
+			Just headsha -> inRepo $ \r ->
+				writeFile (Git.Ref.headFile r) (fromRef headsha)
+			_ -> noop
+	
+		adjustBranch adj origbranch
+	
+	-- Make git checkout quiet to avoid warnings about disconnected
+	-- branch tips being lost.
+	checkoutAdjustedBranch b [Param "--quiet"]
+updateAdjustedBranch adj@(LinkAdjustment _) _ origbranch = preventCommits $ \commitlck -> do
+	-- Not really needed here, but done for consistency.
+	_ <- propigateAdjustedCommits' origbranch adj commitlck
+	-- No need to do anything else, because link adjustments are stable.
+	return True
+
 adjustToCrippledFileSystem :: Annex ()
 adjustToCrippledFileSystem = do
 	warning "Entering an adjusted branch where files are unlocked as this filesystem does not support locked files."
@@ -227,7 +234,7 @@
 			, Param "-m"
 			, Param "commit before entering adjusted unlocked branch"
 			]
-	unlessM (enterAdjustedBranch UnlockAdjustment) $
+	unlessM (enterAdjustedBranch (LinkAdjustment UnlockAdjustment)) $
 		warning "Failed to enter adjusted branch!"
 
 setBasisBranch :: BasisBranch -> Ref -> Annex ()
@@ -313,8 +320,8 @@
 {- Update the currently checked out adjusted branch, merging the provided
  - branch into it. Note that the provided branch should be a non-adjusted
  - branch. -}
-updateAdjustedBranch :: Branch -> (OrigBranch, Adjustment) -> [Git.Merge.MergeConfig] -> Annex Bool -> Git.Branch.CommitMode -> Annex Bool
-updateAdjustedBranch tomerge (origbranch, adj) mergeconfig canresolvemerge commitmode = catchBoolIO $
+mergeToAdjustedBranch :: Branch -> (OrigBranch, Adjustment) -> [Git.Merge.MergeConfig] -> Annex Bool -> Git.Branch.CommitMode -> Annex Bool
+mergeToAdjustedBranch tomerge (origbranch, adj) mergeconfig canresolvemerge commitmode = catchBoolIO $
 	join $ preventCommits go
   where
 	adjbranch@(AdjBranch currbranch) = originalToAdjusted origbranch adj
@@ -603,10 +610,8 @@
 				, return NeedUpgradeForAdjustedClone
 				)
 
--- git 2.2.0 needed for GIT_COMMON_DIR which is needed
--- by updateAdjustedBranch to use withWorkTreeRelated.
-isGitVersionSupported :: IO Bool
-isGitVersionSupported = not <$> Git.Version.older "2.2.0"
+isSupported :: Annex Bool
+isSupported = versionSupportsAdjustedBranch <&&> liftIO isGitVersionSupported
 
 checkVersionSupported :: Annex ()
 checkVersionSupported = do
@@ -614,3 +619,8 @@
 		giveup "Adjusted branches are only supported in v6 or newer repositories."
 	unlessM (liftIO isGitVersionSupported) $
 		giveup "Your version of git is too old; upgrade it to 2.2.0 or newer to use adjusted branches."
+
+-- git 2.2.0 needed for GIT_COMMON_DIR which is needed
+-- by updateAdjustedBranch to use withWorkTreeRelated.
+isGitVersionSupported :: IO Bool
+isGitVersionSupported = not <$> Git.Version.older "2.2.0"
diff --git a/Annex/AdjustedBranch/Name.hs b/Annex/AdjustedBranch/Name.hs
new file mode 100644
--- /dev/null
+++ b/Annex/AdjustedBranch/Name.hs
@@ -0,0 +1,83 @@
+{- adjusted branch names
+ -
+ - Copyright 2016-2018 Joey Hess <id@joeyh.name>
+ -
+ - Licensed under the GNU AGPL version 3 or higher.
+ -}
+
+module Annex.AdjustedBranch.Name (
+	originalToAdjusted,
+	adjustedToOriginal,
+	AdjBranch(..),
+	OrigBranch,
+) where
+
+import Types.AdjustedBranch
+import Git
+import qualified Git.Ref
+import Utility.Misc
+
+import Control.Applicative
+import Data.List
+
+adjustedBranchPrefix :: String
+adjustedBranchPrefix = "refs/heads/adjusted/"
+
+class SerializeAdjustment t where
+	serializeAdjustment :: t -> String
+	deserializeAdjustment :: String -> Maybe t
+
+instance SerializeAdjustment Adjustment where
+	serializeAdjustment (LinkAdjustment l) =
+		serializeAdjustment l
+	serializeAdjustment (PresenceAdjustment p Nothing) =
+		serializeAdjustment p
+	serializeAdjustment (PresenceAdjustment p (Just l)) = 
+		serializeAdjustment p ++ "-" ++ serializeAdjustment l
+	deserializeAdjustment s = 
+		(LinkAdjustment <$> deserializeAdjustment s)
+			<|>
+		(PresenceAdjustment <$> deserializeAdjustment s1 <*> pure (deserializeAdjustment s2))
+			<|>
+		(PresenceAdjustment <$> deserializeAdjustment s <*> pure Nothing)
+	  where
+		(s1, s2) = separate (== '-') s
+
+instance SerializeAdjustment LinkAdjustment where
+	serializeAdjustment UnlockAdjustment = "unlocked"
+	serializeAdjustment LockAdjustment = "locked"
+	serializeAdjustment FixAdjustment = "fixed"
+	serializeAdjustment UnFixAdjustment = "unfixed"
+	deserializeAdjustment "unlocked" = Just UnlockAdjustment
+	deserializeAdjustment "locked" = Just UnlockAdjustment
+	deserializeAdjustment "fixed" = Just FixAdjustment
+	deserializeAdjustment "unfixed" = Just UnFixAdjustment
+	deserializeAdjustment _ = Nothing
+
+instance SerializeAdjustment PresenceAdjustment where
+	serializeAdjustment HideMissingAdjustment = "hidemissing"
+	serializeAdjustment ShowMissingAdjustment = "showmissing"
+	deserializeAdjustment "hidemissing" = Just HideMissingAdjustment
+	deserializeAdjustment "showmissing" = Just ShowMissingAdjustment
+	deserializeAdjustment _ = Nothing
+
+newtype AdjBranch = AdjBranch { adjBranch :: Branch }
+
+originalToAdjusted :: OrigBranch -> Adjustment -> AdjBranch
+originalToAdjusted orig adj = AdjBranch $ Ref $
+	adjustedBranchPrefix ++ base ++ '(' : serializeAdjustment adj ++ ")"
+  where
+	base = fromRef (Git.Ref.base orig)
+
+type OrigBranch = Branch
+
+adjustedToOriginal :: Branch -> Maybe (Adjustment, OrigBranch)
+adjustedToOriginal b
+	| adjustedBranchPrefix `isPrefixOf` bs = do
+		let (base, as) = separate (== '(') (drop prefixlen bs)
+		adj <- deserializeAdjustment (takeWhile (/= ')') as)
+		Just (adj, Git.Ref.branchRef (Ref base))
+	| otherwise = Nothing
+  where
+	bs = fromRef b
+	prefixlen = length adjustedBranchPrefix
diff --git a/Annex/CatFile.hs b/Annex/CatFile.hs
--- a/Annex/CatFile.hs
+++ b/Annex/CatFile.hs
@@ -1,6 +1,6 @@
 {- git cat-file interface, with handle automatically stored in the Annex monad
  -
- - Copyright 2011-2015 Joey Hess <id@joeyh.name>
+ - Copyright 2011-2018 Joey Hess <id@joeyh.name>
  -
  - Licensed under the GNU GPL version 3 or higher.
  -}
@@ -16,9 +16,11 @@
 	catObjectMetaData,
 	catFileStop,
 	catKey,
+	catSymLinkTarget,
 	catKeyFile,
 	catKeyFileHEAD,
-	catSymLinkTarget,
+	catKeyFileHidden,
+	catObjectMetaDataHidden,
 ) where
 
 import qualified Data.ByteString.Lazy as L
@@ -34,6 +36,8 @@
 import Git.Index
 import qualified Git.Ref
 import Annex.Link
+import Annex.CurrentBranch
+import Types.AdjustedBranch
 import Utility.FileSystemEncoding
 
 catFile :: Git.Branch -> FilePath -> Annex L.ByteString
@@ -142,3 +146,16 @@
 
 catKeyFileHEAD :: FilePath -> Annex (Maybe Key)
 catKeyFileHEAD f = catKey $ Git.Ref.fileFromRef Git.Ref.headRef f
+
+{- Look in the original branch from whence an adjusted branch is based
+ - to find the file. But only when the adjustment hides some files. -}
+catKeyFileHidden :: FilePath -> CurrBranch -> Annex (Maybe Key) 
+catKeyFileHidden = hiddenCat catKey
+
+catObjectMetaDataHidden :: FilePath -> CurrBranch -> Annex (Maybe (Integer, ObjectType))
+catObjectMetaDataHidden = hiddenCat catObjectMetaData
+
+hiddenCat :: (Ref -> Annex (Maybe a)) -> FilePath -> CurrBranch -> Annex (Maybe a)
+hiddenCat a f (Just origbranch, Just adj)
+	| adjustmentHidesFiles adj = a (Git.Ref.fileFromRef origbranch f)
+hiddenCat _ _ _ = return Nothing
diff --git a/Annex/Content.hs b/Annex/Content.hs
--- a/Annex/Content.hs
+++ b/Annex/Content.hs
@@ -46,6 +46,7 @@
 	staleKeysPrune,
 	pruneTmpWorkDirBefore,
 	isUnmodified,
+	isUnmodifiedCheap,
 	verifyKeyContent,
 	VerifyConfig(..),
 	Verification(..),
@@ -97,29 +98,29 @@
 inAnnexCheck :: Key -> (FilePath -> Annex Bool) -> Annex Bool
 inAnnexCheck key check = inAnnex' id False check key
 
-{- inAnnex that performs an arbitrary check of the key's content.
- -
- - When the content is unlocked, it must also be unmodified, or the bad
- - value will be returned.
- -
- - In direct mode, at least one of the associated files must pass the
- - check. Additionally, the file must be unmodified.
- -}
+{- inAnnex that performs an arbitrary check of the key's content. -}
 inAnnex' :: (a -> Bool) -> a -> (FilePath -> Annex a) -> Key -> Annex a
 inAnnex' isgood bad check key = withObjectLoc key checkindirect checkdirect
   where
 	checkindirect loc = do
 		r <- check loc
 		if isgood r
-			then do
-				cache <- Database.Keys.getInodeCaches key
-				if null cache
-					then return r
-					else ifM (sameInodeCache loc cache)
-						( return r
-						, return bad
-						)
+			then ifM (annexThin <$> Annex.getGitConfig)
+				-- When annex.thin is set, the object file
+				-- could be modified; make sure it's not.
+				-- (Suppress any messages about
+				-- checksumming, to avoid them cluttering
+				-- the display.)
+				( ifM (doQuietAction $ isUnmodified key loc)
+					( return r
+					, return bad
+					)
+				, return r
+				)
 			else return bad
+ 
+	-- In direct mode, at least one of the associated files must pass the
+	-- check. Additionally, the file must be unmodified.
 	checkdirect [] = return bad
 	checkdirect (loc:locs) = do
 		r <- check loc
@@ -746,17 +747,38 @@
 isUnmodified key f = go =<< geti
   where
 	go Nothing = return False
-	go (Just fc) = cheapcheck fc <||> expensivecheck fc
-	cheapcheck fc = anyM (compareInodeCaches fc)
-		=<< Database.Keys.getInodeCaches key
+	go (Just fc) = isUnmodifiedCheap' key fc <||> expensivecheck fc
 	expensivecheck fc = ifM (verifyKeyContent RetrievalAllKeysSecure AlwaysVerify UnVerified key f)
-		-- The file could have been modified while it was
-		-- being verified. Detect that.
-		( geti >>= maybe (return False) (compareInodeCaches fc)
+		( do
+			-- The file could have been modified while it was
+			-- being verified. Detect that.
+			ifM (geti >>= maybe (return False) (compareInodeCaches fc))
+				( do
+					-- Update the InodeCache to avoid
+					-- performing this expensive check again.
+					Database.Keys.addInodeCaches key [fc]
+					return True
+				, return False
+				)
 		, return False
 		)
 	geti = withTSDelta (liftIO . genInodeCache f)
 
+{- Cheap check if a file contains the unmodified content of the key,
+ - only checking the InodeCache of the key.
+ -
+ - Note that, on systems not supporting high-resolution mtimes,
+ - this may report a false positive when repeated edits are made to a file
+ - within a small time window (eg 1 second).
+ -}
+isUnmodifiedCheap :: Key -> FilePath -> Annex Bool
+isUnmodifiedCheap key f = maybe (return False) (isUnmodifiedCheap' key) 
+	=<< withTSDelta (liftIO . genInodeCache f)
+
+isUnmodifiedCheap' :: Key -> InodeCache -> Annex Bool
+isUnmodifiedCheap' key fc = 
+	anyM (compareInodeCaches fc) =<< Database.Keys.getInodeCaches key
+
 {- Moves a key out of .git/annex/objects/ into .git/annex/bad, and
  - returns the file it was moved to. -}
 moveBad :: Key -> Annex FilePath
@@ -845,6 +867,7 @@
 saveState :: Bool -> Annex ()
 saveState nocommit = doSideAction $ do
 	Annex.Queue.flush
+	Database.Keys.closeDb
 	unless nocommit $
 		whenM (annexAlwaysCommit <$> Annex.getGitConfig) $
 			Annex.Branch.commit =<< Annex.Branch.commitMessage
diff --git a/Annex/Content/LowLevel.hs b/Annex/Content/LowLevel.hs
--- a/Annex/Content/LowLevel.hs
+++ b/Annex/Content/LowLevel.hs
@@ -49,7 +49,6 @@
 
 linkOrCopy' :: Annex Bool -> Key -> FilePath -> FilePath -> Maybe FileMode -> Annex (Maybe LinkedOrCopied)
 linkOrCopy' canhardlink key src dest destmode
-	| maybe False isExecutable destmode = copy =<< getstat
 	| otherwise = catchDefaultIO Nothing $
 		ifM canhardlink
 			( hardlink
diff --git a/Annex/CurrentBranch.hs b/Annex/CurrentBranch.hs
new file mode 100644
--- /dev/null
+++ b/Annex/CurrentBranch.hs
@@ -0,0 +1,41 @@
+{- currently checked out branch
+ -
+ - Copyright 2018 Joey Hess <id@joeyh.name>
+ -
+ - Licensed under the GNU AGPL version 3 or higher.
+ -}
+
+module Annex.CurrentBranch where
+
+import Annex.Common
+import Types.AdjustedBranch
+import Annex.AdjustedBranch.Name
+import qualified Annex
+import qualified Git
+import qualified Git.Branch
+
+type CurrBranch = (Maybe Git.Branch, Maybe Adjustment)
+
+{- Gets the currently checked out branch.
+ - When on an adjusted branch, gets the original branch, and the adjustment.
+ -
+ - Cached for speed.
+ -
+ - Until a commit is made in a new repository, no branch is checked out.
+ - Since git-annex may make the first commit, this does not cache
+ - the absence of a branch.
+ -}
+getCurrentBranch :: Annex CurrBranch
+getCurrentBranch = maybe cache return
+	=<< Annex.getState Annex.cachedcurrentbranch
+  where
+	cache = inRepo Git.Branch.current >>= \case
+		Just b -> do
+			let v = case adjustedToOriginal b of 
+                        	Nothing -> (Just b, Nothing) 
+                                Just (adj, origbranch) -> 
+                                	(Just origbranch, Just adj)
+			Annex.changeState $ \s ->
+				s { Annex.cachedcurrentbranch = Just v }
+			return v
+		Nothing -> return (Nothing, Nothing)
diff --git a/Annex/Environment.hs b/Annex/Environment.hs
--- a/Annex/Environment.hs
+++ b/Annex/Environment.hs
@@ -5,8 +5,6 @@
  - Licensed under the GNU GPL version 3 or higher.
  -}
 
-{-# LANGUAGE CPP #-}
-
 module Annex.Environment where
 
 import Annex.Common
@@ -37,14 +35,8 @@
 	ensureEnv "GIT_AUTHOR_NAME" username
 	ensureEnv "GIT_COMMITTER_NAME" username
   where
-#ifndef __ANDROID__
 	-- existing environment is not overwritten
 	ensureEnv var val = setEnv var val False
-#else
-	-- Environment setting is broken on Android, so this is dealt with
-	-- in runshell instead.
-	ensureEnv _ _ = noop
-#endif
 
 {- Runs an action that commits to the repository, and if it fails, 
  - sets user.email and user.name to a dummy value and tries the action again. -}
diff --git a/Annex/GitOverlay.hs b/Annex/GitOverlay.hs
--- a/Annex/GitOverlay.hs
+++ b/Annex/GitOverlay.hs
@@ -14,6 +14,7 @@
 import Git.Types
 import Git.Index
 import Git.Env
+import Utility.Env
 import qualified Annex
 import qualified Annex.Queue
 
@@ -27,8 +28,8 @@
 		a
   where
 	-- This is an optimisation. Since withIndexFile is run repeatedly,
-	-- and addGitEnv uses the slow copyGitEnv when gitEnv is Nothing, 
-	-- we cache the copied environment the first time, and reuse it in
+	-- and addGitEnv uses the slow getEnvironment when gitEnv is Nothing, 
+	-- we cache the environment the first time, and reuse it in
 	-- subsequent calls.
 	--
 	-- (This could be done at another level; eg when creating the
@@ -40,7 +41,7 @@
 		Nothing -> do
 			e <- Annex.withState $ \s -> case Annex.cachedgitenv s of
 				Nothing -> do
-					e <- copyGitEnv
+					e <- getEnvironment
 					return (s { Annex.cachedgitenv = Just e }, e)
 				Just e -> return (s, e)
 			m (g { gitEnv = Just e })
diff --git a/Annex/Hook.hs b/Annex/Hook.hs
--- a/Annex/Hook.hs
+++ b/Annex/Hook.hs
@@ -32,6 +32,17 @@
 	[ mkHookScript "git annex post-receive"
 	]
 
+postCheckoutHook :: Git.Hook
+postCheckoutHook = Git.Hook "post-checkout" smudgeHook []
+
+postMergeHook :: Git.Hook
+postMergeHook = Git.Hook "post-merge" smudgeHook []
+
+-- Older versions of git-annex didn't support this command, but neither did
+-- they support v7 repositories.
+smudgeHook :: String
+smudgeHook = mkHookScript "git annex smudge --update"
+
 preCommitAnnexHook :: Git.Hook
 preCommitAnnexHook = Git.Hook "pre-commit-annex" "" []
 
@@ -40,7 +51,7 @@
 
 mkHookScript :: String -> String
 mkHookScript s = unlines
-	[ shebang_local
+	[ shebang
 	, "# automatically configured by git-annex"
 	, s
 	]
diff --git a/Annex/Ingest.hs b/Annex/Ingest.hs
--- a/Annex/Ingest.hs
+++ b/Annex/Ingest.hs
@@ -32,13 +32,12 @@
 import Annex.Perms
 import Annex.Link
 import Annex.MetaData
+import Annex.CurrentBranch
 import Annex.Version
 import Logs.Location
 import qualified Annex
 import qualified Annex.Queue
 import qualified Database.Keys
-import qualified Git
-import qualified Git.Branch
 import Config
 import Utility.InodeCache
 import Annex.ReplaceFile
@@ -288,7 +287,7 @@
 	-- touch symlink to have same time as the original file,
 	-- as provided in the InodeCache
 	case mcache of
-		Just c -> liftIO $ touch file (TimeSpec $ inodeCacheToMtime c) False
+		Just c -> liftIO $ touch file (inodeCacheToMtime c) False
 		Nothing -> noop
 
 	return l
@@ -329,21 +328,13 @@
 	(versionSupportsUnlockedPointers <&&>
 	 ((not . coreSymlinks <$> Annex.getGitConfig) <||>
 	  (annexAddUnlocked <$> Annex.getGitConfig) <||>
-	  (maybe False (\b -> getAdjustment b == Just UnlockAdjustment) <$> cachedCurrentBranch)
+	  (maybe False isadjustedunlocked . snd <$> getCurrentBranch)
 	 )
 	)
-
-cachedCurrentBranch :: Annex (Maybe Git.Branch)
-cachedCurrentBranch = maybe cache (return . Just)
-	=<< Annex.getState Annex.cachedcurrentbranch
   where
-	cache :: Annex (Maybe Git.Branch)
-	cache = inRepo Git.Branch.currentUnsafe >>= \case
-		Nothing -> return Nothing
-		Just b -> do
-			Annex.changeState $ \s ->
-				s { Annex.cachedcurrentbranch = Just b }
-			return (Just b)
+	isadjustedunlocked (LinkAdjustment UnlockAdjustment) = True
+	isadjustedunlocked (PresenceAdjustment _ (Just UnlockAdjustment)) = True
+	isadjustedunlocked _ = False
 
 {- Adds a file to the work tree for the key, and stages it in the index.
  - The content of the key may be provided in a temp file, which will be
diff --git a/Annex/Init.hs b/Annex/Init.hs
--- a/Annex/Init.hs
+++ b/Annex/Init.hs
@@ -21,7 +21,6 @@
 import Annex.Common
 import qualified Annex
 import qualified Git
-import qualified Git.LsFiles
 import qualified Git.Config
 import qualified Git.Objects
 import qualified Annex.Branch
@@ -29,10 +28,10 @@
 import Logs.Trust.Basic
 import Logs.Config
 import Types.TrustLevel
+import Types.RepoVersion
 import Annex.Version
 import Annex.Difference
 import Annex.UUID
-import Annex.Link
 import Annex.WorkTree
 import Config
 import Config.Smudge
@@ -78,7 +77,7 @@
 		Right username -> [username, at, hostname, ":", reldir]
 		Left _ -> [hostname, ":", reldir]
 
-initialize :: AutoInit -> Maybe String -> Maybe Version -> Annex ()
+initialize :: AutoInit -> Maybe String -> Maybe RepoVersion -> Annex ()
 initialize ai mdescription mversion = checkCanInitialize ai $ do
 	{- Has to come before any commits are made as the shared
 	 - clone heuristic expects no local objects. -}
@@ -98,7 +97,7 @@
 
 -- Everything except for uuid setup, shared clone setup, and initial
 -- description.
-initialize' :: AutoInit -> Maybe Version -> Annex ()
+initialize' :: AutoInit -> Maybe RepoVersion -> Annex ()
 initialize' ai mversion = checkCanInitialize ai $ do
 	checkLockSupport
 	checkFifoSupport
@@ -112,18 +111,16 @@
 	whenM versionSupportsUnlockedPointers $ do
 		configureSmudgeFilter
 		scanUnlockedFiles
+		unlessM isBareRepo $ do
+			hookWrite postCheckoutHook
+			hookWrite postMergeHook
 	checkAdjustedClone >>= \case
 		NeedUpgradeForAdjustedClone -> 
-			void $ upgrade True  versionForAdjustedClone
+			void $ upgrade True versionForAdjustedClone
 		InAdjustedClone -> return ()
 		NotInAdjustedClone ->
 			ifM (crippledFileSystem <&&> (not <$> isBareRepo))
-				( ifM versionSupportsUnlockedPointers
-					( adjustToCrippledFileSystem
-					, do
-						enableDirectMode
-						setDirect True
-					)
+				( adjustToCrippledFileSystem
 				-- Handle case where this repo was cloned from a
 				-- direct mode repo
 				, unlessM isBareRepo
@@ -265,15 +262,6 @@
 	warning "Detected a filesystem without fifo support."
 	warning "Disabling ssh connection caching."
 	setConfig (annexConfig "sshcaching") (Git.Config.boolConfig False)
-
-enableDirectMode :: Annex ()
-enableDirectMode = unlessM isDirect $ do
-	warning "Enabling direct mode."
-	top <- fromRepo Git.repoPath
-	(l, clean) <- inRepo $ Git.LsFiles.inRepo [top]
-	forM_ l $ \f ->
-		maybe noop (`toDirect` f) =<< isAnnexLink f
-	void $ liftIO clean
 
 checkSharedClone :: Annex Bool
 checkSharedClone = inRepo Git.Objects.isSharedClone
diff --git a/Annex/Locations.hs b/Annex/Locations.hs
--- a/Annex/Locations.hs
+++ b/Annex/Locations.hs
@@ -38,6 +38,8 @@
 	gitAnnexFsckDbDir,
 	gitAnnexFsckDbLock,
 	gitAnnexFsckResultsLog,
+	gitAnnexSmudgeLog,
+	gitAnnexSmudgeLock,
 	gitAnnexExportDbDir,
 	gitAnnexExportLock,
 	gitAnnexScheduleState,
@@ -311,6 +313,14 @@
 {- .git/annex/fsckresults/uuid is used to store results of git fscks -}
 gitAnnexFsckResultsLog :: UUID -> Git.Repo -> FilePath
 gitAnnexFsckResultsLog u r = gitAnnexDir r </> "fsckresults" </> fromUUID u
+
+{- .git/annex/smudge.log is used to log smudges worktree files that need to
+ - be updated. -}
+gitAnnexSmudgeLog :: Git.Repo -> FilePath
+gitAnnexSmudgeLog r = gitAnnexDir r </> "smudge.log"
+
+gitAnnexSmudgeLock :: Git.Repo -> FilePath
+gitAnnexSmudgeLock r = gitAnnexDir r </> "smudge.lck"
 
 {- .git/annex/export/uuid/ is used to store information about
  - exports to special remotes. -}
diff --git a/Annex/NumCopies.hs b/Annex/NumCopies.hs
--- a/Annex/NumCopies.hs
+++ b/Annex/NumCopies.hs
@@ -5,7 +5,7 @@
  - Licensed under the GNU GPL version 3 or higher.
  -}
 
-{-# LANGUAGE CPP, ScopedTypeVariables, DeriveDataTypeable #-}
+{-# LANGUAGE ScopedTypeVariables, DeriveDataTypeable #-}
 
 module Annex.NumCopies (
 	module Types.NumCopies,
@@ -165,9 +165,7 @@
 				cont v `catchNonAsync` (throw . DropException)
 			a `M.catches`
 				[ M.Handler (\ (e :: AsyncException) -> throwM e)
-#if MIN_VERSION_base(4,7,0)
 				, M.Handler (\ (e :: SomeAsyncException) -> throwM e)
-#endif
 				, M.Handler (\ (DropException e') -> throwM e')
 				, M.Handler (\ (_e :: SomeException) -> fallback)
 				]
diff --git a/Annex/VectorClock.hs b/Annex/VectorClock.hs
--- a/Annex/VectorClock.hs
+++ b/Annex/VectorClock.hs
@@ -15,7 +15,7 @@
 import Prelude
 
 import Utility.Env
-import Logs.TimeStamp
+import Utility.TimeStamp
 import Utility.QuickCheck
 
 -- | Some very old logs did not have any time stamp at all;
diff --git a/Annex/Version.hs b/Annex/Version.hs
--- a/Annex/Version.hs
+++ b/Annex/Version.hs
@@ -1,8 +1,8 @@
 {- git-annex repository versioning
  -
- - Copyright 2010,2013 Joey Hess <id@joeyh.name>
+ - Copyright 2010-2018 Joey Hess <id@joeyh.name>
  -
- - Licensed under the GNU GPL version 3 or higher.
+ - Licensed under the GNU AGPL version 3 or higher.
  -}
 
 {-# LANGUAGE CPP #-}
@@ -11,48 +11,53 @@
 
 import Annex.Common
 import Config
+import Types.RepoVersion
 import qualified Annex
 
-type Version = String
+import qualified Data.Map as M
 
-defaultVersion :: Version
-defaultVersion = "5"
+defaultVersion :: RepoVersion
+defaultVersion = RepoVersion 5
 
-latestVersion :: Version
-latestVersion = "6"
+latestVersion :: RepoVersion
+latestVersion = RepoVersion 7
 
-supportedVersions :: [Version]
-supportedVersions = ["3", "5", "6"]
+supportedVersions :: [RepoVersion]
+supportedVersions = map RepoVersion [5, 7]
 
-versionForAdjustedClone :: Version
-versionForAdjustedClone = "6"
+versionForAdjustedClone :: RepoVersion
+versionForAdjustedClone = RepoVersion 7
 
-upgradableVersions :: [Version]
+upgradableVersions :: [RepoVersion]
 #ifndef mingw32_HOST_OS
-upgradableVersions = ["0", "1", "2", "3", "4", "5"]
+upgradableVersions = map RepoVersion [0..6]
 #else
-upgradableVersions = ["2", "3", "4", "5"]
+upgradableVersions = map RepoVersion [2..6]
 #endif
 
-autoUpgradeableVersions :: [Version]
-autoUpgradeableVersions = ["3", "4"]
+autoUpgradeableVersions :: M.Map RepoVersion RepoVersion
+autoUpgradeableVersions = M.fromList
+	[ (RepoVersion 3, RepoVersion 5)
+	, (RepoVersion 4, RepoVersion 5)
+	, (RepoVersion 6, RepoVersion 7)
+	]
 
 versionField :: ConfigKey
 versionField = annexConfig "version"
 
-getVersion :: Annex (Maybe Version)
+getVersion :: Annex (Maybe RepoVersion)
 getVersion = annexVersion <$> Annex.getGitConfig
 
 versionSupportsDirectMode :: Annex Bool
 versionSupportsDirectMode = go <$> getVersion
   where
-	go (Just "6") = False
+	go (Just v) | v >= RepoVersion 6 = False
 	go _ = True
 
 versionSupportsUnlockedPointers :: Annex Bool
 versionSupportsUnlockedPointers = go <$> getVersion
   where
-	go (Just "6") = True
+	go (Just v) | v >= RepoVersion 6 = True
 	go _ = False
 
 versionSupportsAdjustedBranch :: Annex Bool
@@ -61,8 +66,8 @@
 versionUsesKeysDatabase :: Annex Bool
 versionUsesKeysDatabase = versionSupportsUnlockedPointers
 
-setVersion :: Version -> Annex ()
-setVersion = setConfig versionField
+setVersion :: RepoVersion -> Annex ()
+setVersion (RepoVersion v) = setConfig versionField (show v)
 
 removeVersion :: Annex ()
 removeVersion = unsetConfig versionField
diff --git a/Annex/WorkTree.hs b/Annex/WorkTree.hs
--- a/Annex/WorkTree.hs
+++ b/Annex/WorkTree.hs
@@ -1,6 +1,6 @@
 {- git-annex worktree files
  -
- - Copyright 2013-2016 Joey Hess <id@joeyh.name>
+ - Copyright 2013-2018 Joey Hess <id@joeyh.name>
  -
  - Licensed under the GNU GPL version 3 or higher.
  -}
@@ -13,6 +13,7 @@
 import Annex.Version
 import Annex.Content
 import Annex.ReplaceFile
+import Annex.CurrentBranch
 import Config
 import Git.FilePath
 import qualified Git.Ref
@@ -28,19 +29,20 @@
  -
  - An unlocked file will not have a link on disk, so fall back to
  - looking for a pointer to a key in git.
+ -
+ - When in an adjusted branch that may have hidden the file, looks for a
+ - pointer to a key in the original branch.
  -}
 lookupFile :: FilePath -> Annex (Maybe Key)
 lookupFile file = isAnnexLink file >>= \case
-	Just key -> makeret key
+	Just key -> return (Just key)
 	Nothing -> ifM (versionSupportsUnlockedPointers <||> isDirect)
 		( ifM (liftIO $ doesFileExist file)
-			( maybe (return Nothing) makeret =<< catKeyFile file
-			, return Nothing
+			( catKeyFile file
+			, catKeyFileHidden file =<< getCurrentBranch
 			)
 		, return Nothing 
 		)
-  where
-	makeret = return . Just
 
 {- Modifies an action to only act on files that are already annexed,
  - and passes the key on to it. -}
diff --git a/Assistant/DaemonStatus.hs b/Assistant/DaemonStatus.hs
--- a/Assistant/DaemonStatus.hs
+++ b/Assistant/DaemonStatus.hs
@@ -16,7 +16,7 @@
 import Types.Transfer
 import Logs.Transfer
 import Logs.Trust
-import Logs.TimeStamp
+import Utility.TimeStamp
 import qualified Remote
 import qualified Types.Remote as Remote
 import Config.DynamicConfig
diff --git a/Assistant/Install.hs b/Assistant/Install.hs
--- a/Assistant/Install.hs
+++ b/Assistant/Install.hs
@@ -80,7 +80,7 @@
 		let rungitannexshell var = runshell $ "git-annex-shell -c \"" ++ var ++ "\""
 
 		installWrapper (sshdir </> "git-annex-shell") $ unlines
-			[ shebang_local
+			[ shebang
 			, "set -e"
 			, "if [ \"x$SSH_ORIGINAL_COMMAND\" != \"x\" ]; then"
 			,   rungitannexshell "$SSH_ORIGINAL_COMMAND"
@@ -89,7 +89,7 @@
 			, "fi"
 			]
 		installWrapper (sshdir </> "git-annex-wrapper") $ unlines
-			[ shebang_local
+			[ shebang
 			, "set -e"
 			, runshell "\"$@\""
 			]
@@ -124,7 +124,7 @@
   where
 	genNautilusScript scriptdir action =
 		installscript (scriptdir </> scriptname action) $ unlines
-			[ shebang_local
+			[ shebang
 			, autoaddedcomment
 			, "exec " ++ program ++ " " ++ action ++ " --notify-start --notify-finish -- \"$@\""
 			]
diff --git a/Assistant/Pairing.hs b/Assistant/Pairing.hs
--- a/Assistant/Pairing.hs
+++ b/Assistant/Pairing.hs
@@ -5,8 +5,6 @@
  - Licensed under the GNU GPL version 3 or higher.
  -}
 
-{-# LANGUAGE CPP #-}
-
 module Assistant.Pairing where
 
 import Annex.Common
@@ -84,11 +82,7 @@
 data AddrClass = IPv4AddrClass | IPv6AddrClass
 
 data SomeAddr = IPv4Addr HostAddress
-{- My Android build of the Network library does not currently have IPV6
- - support. -}
-#ifndef __ANDROID__
 	| IPv6Addr HostAddress6
-#endif
 	deriving (Ord, Eq, Read, Show)
 
 {- This contains the whole secret, just lightly obfuscated to make it not
diff --git a/Assistant/Ssh.hs b/Assistant/Ssh.hs
--- a/Assistant/Ssh.hs
+++ b/Assistant/Ssh.hs
@@ -189,7 +189,7 @@
 	echoval v = "echo " ++ shellEscape v
 	wrapper = "~/.ssh/git-annex-shell"
 	script =
-		[ shebang_portable
+		[ shebang
 		, "set -e"
 		, "if [ \"x$SSH_ORIGINAL_COMMAND\" != \"x\" ]; then"
 		,   runshell "$SSH_ORIGINAL_COMMAND"
diff --git a/Assistant/Sync.hs b/Assistant/Sync.hs
--- a/Assistant/Sync.hs
+++ b/Assistant/Sync.hs
@@ -25,6 +25,7 @@
 import Annex.UUID
 import Annex.TaggedPush
 import Annex.Ssh
+import Annex.CurrentBranch
 import qualified Config
 import Git.Config
 import Config.DynamicConfig
@@ -79,8 +80,7 @@
 	{- No local branch exists yet, but we can try pulling. -}
 	sync (Nothing, _) = manualPull (Nothing, Nothing) =<< gitremotes
 	go = do
-		(failed, diverged) <- sync
-			=<< liftAnnex (join Command.Sync.getCurrBranch)
+		(failed, diverged) <- sync =<< liftAnnex getCurrentBranch
 		addScanRemotes diverged =<<
 			filterM (not <$$> liftIO . getDynamicConfig . remoteAnnexIgnore . Remote.gitconfig) rs
 		return failed
@@ -127,7 +127,7 @@
 		Annex.Branch.commit =<< Annex.Branch.commitMessage
 		(,,)
 			<$> gitRepo
-			<*> join Command.Sync.getCurrBranch
+			<*> getCurrentBranch
 			<*> getUUID
 	ret <- go True branch g u remotes
 	return ret
diff --git a/Assistant/Threads/Committer.hs b/Assistant/Threads/Committer.hs
--- a/Assistant/Threads/Committer.hs
+++ b/Assistant/Threads/Committer.hs
@@ -32,6 +32,7 @@
 import Annex.CatFile
 import Annex.InodeSentinal
 import Annex.Version
+import Annex.CurrentBranch
 import qualified Annex
 import Utility.InodeCache
 import Annex.Content.Direct
@@ -228,7 +229,7 @@
 		Right _ -> do
 			ok <- Command.Sync.commitStaged Git.Branch.AutomaticCommit msg
 			when ok $
-				Command.Sync.updateSyncBranch =<< join Command.Sync.getCurrBranch
+				Command.Sync.updateBranches =<< getCurrentBranch
 			return ok
 
 {- OSX needs a short delay after a file is added before locking it down,
diff --git a/Assistant/Threads/Exporter.hs b/Assistant/Threads/Exporter.hs
--- a/Assistant/Threads/Exporter.hs
+++ b/Assistant/Threads/Exporter.hs
@@ -12,6 +12,7 @@
 import Assistant.Pushes
 import Assistant.DaemonStatus
 import Annex.Concurrent
+import Annex.CurrentBranch
 import Utility.ThreadScheduler
 import qualified Annex
 import qualified Remote
@@ -64,7 +65,7 @@
 			Annex.changeState $ \st -> st { Annex.errcounter = 0 }
 			start <- liftIO getCurrentTime
 			void $ Command.Sync.seekExportContent rs
-				=<< join Command.Sync.getCurrBranch
+				=<< getCurrentBranch
 			-- Look at command error counter to see if the export
 			-- didn't work.
 			failed <- (> 0) <$> Annex.getState Annex.errcounter
diff --git a/Assistant/Threads/Merger.hs b/Assistant/Threads/Merger.hs
--- a/Assistant/Threads/Merger.hs
+++ b/Assistant/Threads/Merger.hs
@@ -13,6 +13,7 @@
 import Assistant.Sync
 import Utility.DirWatcher
 import Utility.DirWatcher.Types
+import Annex.CurrentBranch
 import qualified Annex.Branch
 import qualified Git
 import qualified Git.Branch
@@ -71,7 +72,7 @@
 	changedbranch = fileToBranch file
 
 	mergecurrent =
-		mergecurrent' =<< liftAnnex (join Command.Sync.getCurrBranch)
+		mergecurrent' =<< liftAnnex getCurrentBranch
 	mergecurrent' currbranch@(Just b, _)
 		| changedbranch `isRelatedTo` b =
 			whenM (liftAnnex $ inRepo $ Git.Branch.changed b changedbranch) $ do
diff --git a/Assistant/Threads/WebApp.hs b/Assistant/Threads/WebApp.hs
--- a/Assistant/Threads/WebApp.hs
+++ b/Assistant/Threads/WebApp.hs
@@ -7,7 +7,6 @@
 
 {-# LANGUAGE TemplateHaskell, MultiParamTypeClasses #-}
 {-# LANGUAGE ViewPatterns, OverloadedStrings #-}
-{-# LANGUAGE CPP #-}
 {-# OPTIONS_GHC -fno-warn-orphans #-}
 
 module Assistant.Threads.WebApp where
@@ -69,11 +68,6 @@
 		then pure listenhost
 		else getAnnex $ annexListen <$> Annex.getGitConfig
 	tlssettings <- getAnnex getTlsSettings
-#ifdef __ANDROID__
-	when (isJust listenhost') $
-		-- See Utility.WebApp
-		giveup "Sorry, --listen is not currently supported on Android"
-#endif
 	webapp <- WebApp
 		<$> pure assistantdata
 		<*> genAuthToken 128
diff --git a/Assistant/WebApp/Configurators/Local.hs b/Assistant/WebApp/Configurators/Local.hs
--- a/Assistant/WebApp/Configurators/Local.hs
+++ b/Assistant/WebApp/Configurators/Local.hs
@@ -20,7 +20,6 @@
 import qualified Git
 import qualified Git.Config
 import qualified Git.Command
-import qualified Command.Sync
 import Config.Files
 import Utility.FreeDesktop
 import Utility.DiskFree
@@ -30,6 +29,7 @@
 import Utility.DataUnits
 import Remote (prettyUUID)
 import Annex.UUID
+import Annex.CurrentBranch
 import Types.StandardGroups
 import Logs.PreferredContent
 import Logs.UUID
@@ -165,13 +165,8 @@
 postFirstRepositoryR = page "Getting started" (Just Configuration) $ do
 	unlessM (liftIO $ inPath "git") $
 		giveup "You need to install git in order to use git-annex!"
-#ifdef __ANDROID__
-	androidspecial <- liftIO $ doesDirectoryExist "/sdcard/DCIM"
-	let path = "/sdcard/annex"
-#else
 	androidspecial <- liftIO osAndroid
 	path <- liftIO . defaultRepositoryPath =<< liftH inFirstRun
-#endif
 	((res, form), enctype) <- liftH $ runFormPostNoToken $ newRepositoryForm path
 	case res of
 		FormSuccess (RepositoryPath p) -> liftH $
@@ -180,12 +175,8 @@
 
 getAndroidCameraRepositoryR :: Handler ()
 getAndroidCameraRepositoryR = do
-#ifdef __ANDROID__
-	let dcim = "/sdcard/DCIM"
-#else
 	home <- liftIO myHomeDir
 	let dcim = home </> "storage" </> "dcim"
-#endif
 	startFullAssistant dcim SourceGroup $ Just addignore	
   where
 	addignore = do
@@ -221,7 +212,7 @@
  - immediately pulling from it. Also spawns a sync to push to it as well. -}
 immediateSyncRemote :: Remote -> Assistant ()
 immediateSyncRemote r = do
-	currentbranch <- liftAnnex $ join Command.Sync.getCurrBranch
+	currentbranch <- liftAnnex $ getCurrentBranch
 	void $ manualPull currentbranch [r]
 	syncRemote r
 
@@ -392,10 +383,6 @@
 		| dir == "/tmp" = False
 		| dir == "/run/shm" = False
 		| dir == "/run/lock" = False
-#ifdef __ANDROID__
-		| dir == "/mnt/sdcard" = False
-		| dir == "/sdcard" = False
-#endif
 		| otherwise = True
 #endif
 
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
@@ -116,7 +116,6 @@
 		bad_username textField
 
 	bad_username = "bad user name" :: Text
-#ifndef __ANDROID__
 	bad_hostname = "cannot resolve host name" :: Text
 
 	check_hostname = checkM (liftIO . checkdns) hostnamefield
@@ -131,10 +130,6 @@
 				| otherwise -> Right $ T.pack fullname
 			Just [] -> Right t
 			Nothing -> Left bad_hostname
-#else
-	-- getAddrInfo currently broken on Android
-	check_hostname = hostnamefield -- unchecked
-#endif
 
 	-- The directory is implicitly in home, so remove any leading ~/
 	normalize i = i { inputDirectory = normalizedir <$> inputDirectory i }
diff --git a/Assistant/WebApp/Configurators/Upgrade.hs b/Assistant/WebApp/Configurators/Upgrade.hs
--- a/Assistant/WebApp/Configurators/Upgrade.hs
+++ b/Assistant/WebApp/Configurators/Upgrade.hs
@@ -5,7 +5,7 @@
  - Licensed under the GNU AGPL version 3 or higher.
  -}
 
-{-# LANGUAGE CPP, QuasiQuotes, TemplateHaskell, OverloadedStrings #-}
+{-# LANGUAGE QuasiQuotes, TemplateHaskell, OverloadedStrings #-}
 
 module Assistant.WebApp.Configurators.Upgrade where
 
@@ -15,22 +15,11 @@
 import Assistant.Restart
 import Config
 
-{- On Android, just point the user at the apk file to download.
- - Installation will be handled by selecting the downloaded file.
- -
- - Otherwise, start the upgrade process, which will run fully
- - noninteractively.
- - -}
+{- Start the upgrade process. -}
 getConfigStartUpgradeR :: GitAnnexDistribution -> Handler Html
 getConfigStartUpgradeR d = do
-#ifdef ANDROID_SPLICES
-	let url = distributionUrl d
-	page "Upgrade" (Just Configuration) $
-		$(widgetFile "configurators/upgrade/android")
-#else
 	liftAssistant $ startDistributionDownload d
 	redirect DashboardR
-#endif
 
 {- Finish upgrade by starting the new assistant in the same repository this
  - one is running in, and redirecting to it. -}
diff --git a/Assistant/WebApp/Page.hs b/Assistant/WebApp/Page.hs
--- a/Assistant/WebApp/Page.hs
+++ b/Assistant/WebApp/Page.hs
@@ -5,7 +5,7 @@
  - Licensed under the GNU AGPL version 3 or higher.
  -}
 
-{-# LANGUAGE TypeFamilies, QuasiQuotes, MultiParamTypeClasses, TemplateHaskell, OverloadedStrings, RankNTypes, CPP #-}
+{-# LANGUAGE TypeFamilies, QuasiQuotes, MultiParamTypeClasses, TemplateHaskell, OverloadedStrings, RankNTypes #-}
 
 module Assistant.WebApp.Page where
 
@@ -70,13 +70,6 @@
 		Just msg -> error msg
   where
 	navdetails i = (navBarName i, navBarRoute i, Just i == navbaritem)
-
-hasFileBrowser :: Bool
-#ifdef ANDROID_SPLICES
-hasFileBrowser = False
-#else
-hasFileBrowser = True
-#endif
 
 controlMenu :: Widget
 controlMenu = $(widgetFile "controlmenu")
diff --git a/BuildFlags.hs b/BuildFlags.hs
--- a/BuildFlags.hs
+++ b/BuildFlags.hs
@@ -62,11 +62,6 @@
 #ifdef WITH_DESKTOP_NOTIFY
 	, "DesktopNotify"
 #endif
-#ifdef WITH_CONCURRENTOUTPUT
-	, "ConcurrentOutput"
-#else
-#warning Building without ConcurrentOutput
-#endif
 #ifdef WITH_TORRENTPARSER
 	, "TorrentParser"
 #endif
diff --git a/CHANGELOG b/CHANGELOG
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -1,3 +1,64 @@
+git-annex (7.20181031) upstream; urgency=medium
+
+  * Added v7 repository mode. v6 upgrades automatically to v7, but
+    v5 is still the default for now. While v6 was always experimental
+    to some degree, its successor v7 is ready for production use!
+    http://git-annex.branchable.com/tips/unlocked_files/
+  * Direct mode repositories are deprecated; they have many problems
+    that v7 fixes, so upgrading them now is recommended (but not yet
+    required): git annex upgrade --version=7
+  * init: When in a crippled filesystem, initialize a v7 repository
+    using an adjusted unlocked branch, instead of a direct mode repository.
+  * At long last there's a way to hide annexed files whose content
+    is missing from the working tree: git-annex adjust --hide-missing
+    See https://git-annex.branchable.com/tips/hiding_missing_files/
+  * When already in an adjusted branch, running git-annex adjust
+    again will update the branch as needed. This is mostly
+    useful with --hide-missing to hide/unhide files after their content
+    has been dropped or received.
+  * git-annex sync --content supports --hide-missing; it can
+    be used to get the content of hidden files, and it updates the
+    adjusted branch to hide/unhide files as necessary.
+  * smudge: The smudge filter no longer provides git with annexed
+    file content, to avoid a git memory leak, and because that did not
+    honor annex.thin. Now git annex smudge --update has to be run
+    after a checkout to update unlocked files in the working tree 
+    with annexed file contents.
+  * v7 init, upgrade: Install git post-checkout and post-merge hooks that run 
+    git annex smudge --update.
+  * precommit: Run git annex smudge --update, because the post-merge
+    hook is not run when there is a merge conflict. So the work tree will
+    be updated when a commit is made to resolve the merge conflict.
+  * Note that git has no hooks run after git stash or git cherry-pick,
+    so the user will have to manually run git annex smudge --update
+    after such commands.
+  * Removed the old Android app.
+  * Removed support for building with very old ghc < 8.0.1,
+    and with yesod < 1.4.3, and without concurrent-output,
+    which were only being used for the Android cross build.
+  * Webapp: Fix termux detection.
+  * runshell: Use system locales when built with 
+    GIT_ANNEX_PACKAGE_INSTALL set. (For Neurodebian packages.)
+  * Fix database inconsistency that could cause git-annex to
+    get confused about whether a locked file's content was present.
+  * Fix concurrency bug that occurred on the first download from an
+    exporttree remote.
+  * init --version=6 will still work, but the repository is auto-upgraded
+    immediately to v7.
+  * When annex.thin is set, allow hard links to be made between executable
+    work tree files and annex objects.
+  * addurl: Removed undocumented special case in handling of a CHECKURL-MULTI
+    response with only a single file listed. Rather than ignoring the url that
+    was in the response, use it.
+  * webapp: Fixed a crash when adding a git remote.
+    (Reversion introduced in version 6.20180112)
+  * migrate: Fix failure to migrate from URL keys.
+    (Reversion introduced in version 6.20180926)
+  * Cache high-resolution mtimes for improved detection of modified files
+    in v7 (and direct mode).
+
+ -- Joey Hess <id@joeyh.name>  Wed, 31 Oct 2018 09:21:50 -0400
+
 git-annex (6.20181011) upstream; urgency=medium
 
   * sync: Warn when a remote's export is not updated to the current
diff --git a/COPYRIGHT b/COPYRIGHT
--- a/COPYRIGHT
+++ b/COPYRIGHT
@@ -33,7 +33,7 @@
 Copyright: 2012-2018 Joey Hess <id@joeyh.name>
 License: BSD-2-clause
 
-Files: doc/logo* */favicon.ico standalone/osx/git-annex.app/Contents/Resources/git-annex.icns standalone/android/icons/*
+Files: doc/logo* */favicon.ico standalone/osx/git-annex.app/Contents/Resources/git-annex.icns
 Copyright: 2007 Henrik Nyh <http://henrik.nyh.se/>
            2010 Joey Hess <id@joeyh.name>
 	   2013 John Lawrence
diff --git a/CmdLine/Action.hs b/CmdLine/Action.hs
--- a/CmdLine/Action.hs
+++ b/CmdLine/Action.hs
@@ -24,10 +24,7 @@
 import Control.Exception (throwIO)
 import Data.Either
 import qualified Data.Map.Strict as M
-
-#ifdef WITH_CONCURRENTOUTPUT
 import qualified System.Console.Regions as Regions
-#endif
 
 {- Runs a command, starting with the check stage, and then
  - the seek stage. Finishes by running the continutation, and 
@@ -169,7 +166,6 @@
 
 {- Do concurrent output when that has been requested. -}
 allowConcurrentOutput :: Annex a -> Annex a
-#ifdef WITH_CONCURRENTOUTPUT
 allowConcurrentOutput a = do
 	fromcmdline <- Annex.getState Annex.concurrency
 	fromgitcfg <- annexJobs <$> Annex.getGitConfig
@@ -197,9 +193,6 @@
 		setconcurrentoutputenabled False
 	setconcurrentoutputenabled b = Annex.changeState $ \s ->
 		s { Annex.output = (Annex.output s) { concurrentOutputEnabled = b } }
-#else
-allowConcurrentOutput = id
-#endif
 
 {- Ensures that only one thread processes a key at a time.
  - Other threads will block until it's done. -}
diff --git a/CmdLine/Seek.hs b/CmdLine/Seek.hs
--- a/CmdLine/Seek.hs
+++ b/CmdLine/Seek.hs
@@ -29,6 +29,7 @@
 import Remote.List
 import qualified Remote
 import Annex.CatFile
+import Annex.CurrentBranch
 import Annex.Content
 import Annex.InodeSentinal
 import qualified Database.Keys
@@ -270,17 +271,33 @@
 -- An item in the work tree, which may be a file or a directory.
 newtype WorkTreeItem = WorkTreeItem FilePath
 
+-- When in an adjusted branch that hides some files, it may not exist
+-- in the current work tree, but in the original branch. This allows
+-- seeking for such files.
+newtype AllowHidden = AllowHidden Bool
+
 -- Many git commands seek work tree items matching some criteria,
 -- and silently skip over anything that does not exist. But users expect
 -- an error message when one of the files they provided as a command-line
 -- parameter doesn't exist, so this checks that each exists.
 workTreeItems :: CmdParams -> Annex [WorkTreeItem]
-workTreeItems ps = do
+workTreeItems = workTreeItems' (AllowHidden False)
+
+workTreeItems' :: AllowHidden -> CmdParams -> Annex [WorkTreeItem]
+workTreeItems' (AllowHidden allowhidden) ps = do
+	currbranch <- getCurrentBranch
 	forM_ ps $ \p ->
-		unlessM (isJust <$> liftIO (catchMaybeIO $ getSymbolicLinkStatus p)) $ do
+		unlessM (exists p <||> hidden currbranch p) $ do
 			toplevelWarning False (p ++ " not found")
 			Annex.incError
 	return (map WorkTreeItem ps)
+  where
+	exists p = isJust <$> liftIO (catchMaybeIO $ getSymbolicLinkStatus p)
+	hidden currbranch p
+		| allowhidden = do
+			f <- liftIO $ relPathCwdToFile p
+			isJust <$> catObjectMetaDataHidden f currbranch
+		| otherwise = return False
 
 notSymlink :: FilePath -> IO Bool
 notSymlink f = liftIO $ not . isSymbolicLink <$> getSymbolicLinkStatus f
diff --git a/Command/AddUrl.hs b/Command/AddUrl.hs
--- a/Command/AddUrl.hs
+++ b/Command/AddUrl.hs
@@ -132,17 +132,21 @@
 	go deffile (Right (UrlContents sz mf)) = do
 		let f = adjustFile o (fromMaybe (maybe deffile fromSafeFilePath mf) (fileOption (downloadOptions o)))
 		void $ commandAction $ startRemote r o f u sz
-	go deffile (Right (UrlMulti l))
-		| isNothing (fileOption (downloadOptions o)) =
+	go deffile (Right (UrlMulti l)) = case fileOption (downloadOptions o) of
+		Nothing ->
 			forM_ l $ \(u', sz, f) -> do
 				let f' = adjustFile o (deffile </> fromSafeFilePath f)
-				void $ commandAction $
-					startRemote r o f' u' sz
-		| otherwise = giveup $ unwords
-			[ "That url contains multiple files according to the"
-			, Remote.name r
-			, " remote; cannot add it to a single file."
-			]
+				void $ commandAction $ startRemote r o f' u' sz
+		Just f -> case l of
+			[] -> noop
+			((u',sz,_):[]) -> do
+				let f' = adjustFile o f
+				void $ commandAction $ startRemote r o f' u' sz
+			_ -> giveup $ unwords
+				[ "That url contains multiple files according to the"
+				, Remote.name r
+				, " remote; cannot add it to a single file."
+				]
 
 startRemote :: Remote -> AddUrlOptions -> FilePath -> URLString -> Maybe Integer -> CommandStart
 startRemote r o file uri sz = do
diff --git a/Command/Adjust.hs b/Command/Adjust.hs
--- a/Command/Adjust.hs
+++ b/Command/Adjust.hs
@@ -1,6 +1,6 @@
 {- git-annex command
  -
- - Copyright 2016 Joey Hess <id@joeyh.name>
+ - Copyright 2016-2018 Joey Hess <id@joeyh.name>
  -
  - Licensed under the GNU GPL version 3 or higher.
  -}
@@ -16,7 +16,12 @@
 		paramNothing (seek <$$> optParser)
 
 optParser :: CmdParamsDesc -> Parser Adjustment
-optParser _ = 
+optParser _ =
+	(LinkAdjustment <$> linkAdjustmentParser)
+	<|> (PresenceAdjustment <$> presenceAdjustmentParser <*> maybeLinkAdjustmentParser)
+
+linkAdjustmentParser :: Parser LinkAdjustment
+linkAdjustmentParser =
 	flag' UnlockAdjustment
 		( long "unlock"
 		<> help "unlock annexed files"
@@ -25,12 +30,16 @@
 		( long "fix"
 		<> help "fix symlinks to annnexed files"
 		)
-	{- Not ready yet
-	<|> flag' HideMissingAdjustment
+
+maybeLinkAdjustmentParser :: Parser (Maybe LinkAdjustment)
+maybeLinkAdjustmentParser = Just <$> linkAdjustmentParser <|> pure Nothing
+
+presenceAdjustmentParser :: Parser PresenceAdjustment
+presenceAdjustmentParser =
+	flag' HideMissingAdjustment
 		( long "hide-missing"
-		<> help "omit annexed files whose content is not present"
+		<> help "hide annexed files whose content is not present"
 		)
-	-}
 
 seek :: Adjustment -> CommandSeek
 seek = commandAction . start
diff --git a/Command/EnableTor.hs b/Command/EnableTor.hs
--- a/Command/EnableTor.hs
+++ b/Command/EnableTor.hs
@@ -122,6 +122,7 @@
 			, connCheckAuth = const False
 			, connIhdl = h
 			, connOhdl = h
+			, connIdent = ConnIdent Nothing
 			}
 		runst <- mkRunState Client
 		void $ runNetProto runst conn $ P2P.serveAuth u
diff --git a/Command/Find.hs b/Command/Find.hs
--- a/Command/Find.hs
+++ b/Command/Find.hs
@@ -18,7 +18,7 @@
 import Utility.DataUnits
 
 cmd :: Command
-cmd = withGlobalOptions [annexedMatchingOptions] $ mkCommand $
+cmd = notBareRepo $ withGlobalOptions [annexedMatchingOptions] $ mkCommand $
 	command "find" SectionQuery "lists available files"
 		paramPaths (seek <$$> optParser)
 
diff --git a/Command/Fix.hs b/Command/Fix.hs
--- a/Command/Fix.hs
+++ b/Command/Fix.hs
@@ -18,8 +18,10 @@
 import Annex.Perms
 import qualified Annex.Queue
 import qualified Database.Keys
-#if ! defined(mingw32_HOST_OS) && ! defined(__ANDROID__)
+
+#if ! defined(mingw32_HOST_OS)
 import Utility.Touch
+import System.Posix.Files
 #endif
 
 cmd :: Command
@@ -91,15 +93,15 @@
 fixSymlink :: FilePath -> FilePath -> CommandPerform
 fixSymlink file link = do
 	liftIO $ do
-#if ! defined(mingw32_HOST_OS) && ! defined(__ANDROID__)
+#if ! defined(mingw32_HOST_OS)
 		-- preserve mtime of symlink
-		mtime <- catchMaybeIO $ TimeSpec . modificationTime
+		mtime <- catchMaybeIO $ modificationTimeHiRes
 			<$> getSymbolicLinkStatus file
 #endif
 		createDirectoryIfMissing True (parentDir file)
 		removeFile file
 		createSymbolicLink link file
-#if ! defined(mingw32_HOST_OS) && ! defined(__ANDROID__)
+#if ! defined(mingw32_HOST_OS)
 		maybe noop (\t -> touch file t False) mtime
 #endif
 	next $ cleanupSymlink file
diff --git a/Command/Fsck.hs b/Command/Fsck.hs
--- a/Command/Fsck.hs
+++ b/Command/Fsck.hs
@@ -22,7 +22,7 @@
 import Logs.Location
 import Logs.Trust
 import Logs.Activity
-import Logs.TimeStamp
+import Utility.TimeStamp
 import Logs.PreferredContent
 import Annex.NumCopies
 import Annex.UUID
diff --git a/Command/Info.hs b/Command/Info.hs
--- a/Command/Info.hs
+++ b/Command/Info.hs
@@ -13,9 +13,7 @@
 import qualified Data.Map.Strict as M
 import qualified Data.Vector as V
 import Data.Ord
-#if MIN_VERSION_base(4,9,0)
 import qualified Data.Semigroup as Sem
-#endif
 import Prelude
 
 import Command
@@ -60,26 +58,18 @@
 	, backendsKeys :: M.Map KeyVariety Integer
 	}
 	
-appendKeyData :: KeyData -> KeyData -> KeyData
-appendKeyData a b = KeyData
-	{ countKeys = countKeys a + countKeys b
-	, sizeKeys = sizeKeys a + sizeKeys b
-	, unknownSizeKeys = unknownSizeKeys a + unknownSizeKeys b
-	, backendsKeys = backendsKeys a <> backendsKeys b
-	}
-	
-#if MIN_VERSION_base(4,9,0)
 instance Sem.Semigroup KeyData where
-	(<>) = appendKeyData
-#endif
+	a <> b = KeyData
+		{ countKeys = countKeys a + countKeys b
+		, sizeKeys = sizeKeys a + sizeKeys b
+		, unknownSizeKeys = unknownSizeKeys a + unknownSizeKeys b
+		, backendsKeys = backendsKeys a <> backendsKeys b
+		}
 
 instance Monoid KeyData where
 	mempty = KeyData 0 0 0 M.empty
-#if MIN_VERSION_base(4,11,0)
-#elif MIN_VERSION_base(4,9,0)
+#if ! MIN_VERSION_base(4,11,0)
 	mappend = (Sem.<>)
-#else
-	mappend = appendKeyData
 #endif
 
 data NumCopiesStats = NumCopiesStats
diff --git a/Command/Init.hs b/Command/Init.hs
--- a/Command/Init.hs
+++ b/Command/Init.hs
@@ -10,7 +10,10 @@
 import Command
 import Annex.Init
 import Annex.Version
+import Types.RepoVersion
 import qualified Annex.SpecialRemote
+
+import qualified Data.Map as M
 	
 cmd :: Command
 cmd = dontCheck repoExists $
@@ -19,21 +22,25 @@
 
 data InitOptions = InitOptions
 	{ initDesc :: String
-	, initVersion :: Maybe Version
+	, initVersion :: Maybe RepoVersion
 	}
 
 optParser :: CmdParamsDesc -> Parser InitOptions
 optParser desc = InitOptions
 	<$> (unwords <$> cmdParams desc)
-	<*> optional (option (str >>= parseVersion)
+	<*> optional (option (str >>= parseRepoVersion)
 		( long "version" <> metavar paramValue
 		<> help "Override default annex.version"
 		))
 
-parseVersion :: Monad m => String -> m Version
-parseVersion v
-	| v `elem` supportedVersions = return v
-	| otherwise = fail $ v ++ " is not a currently supported repository version"
+parseRepoVersion :: Monad m => String -> m RepoVersion
+parseRepoVersion s = case RepoVersion <$> readish s of
+	Nothing -> fail $ "version parse error"
+	Just v
+		| v `elem` supportedVersions -> return v
+		| otherwise -> case M.lookup v autoUpgradeableVersions of
+			Just v' -> return v'
+			Nothing -> fail $ s ++ " is not a currently supported repository version"
 
 seek :: InitOptions -> CommandSeek
 seek = commandAction . start
diff --git a/Command/Merge.hs b/Command/Merge.hs
--- a/Command/Merge.hs
+++ b/Command/Merge.hs
@@ -9,7 +9,8 @@
 
 import Command
 import qualified Annex.Branch
-import Command.Sync (prepMerge, mergeLocal, getCurrBranch, mergeConfig)
+import Annex.CurrentBranch
+import Command.Sync (prepMerge, mergeLocal, mergeConfig)
 
 cmd :: Command
 cmd = command "merge" SectionMaintenance
@@ -33,4 +34,4 @@
 mergeSynced :: CommandStart
 mergeSynced = do
 	prepMerge
-	mergeLocal mergeConfig def =<< join getCurrBranch
+	mergeLocal mergeConfig def =<< getCurrentBranch
diff --git a/Command/Migrate.hs b/Command/Migrate.hs
--- a/Command/Migrate.hs
+++ b/Command/Migrate.hs
@@ -80,20 +80,20 @@
 			forM_ urls $ \url ->
 				setUrlPresent newkey url
 			next $ Command.ReKey.cleanup file oldkey newkey
-		, error "failed"
+		, giveup "failed creating link from old to new key"
 		)
-	genkey Nothing = return Nothing
+	genkey Nothing = do
+		content <- calcRepo $ gitAnnexLocation oldkey
+		let source = KeySource
+			{ keyFilename = file
+			, contentLocation = content
+			, inodeCache = Nothing
+			}
+		v <- genKey source (Just newbackend)
+		return $ case v of
+			Just (newkey, _) -> Just (newkey, False)
+			_ -> Nothing
 	genkey (Just fm) = fm oldkey newbackend afile >>= \case
-		Just newkey -> return $ Just (newkey, True)
-		Nothing -> do
-			content <- calcRepo $ gitAnnexLocation oldkey
-			let source = KeySource
-				{ keyFilename = file
-				, contentLocation = content
-				, inodeCache = Nothing
-				}
-			v <- genKey source (Just newbackend)
-			return $ case v of
-				Just (newkey, _) -> Just (newkey, False)
-				_ -> Nothing
+		Just newkey -> return (Just (newkey, True))
+		Nothing -> genkey Nothing
 	afile = AssociatedFile (Just file)
diff --git a/Command/PostReceive.hs b/Command/PostReceive.hs
--- a/Command/PostReceive.hs
+++ b/Command/PostReceive.hs
@@ -11,7 +11,8 @@
 import qualified Annex
 import Git.Types
 import Annex.UpdateInstead
-import Command.Sync (mergeLocal, prepMerge, mergeConfig, getCurrBranch)
+import Annex.CurrentBranch
+import Command.Sync (mergeLocal, prepMerge, mergeConfig)
 
 -- This does not need to modify the git-annex branch to update the 
 -- work tree, but auto-initialization might change the git-annex branch.
@@ -48,4 +49,4 @@
 updateInsteadEmulation :: CommandStart
 updateInsteadEmulation = do
 	prepMerge
-	mergeLocal mergeConfig def =<< join getCurrBranch
+	mergeLocal mergeConfig def =<< getCurrentBranch
diff --git a/Command/PreCommit.hs b/Command/PreCommit.hs
--- a/Command/PreCommit.hs
+++ b/Command/PreCommit.hs
@@ -13,6 +13,7 @@
 import Config
 import qualified Command.Add
 import qualified Command.Fix
+import qualified Command.Smudge
 import Annex.Direct
 import Annex.Hook
 import Annex.Link
@@ -54,11 +55,21 @@
 				flip withFilesToBeCommitted l $ \f -> commandAction $
 					maybe stop (Command.Fix.start Command.Fix.FixSymlinks f)
 						=<< isAnnexLink f
-				-- inject unlocked files into the annex
-				-- (not needed when repo version uses
-				-- unlocked pointer files)
-				unlessM versionSupportsUnlockedPointers $
-					withFilesOldUnlockedToBeCommitted (commandAction . startInjectUnlocked) l
+				ifM versionSupportsUnlockedPointers
+					-- after a merge conflict or git
+					-- cherry-pick or stash, pointer
+					-- files in the worktree won't
+					-- be populated, so populate them
+					-- here
+					( Command.Smudge.updateSmudged 
+						-- When there's a false index,
+						-- restaging the files won't work.
+						. Restage =<< liftIO Git.haveFalseIndex
+					-- inject unlocked files into the annex
+					-- (not needed when repo version uses
+					-- unlocked pointer files)
+					, withFilesOldUnlockedToBeCommitted (commandAction . startInjectUnlocked) l
+					)
 			)
 		runAnnexHook preCommitAnnexHook
 		-- committing changes to a view updates metadata
diff --git a/Command/ReKey.hs b/Command/ReKey.hs
--- a/Command/ReKey.hs
+++ b/Command/ReKey.hs
@@ -68,7 +68,7 @@
 perform file oldkey newkey = do
 	ifM (inAnnex oldkey) 
 		( unlessM (linkKey file oldkey newkey) $
-			giveup "failed"
+			giveup "failed creating link from old to new key"
 		, unlessM (Annex.getState Annex.force) $
 			giveup $ file ++ " is not available (use --force to override)"
 		)
@@ -87,18 +87,18 @@
 		oldobj <- calcRepo (gitAnnexLocation oldkey)
 		isJust <$> linkOrCopy' (return True) newkey oldobj tmp Nothing
 	, do
-		ic <- withTSDelta (liftIO . genInodeCache file)
-	 	{- The file being rekeyed is itself an unlocked file, so if
-		 - it's linked to the old key, that link must be broken. -}
+	 	{- The file being rekeyed is itself an unlocked file; if
+		 - it's hard linked to the old key, that link must be broken. -}
 		oldobj <- calcRepo (gitAnnexLocation oldkey)
-		v <- tryNonAsync $ modifyContent oldobj $ do
-			replaceFile oldobj $ \tmp ->
-				unlessM (checkedCopyFile oldkey file tmp Nothing) $
-					error "can't lock old key"
-			freezeContent oldobj
-			oldic <- withTSDelta (liftIO . genInodeCache oldobj)
-			whenM (isUnmodified oldkey oldobj) $
-				Database.Keys.addInodeCaches oldkey (catMaybes [oldic])
+		v <- tryNonAsync $ do
+			st <- liftIO $ getFileStatus file
+			when (linkCount st > 1) $ do
+				freezeContent oldobj
+				replaceFile file $ \tmp -> do
+					unlessM (checkedCopyFile oldkey oldobj tmp Nothing) $
+						error "can't lock old key"
+					thawContent tmp
+		ic <- withTSDelta (liftIO . genInodeCache file)
 		case v of
 			Left e -> do
 				warning (show e)
diff --git a/Command/Smudge.hs b/Command/Smudge.hs
--- a/Command/Smudge.hs
+++ b/Command/Smudge.hs
@@ -8,12 +8,12 @@
 module Command.Smudge where
 
 import Command
-import qualified Annex
 import Annex.Content
 import Annex.Link
 import Annex.FileMatcher
 import Annex.Ingest
 import Annex.CatFile
+import Logs.Smudge
 import Logs.Location
 import qualified Database.Keys
 import qualified Git.BuildVersion
@@ -29,43 +29,46 @@
 		"git smudge filter"
 		paramFile (seek <$$> optParser)
 
-data SmudgeOptions = SmudgeOptions
+data SmudgeOptions = UpdateOption | SmudgeOptions
 	{ smudgeFile :: FilePath
 	, cleanOption :: Bool
 	}
 
 optParser :: CmdParamsDesc -> Parser SmudgeOptions
-optParser desc = SmudgeOptions
-	<$> argument str ( metavar desc )
-	<*> switch ( long "clean" <> help "clean filter" )
+optParser desc = smudgeoptions <|> updateoption
+  where
+	smudgeoptions = SmudgeOptions
+		<$> argument str ( metavar desc )
+		<*> switch ( long "clean" <> help "clean filter" )
+	updateoption = flag' UpdateOption
+		( long "update" <> help "populate annexed worktree files" )
 
 seek :: SmudgeOptions -> CommandSeek
-seek o = commandAction $
-	(if cleanOption o then clean else smudge) (smudgeFile o)
+seek (SmudgeOptions f False) = commandAction (smudge f)
+seek (SmudgeOptions f True) = commandAction (clean f)
+seek UpdateOption = commandAction update
 
 -- Smudge filter is fed git file content, and if it's a pointer to an
--- available annex object, should output its content.
+-- available annex object, git expects it to output its content.
+--
+-- However, this does not do that. It outputs the pointer, and records
+-- the filename in the smudge log. Git hooks run after commands like checkout
+-- then run git annex smudge --update which populates the work tree files
+-- with annex content. This is done for several reasons:
+--
+-- * To support annex.thin
+-- * Because git currently buffers the whole object received from the
+--   smudge filter in memory, which is a problem with large files.
 smudge :: FilePath -> CommandStart
 smudge file = do
 	b <- liftIO $ B.hGetContents stdin
 	case parseLinkOrPointer b of
-		Nothing -> liftIO $ B.putStr b
+		Nothing -> noop
 		Just k -> do
-			Database.Keys.addAssociatedFile k =<< inRepo (toTopFilePath file)
-			-- A previous unlocked checkout of the file may have
-			-- led to the annex object getting modified;
-			-- don't provide such modified content as it
-			-- will be confusing. inAnnex will detect such
-			-- modifications.
-			ifM (inAnnex k)
-				( do
-					content <- calcRepo (gitAnnexLocation k)
-					whenM (annexThin <$> Annex.getGitConfig) $
-						warning $ "Not able to honor annex.thin when git is checking out " ++ file ++ " (run git annex fix to re-thin files)"
-					liftIO $ B.putStr . fromMaybe b
-						=<< catchMaybeIO (B.readFile content)
-				, liftIO $ B.putStr b
-				)
+			topfile <- inRepo (toTopFilePath file)
+			Database.Keys.addAssociatedFile k topfile
+			void $ smudgeLog k topfile
+	liftIO $ B.putStr b
 	stop
 
 -- Clean filter is fed file content on stdin, decides if a file
@@ -92,19 +95,30 @@
 			if Git.BuildVersion.older "2.5"
 				then B.length b `seq` return ()
 				else liftIO $ hClose stdin
-			-- Look up the backend that was used for this file
-			-- before, so that when git re-cleans a file its
-			-- backend does not change.
-			let oldbackend = maybe Nothing (maybeLookupBackendVariety . keyVariety) oldkey
-			-- Can't restage associated files because git add
-			-- runs this and has the index locked.
-			let norestage = Restage False
-			liftIO . emitPointer
-				=<< postingest
-				=<< (\ld -> ingest' oldbackend ld Nothing norestage)
-				=<< lockDown cfg file
+
+			-- Optimization for the case when the file is already
+			-- annexed and is unmodified.
+			case oldkey of
+				Nothing -> doingest oldkey
+				Just ko -> ifM (isUnmodifiedCheap ko file)
+					( liftIO $ emitPointer ko
+					, doingest oldkey
+					)
 		, liftIO $ B.hPut stdout b
 		)
+	
+	doingest oldkey = do
+		-- Look up the backend that was used for this file
+		-- before, so that when git re-cleans a file its
+		-- backend does not change.
+		let oldbackend = maybe Nothing (maybeLookupBackendVariety . keyVariety) oldkey
+		-- Can't restage associated files because git add
+		-- runs this and has the index locked.
+		let norestage = Restage False
+		liftIO . emitPointer
+			=<< postingest
+			=<< (\ld -> ingest' oldbackend ld Nothing norestage)
+			=<< lockDown cfg file
 
 	postingest (Just k, _) = do
 		logStatus k InfoPresent
@@ -144,11 +158,26 @@
 -- the pointer copy. It will then be populated with the content.
 getMoveRaceRecovery :: Key -> FilePath -> Annex ()
 getMoveRaceRecovery k file = void $ tryNonAsync $
-	liftIO (isPointerFile file) >>= \k' -> when (Just k == k') $
-		whenM (inAnnex k) $ do
-			obj <- calcRepo (gitAnnexLocation k)
-			-- Cannot restage because git add is running and has
-			-- the index locked.
-			populatePointerFile (Restage False) k obj file >>= \case
-				Nothing -> return ()
-				Just ic -> Database.Keys.addInodeCaches k [ic]
+	whenM (inAnnex k) $ do
+		obj <- calcRepo (gitAnnexLocation k)
+		-- Cannot restage because git add is running and has
+		-- the index locked.
+		populatePointerFile (Restage False) k obj file >>= \case
+			Nothing -> return ()
+			Just ic -> Database.Keys.addInodeCaches k [ic]
+
+update :: CommandStart
+update = do
+	updateSmudged (Restage True)
+	stop
+
+updateSmudged :: Restage -> Annex ()
+updateSmudged restage = streamSmudged $ \k topf -> do
+	f <- fromRepo $ fromTopFilePath topf
+	whenM (inAnnex k) $ do
+		obj <- calcRepo (gitAnnexLocation k)
+		unlessM (isJust <$> populatePointerFile restage k obj f) $
+			liftIO (isPointerFile f) >>= \case
+				Just k' | k' == k -> toplevelWarning False $
+					"unable to populate worktree file " ++ f
+				_ -> noop
diff --git a/Command/Sync.hs b/Command/Sync.hs
--- a/Command/Sync.hs
+++ b/Command/Sync.hs
@@ -9,7 +9,6 @@
 module Command.Sync (
 	cmd,
 	CurrBranch,
-	getCurrBranch,
 	mergeConfig,
 	merge,
 	prepMerge,
@@ -20,7 +19,7 @@
 	pushBranch,
 	updateBranch,
 	syncBranch,
-	updateSyncBranch,
+	updateBranches,
 	seekExportContent,
 ) where
 
@@ -60,6 +59,7 @@
 import Annex.Export
 import Annex.LockFile
 import Annex.TaggedPush
+import Annex.CurrentBranch
 import qualified Database.Export as Export
 import Utility.Bloom
 import Utility.OptParse
@@ -162,8 +162,7 @@
 seek o = allowConcurrentOutput $ do
 	prepMerge
 
-	getbranch <- getCurrBranch 
-	let withbranch a = a =<< getbranch
+	let withbranch a = a =<< getCurrentBranch
 
 	remotes <- syncRemotes (syncWith o)
 	let gitremotes = filter Remote.gitSyncableRemote remotes
@@ -188,7 +187,7 @@
 				]
 			
 			whenM shouldsynccontent $ do
-				syncedcontent <- seekSyncContent o dataremotes
+				syncedcontent <- withbranch $ seekSyncContent o dataremotes
 				exportedcontent <- withbranch $ seekExportContent exportremotes
 				-- Transferring content can take a while,
 				-- and other changes can be pushed to the
@@ -209,35 +208,6 @@
 		<||> pure (not (null (contentOfOption o)))
 		<||> (pure (not (noContentOption o)) <&&> getGitConfigVal annexSyncContent)
 
-type CurrBranch = (Maybe Git.Branch, Maybe Adjustment)
-
-{- There may not be a branch checked out until after the commit,
- - or perhaps after it gets merged from the remote, or perhaps
- - never.
- -
- - So only look it up once it's needed, and once there is a
- - branch, cache it.
- -
- - When on an adjusted branch, gets the original branch, and the adjustment.
- -}
-getCurrBranch :: Annex (Annex CurrBranch)
-getCurrBranch = do
-	mvar <- liftIO newEmptyMVar
-	return $ ifM (liftIO $ isEmptyMVar mvar)
-		( do
-			currbranch <- inRepo Git.Branch.current
-			case currbranch of
-				Nothing -> return (Nothing, Nothing)
-				Just b -> do
-					let v = case adjustedToOriginal b of
-						Nothing -> (Just b, Nothing)
-						Just (adj, origbranch) ->
-							(Just origbranch, Just adj)
-					liftIO $ putMVar mvar v
-					return v
-		, liftIO $ readMVar mvar
-		)
-
 {- Merging may delete the current directory, so go to the top
  - of the repo. This also means that sync always acts on all files in the
  - repository, not just on a subdirectory. -}
@@ -257,7 +227,7 @@
 
 merge :: CurrBranch -> [Git.Merge.MergeConfig] -> ResolveMergeOverride -> Git.Branch.CommitMode -> Git.Branch -> Annex Bool
 merge currbranch mergeconfig resolvemergeoverride commitmode tomerge = case currbranch of
-	(Just b, Just adj) -> updateAdjustedBranch tomerge (b, adj) mergeconfig canresolvemerge commitmode
+	(Just b, Just adj) -> mergeToAdjustedBranch tomerge (b, adj) mergeconfig canresolvemerge commitmode
 	(b, _) -> autoMergeFrom tomerge b mergeconfig canresolvemerge commitmode
   where
 	canresolvemerge = case resolvemergeoverride of
@@ -372,17 +342,29 @@
 
 pushLocal :: CurrBranch -> CommandStart
 pushLocal b = do
-	updateSyncBranch b
+	updateBranches b
 	stop
 
-updateSyncBranch :: CurrBranch -> Annex ()
-updateSyncBranch (Nothing, _) = noop
-updateSyncBranch (Just branch, madj) = do
+updateBranches :: CurrBranch -> Annex ()
+updateBranches (Nothing, _) = noop
+updateBranches (Just branch, madj) = do
 	-- When in an adjusted branch, propigate any changes made to it
-	-- back to the original branch.
-	maybe noop (propigateAdjustedCommits branch) madj
+	-- back to the original branch. The adjusted branch may also need
+	-- to be updated to hide/expose files.
+	case madj of
+		Nothing -> noop
+		Just adj -> do
+			let origbranch = branch
+			propigateAdjustedCommits origbranch adj
+			when (adjustmentHidesFiles adj) $ do
+				showSideAction "updating adjusted branch"
+				let adjbranch = originalToAdjusted origbranch adj
+				unlessM (updateAdjustedBranch adj adjbranch origbranch) $
+					warning $ unwords [ "Updating adjusted branch failed." ]
+					
 	-- Update the sync branch to match the new state of the branch
 	inRepo $ updateBranch (syncBranch branch) branch
+
 	-- In direct mode, we're operating on some special direct mode
 	-- branch, rather than the intended branch, so update the intended
 	-- branch.
@@ -568,8 +550,11 @@
 		, return True
 		)
 
-{- Without --all, only looks at files in the work tree. With --all,
- - makes 2 passes, first looking at the work tree and then all keys.
+{- Without --all, only looks at files in the work tree.
+ - (Or, when in an ajusted branch where some files are hidden, at files in
+ - the original branch.)
+ -
+ - With --all, makes a second pass over all keys.
  - This ensures that preferred content expressions that match on
  - filenames work, even when in --all mode.
  -
@@ -577,25 +562,42 @@
  -
  - When concurrency is enabled, files are processed concurrently.
  -}
-seekSyncContent :: SyncOptions -> [Remote] -> Annex Bool
-seekSyncContent o rs = do
+seekSyncContent :: SyncOptions -> [Remote] -> CurrBranch -> Annex Bool
+seekSyncContent o rs currbranch = do
 	mvar <- liftIO newEmptyMVar
 	bloom <- case keyOptions o of
 		Just WantAllKeys -> Just <$> genBloomFilter (seekworktree mvar [])
-		_ -> do
-			l <- workTreeItems (contentOfOption o)
-			seekworktree mvar l (const noop)
-			pure Nothing
+		_ -> case currbranch of
+                	(Just origbranch, Just adj) | adjustmentHidesFiles adj -> do
+				l <- workTreeItems' (AllowHidden True) (contentOfOption o)
+				seekincludinghidden origbranch mvar l (const noop)
+				pure Nothing
+			_ -> do
+				l <- workTreeItems (contentOfOption o)
+				seekworktree mvar l (const noop)
+				pure Nothing
 	withKeyOptions' (keyOptions o) False
-		(return (seekkeys mvar bloom))
+		(return (gokey mvar bloom))
 		(const noop)
 		[]
 	finishCommandActions
 	liftIO $ not <$> isEmptyMVar mvar
   where
-	seekworktree mvar l bloomfeeder = seekHelper LsFiles.inRepo l >>=
-		mapM_ (\f -> ifAnnexed f (go (Right bloomfeeder) mvar (AssociatedFile (Just f))) noop)
-	seekkeys mvar bloom (k, _) = go (Left bloom) mvar (AssociatedFile Nothing) k
+	seekworktree mvar l bloomfeeder = 
+		seekHelper LsFiles.inRepo l
+			>>= gofiles bloomfeeder mvar
+
+	seekincludinghidden origbranch mvar l bloomfeeder = 
+		seekHelper (LsFiles.inRepoOrBranch origbranch) l 
+			>>= gofiles bloomfeeder mvar
+
+	gofiles bloomfeeder mvar = mapM_ $ \f ->
+		ifAnnexed f
+			(go (Right bloomfeeder) mvar (AssociatedFile (Just f)))
+			noop
+	
+	gokey mvar bloom (k, _) = go (Left bloom) mvar (AssociatedFile Nothing) k
+
 	go ebloom mvar af k = commandAction $ do
 		whenM (syncFile ebloom rs af k) $
 			void $ liftIO $ tryPutMVar mvar ()
diff --git a/Command/Version.hs b/Command/Version.hs
--- a/Command/Version.hs
+++ b/Command/Version.hs
@@ -12,6 +12,7 @@
 import BuildInfo
 import BuildFlags
 import Types.Key
+import Types.RepoVersion
 import qualified Types.Backend as B
 import qualified Types.Remote as R
 import qualified Remote
@@ -49,7 +50,7 @@
 showVersion :: Annex ()
 showVersion = do
 	liftIO showPackageVersion
-	maybe noop (liftIO . vinfo "local repository version")
+	maybe noop (liftIO . vinfo "local repository version" . showRepoVersion)
 		=<< getVersion
 
 showPackageVersion :: IO ()
@@ -62,9 +63,14 @@
 	vinfo "remote types" $ unwords $ map R.typename Remote.remoteTypes
 	vinfo "operating system" $ unwords [os, arch]
 	vinfo "supported repository versions" $
-		unwords supportedVersions
+		verlist supportedVersions
 	vinfo "upgrade supported from repository versions" $
-		unwords upgradableVersions
+		verlist upgradableVersions
+  where
+	verlist = unwords . map showRepoVersion
+
+showRepoVersion :: RepoVersion -> String
+showRepoVersion = show  . fromRepoVersion
 
 showRawVersion :: IO ()
 showRawVersion = do
diff --git a/Command/WebApp.hs b/Command/WebApp.hs
--- a/Command/WebApp.hs
+++ b/Command/WebApp.hs
@@ -19,9 +19,6 @@
 import Annex.Environment
 import Utility.WebApp
 import Utility.Daemon (checkDaemon)
-#ifdef __ANDROID__
-import Utility.Env
-#endif
 import Utility.UserInfo
 import Annex.Init
 import qualified Git
@@ -188,18 +185,7 @@
 			Annex.eval state $
 				startDaemon True True Nothing Nothing (listenAddress o) $ Just $
 					sendurlback v
-	sendurlback v _origout _origerr url _htmlshim = do
-		recordUrl url
-		putMVar v url
-
-recordUrl :: String -> IO ()
-#ifdef __ANDROID__
-{- The Android app has a menu item that opens the url recorded
- - in this file. -}
-recordUrl url = writeFile "/sdcard/git-annex.home/.git-annex-url" url
-#else
-recordUrl _ = noop
-#endif
+	sendurlback v _origout _origerr url _htmlshim = putMVar v url
 
 openBrowser :: Maybe FilePath -> FilePath -> String -> Maybe Handle -> Maybe Handle -> IO ()
 openBrowser mcmd htmlshim realurl outh errh = do
@@ -207,7 +193,6 @@
 	openBrowser' mcmd htmlshim' realurl outh errh
 
 openBrowser' :: Maybe FilePath -> FilePath -> String -> Maybe Handle -> Maybe Handle -> IO ()
-#ifndef __ANDROID__
 openBrowser' mcmd htmlshim realurl outh errh =
 	ifM osAndroid
 		{- Android does not support file:// urls well, but neither
@@ -216,20 +201,6 @@
 		( runbrowser realurl
 		, runbrowser (fileUrl htmlshim)
 		)
-#else
-openBrowser' mcmd htmlshim realurl outh errh = do
-	recordUrl realurl
-	{- Android's `am` command does not work reliably across the
-	 - wide range of Android devices. Intead, FIFO should be set to 
-	 - the filename of a fifo that we can write the URL to. -}
-	v <- getEnv "FIFO"
-	case v of
-		Nothing -> runbrowser realurl
-		Just f -> void $ forkIO $ do
-			fd <- openFd f WriteOnly Nothing defaultFileFlags
-			void $ fdWrite fd realurl
-			closeFd fd
-#endif
   where
 	runbrowser url = do
 		let p = case mcmd of
diff --git a/Database/Handle.hs b/Database/Handle.hs
--- a/Database/Handle.hs
+++ b/Database/Handle.hs
@@ -1,6 +1,6 @@
 {- Persistent sqlite database handles.
  -
- - Copyright 2015 Joey Hess <id@joeyh.name>
+ - Copyright 2015-2018 Joey Hess <id@joeyh.name>
  -
  - Licensed under the GNU GPL version 3 or higher.
  -}
@@ -31,7 +31,6 @@
 import qualified Data.Text as T
 import Control.Monad.Trans.Resource (runResourceT)
 import Control.Monad.Logger (runNoLoggingT)
-import Data.List
 import System.IO
 
 {- A DbHandle is a reference to a worker thread that communicates with
@@ -43,12 +42,8 @@
 
 {- Sqlite only allows a single write to a database at a time; a concurrent
  - write will crash. 
- -
- - While a DbHandle serializes concurrent writes from
- - multiple threads. But, when a database can be written to by
- - multiple processes concurrently, use MultiWriter to make writes
- - to the database be done robustly.
  - 
+ - MultiWrter works around this limitation.
  - The downside of using MultiWriter is that after writing a change to the
  - database, the a query using the same DbHandle will not immediately see
  - the change! This is because the change is actually written using a
@@ -57,9 +52,10 @@
  - you can't rely on seeing values you've just written anyway, as another
  - process may change them.
  -
- - When a database can only be written to by a single process, use
- - SingleWriter. Changes written to the database will always be immediately
- - visible then.
+ - When a database can only be written to by a single process (enforced by
+ - a lock file), use SingleWriter. Changes written to the database will
+ - always be immediately visible then. Multiple threads can write; their
+ - writes will be serialized.
  -}
 data DbConcurrency = SingleWriter | MultiWriter
 
@@ -105,9 +101,10 @@
 
 {- Writes a change to the database.
  -
- - In MultiWriter mode, catches failure to write to the database,
- - and retries repeatedly for up to 10 seconds,  which should avoid
- - all but the most exceptional problems.
+ - In MultiWriter mode, writes can fail if another write is happening
+ - concurrently. So write failures are caught and retried repeatedly
+ - for up to 10 seconds, which should avoid all but the most exceptional
+ - problems.
  -}
 commitDb :: DbHandle -> SqlPersistM () -> IO ()
 commitDb h wa = robustly Nothing 100 (commitDb' h wa)
@@ -177,33 +174,68 @@
 				liftIO (a (runSqliteRobustly tablename db))
 				loop
 	
--- like runSqlite, but calls settle on the raw sql Connection.
+-- Like runSqlite, but more robust.
+--
+-- New database connections can sometimes take a while to become usable.
+-- This may be due to WAL mode recovering after a crash, or perhaps a bug
+-- like described in blob 500f777a6ab6c45ca5f9790e0a63575f8e3cb88f.
+-- So, loop until a select succeeds; once one succeeds the connection will
+-- stay usable.
+--
+-- And sqlite sometimes throws ErrorIO when there's not really an IO problem,
+-- but perhaps just a short read(). That's caught and retried several times.
 runSqliteRobustly :: TableName -> T.Text -> (SqlPersistM a) -> IO a
 runSqliteRobustly tablename db a = do
-	conn <- Sqlite.open db
-	settle conn
-	runResourceT $ runNoLoggingT $
-		withSqlConn (wrapConnection conn) $
-			runSqlConn a
+	conn <- opensettle maxretries
+	go conn maxretries
   where
-	-- Work around a bug in sqlite: New database connections can
-	-- sometimes take a while to become usable; select statements will
-	-- fail with ErrorBusy for some time. So, loop until a select
-	-- succeeds; once one succeeds the connection will stay usable.
-	-- <http://thread.gmane.org/gmane.comp.db.sqlite.general/93116>
-	settle conn = do
-		r <- tryNonAsync $ do
+	maxretries = 100 :: Int
+	
+	rethrow msg e = throwIO $ userError $ show e ++ "(" ++ msg ++ ")"
+	
+	go conn retries = do
+		r <- try $ runResourceT $ runNoLoggingT $
+			withSqlConn (wrapConnection conn) $
+				runSqlConn a
+		case r of
+			Right v -> return v
+			Left ex@(Sqlite.SqliteException { Sqlite.seError = e })
+				| e == Sqlite.ErrorIO ->
+					let retries' = retries - 1
+					in if retries' < 1
+						then rethrow "after successful open" ex
+						else go conn retries'
+				| otherwise -> rethrow "after successful open" ex
+	
+	opensettle retries = do
+		conn <- Sqlite.open db
+		settle conn retries
+
+	settle conn retries = do
+		r <- try $ do
 			stmt <- Sqlite.prepare conn nullselect
 			void $ Sqlite.step stmt
 			void $ Sqlite.finalize stmt
 		case r of
-			Right _ -> return ()
-			Left e -> do
-				if "ErrorBusy" `isInfixOf` show e
-					then do
-						threadDelay 1000 -- 1/1000th second
-						settle conn
-					else throwIO e
+			Right _ -> return conn
+			Left ex@(Sqlite.SqliteException { Sqlite.seError = e })
+				| e == Sqlite.ErrorBusy -> do
+					-- Wait and retry any number of times; it 
+					-- will stop being busy eventually.
+					briefdelay
+					settle conn retries
+				| e == Sqlite.ErrorIO -> do
+					-- Could be a real IO error,
+					-- so don't retry indefinitely.
+					Sqlite.close conn
+					briefdelay
+					let retries' = retries - 1
+					if retries' < 1
+						then rethrow "while opening database connection" ex
+						else opensettle retries'
+				| otherwise -> rethrow "while opening database connection" ex
 	
 	-- This should succeed for any table.
 	nullselect = T.pack $ "SELECT null from " ++ tablename ++ " limit 1"
+
+	briefdelay = threadDelay 1000 -- 1/1000th second
diff --git a/Database/Init.hs b/Database/Init.hs
--- a/Database/Init.hs
+++ b/Database/Init.hs
@@ -1,6 +1,6 @@
 {- Persistent sqlite database initialization
  -
- - Copyright 2015-2017 Joey Hess <id@joeyh.name>
+ - Copyright 2015-2018 Joey Hess <id@joeyh.name>
  -
  - Licensed under the GNU GPL version 3 or higher.
  -}
@@ -12,16 +12,13 @@
 import Utility.FileMode
 
 import Database.Persist.Sqlite
-import qualified Database.Sqlite as Sqlite
 import Control.Monad.IO.Class (liftIO)
 import qualified Data.Text as T
+import Lens.Micro
 
 {- Ensures that the database is freshly initialized. Deletes any
  - existing database. Pass the migration action for the database.
  -
- - The database is initialized using WAL mode, to prevent readers
- - from blocking writers, and prevent a writer from blocking readers.
- -
  - The permissions of the database are set based on the
  - core.sharedRepository setting. Setting these permissions on the main db
  - file causes Sqlite to always use the same permissions for additional
@@ -34,9 +31,7 @@
 	let tmpdb = tmpdbdir </> "db"
 	liftIO $ do
 		createDirectoryIfMissing True tmpdbdir
-		let tdb = T.pack tmpdb
-		enableWAL tdb
-		runSqlite tdb migration
+		runSqliteInfo (mkConnInfo tmpdb) migration
 	setAnnexDirPerm tmpdbdir
 	-- Work around sqlite bug that prevents it from honoring
 	-- less restrictive umasks.
@@ -46,10 +41,14 @@
 		void $ tryIO $ removeDirectoryRecursive dbdir
 		rename tmpdbdir dbdir
 
-enableWAL :: T.Text -> IO ()
-enableWAL db = do
-	conn <- Sqlite.open db
-	stmt <- Sqlite.prepare conn (T.pack "PRAGMA journal_mode=WAL;")
-	void $ Sqlite.step stmt
-	void $ Sqlite.finalize stmt
-	Sqlite.close conn
+{- Make sure that the database uses WAL mode, to prevent readers
+ - from blocking writers, and prevent a writer from blocking readers.
+ -
+ - This is the default in persistent-sqlite currently, but force it on just
+ - in case. 
+ -
+ - Note that once WAL mode is enabled, it will persist whenever the
+ - database is opened. -}
+mkConnInfo :: FilePath -> SqliteConnectionInfo
+mkConnInfo db = over walEnabled (const True) $ 
+	mkSqliteConnectionInfo (T.pack db)
diff --git a/Database/Keys.hs b/Database/Keys.hs
--- a/Database/Keys.hs
+++ b/Database/Keys.hs
@@ -151,7 +151,9 @@
  - data to it.
  -}
 closeDb :: Annex ()
-closeDb = liftIO . closeDbHandle =<< getDbHandle
+closeDb = Annex.getState Annex.keysdbhandle >>= \case
+	Nothing -> return ()
+	Just h -> liftIO (closeDbHandle h)
 
 addAssociatedFile :: Key -> TopFilePath -> Annex ()
 addAssociatedFile k f = runWriterIO $ SQL.addAssociatedFile (toIKey k) f
diff --git a/Git/Env.hs b/Git/Env.hs
--- a/Git/Env.hs
+++ b/Git/Env.hs
@@ -5,8 +5,6 @@
  - Licensed under the GNU GPL version 3 or higher.
  -}
 
-{-# LANGUAGE CPP #-}
-
 module Git.Env where
 
 import Common
@@ -18,27 +16,10 @@
  - does not have any gitEnv yet. -}
 adjustGitEnv :: Repo -> ([(String, String)] -> [(String, String)]) -> IO Repo
 adjustGitEnv g adj = do
-	e <- maybe copyGitEnv return (gitEnv g)
+	e <- maybe getEnvironment return (gitEnv g)
 	let e' = adj e
 	return $ g { gitEnv = Just e' }
   where
-
-{- Copies the current environment, so it can be adjusted when running a git
- - command. -}
-copyGitEnv :: IO [(String, String)]
-copyGitEnv = do
-#ifdef __ANDROID__
-	{- This should not be necessary on Android, but there is some
-	 - weird getEnvironment breakage. See
-	 - https://github.com/neurocyte/ghc-android/issues/7
-	 - Use getEnv to get some key environment variables that
-	 - git expects to have. -}
-	let keyenv = words "USER PATH GIT_EXEC_PATH HOSTNAME HOME"
-	let getEnvPair k = maybe Nothing (\v -> Just (k, v)) <$> getEnv k
-	catMaybes <$> forM keyenv getEnvPair
-#else
-	getEnvironment
-#endif
 
 addGitEnv :: Repo -> String -> String -> IO Repo
 addGitEnv g var val = adjustGitEnv g (addEntry var val)
diff --git a/Git/Fsck.hs b/Git/Fsck.hs
--- a/Git/Fsck.hs
+++ b/Git/Fsck.hs
@@ -26,9 +26,7 @@
 
 import qualified Data.Set as S
 import Control.Concurrent.Async
-#if MIN_VERSION_base(4,9,0)
 import qualified Data.Semigroup as Sem
-#endif
 import Prelude
 
 data FsckResults 
@@ -58,18 +56,13 @@
 appendFsckOutput AllDuplicateEntriesWarning NoFsckOutput = AllDuplicateEntriesWarning
 appendFsckOutput NoFsckOutput AllDuplicateEntriesWarning = AllDuplicateEntriesWarning
 
-#if MIN_VERSION_base(4,9,0)
 instance Sem.Semigroup FsckOutput where
 	(<>) = appendFsckOutput
-#endif
 
 instance Monoid FsckOutput where
 	mempty = NoFsckOutput
-#if MIN_VERSION_base(4,11,0)
-#elif MIN_VERSION_base(4,9,0)
+#if ! MIN_VERSION_base(4,11,0)
 	mappend = (Sem.<>)
-#else
-	mappend = appendFsckOutput
 #endif
 
 {- Runs fsck to find some of the broken objects in the repository.
diff --git a/Git/LsFiles.hs b/Git/LsFiles.hs
--- a/Git/LsFiles.hs
+++ b/Git/LsFiles.hs
@@ -7,6 +7,7 @@
 
 module Git.LsFiles (
 	inRepo,
+	inRepoOrBranch,
 	notInRepo,
 	notInRepoIncludingEmptyDirectories,
 	allFiles,
@@ -34,14 +35,22 @@
 import Numeric
 import System.Posix.Types
 
-{- Scans for files that are checked into git at the specified locations. -}
+{- Scans for files that are checked into git's index at the specified locations. -}
 inRepo :: [FilePath] -> Repo -> IO ([FilePath], IO Bool)
-inRepo l = pipeNullSplit $ 
+inRepo = inRepo' [] 
+
+inRepo' :: [CommandParam] -> [FilePath] -> Repo -> IO ([FilePath], IO Bool)
+inRepo' ps l = pipeNullSplit $ 
 	Param "ls-files" :
 	Param "--cached" :
 	Param "-z" :
-	Param "--" :
-	map File l
+	ps ++
+	(Param "--" : map File l)
+
+{- Files that are checked into the index or have been committed to a
+ - branch. -}
+inRepoOrBranch :: Branch -> [FilePath] -> Repo -> IO ([FilePath], IO Bool)
+inRepoOrBranch (Ref b) = inRepo' [Param $ "--with-tree=" ++ b]
 
 {- Scans for files at the specified locations that are not checked into git. -}
 notInRepo :: Bool -> [FilePath] -> Repo -> IO ([FilePath], IO Bool)
diff --git a/Logs/File.hs b/Logs/File.hs
--- a/Logs/File.hs
+++ b/Logs/File.hs
@@ -2,26 +2,59 @@
  -
  - Copyright 2018 Joey Hess <id@joeyh.name>
  -
- - Licensed under the GNU GPL version 3 or higher.
+ - Licensed under the GNU AGPL version 3 or higher.
  -}
 
-module Logs.File where
+module Logs.File (writeLogFile, appendLogFile, streamLogFile) where
 
 import Annex.Common
 import Annex.Perms
+import Annex.LockFile
+import qualified Git
 import Utility.Tmp
 
 -- | Writes content to a file, replacing the file atomically, and
 -- making the new file have whatever permissions the git repository is
 -- configured to use. Creates the parent directory when necessary.
 writeLogFile :: FilePath -> String -> Annex ()
-writeLogFile f c = go `catchNonAsync` \_e -> do
-	-- Most of the time, the directory will exist, so this is only
-	-- done if writing the file fails.
-	createAnnexDirectory (parentDir f)
-	go
+writeLogFile f c = createDirWhenNeeded f $ viaTmp writelog f c
   where
-	go = viaTmp writelog f c
 	writelog f' c' = do
 		liftIO $ writeFile f' c'
 		setAnnexFilePerm f'
+
+-- | Appends a line to a log file, first locking it to prevent
+-- concurrent writers.
+appendLogFile :: FilePath -> (Git.Repo -> FilePath) -> String -> Annex ()
+appendLogFile f lck c = createDirWhenNeeded f $ withExclusiveLock lck $ do
+	liftIO $ withFile f AppendMode $ \h -> hPutStrLn h c
+	setAnnexFilePerm f
+
+-- | Streams lines from a log file, and then empties the file at the end.
+--
+-- If the action is interrupted or throws an exception, the log file is
+-- left unchanged.
+--
+-- Does nothing if the log file does not exist.
+-- 
+-- Locking is used to prevent writes to to the log file while this
+-- is running.
+streamLogFile :: FilePath -> (Git.Repo -> FilePath) -> (String -> Annex ()) -> Annex ()
+streamLogFile f lck a = withExclusiveLock lck $ bracketOnError setup cleanup go
+  where
+	setup = liftIO $ tryWhenExists $ openFile f ReadMode 
+	cleanup Nothing = noop
+	cleanup (Just h) = liftIO $ hClose h
+	go Nothing = noop
+	go (Just h) = do
+		mapM_ a =<< liftIO (lines <$> hGetContents h)
+		liftIO $ hClose h
+		liftIO $ writeFile f ""
+		setAnnexFilePerm f
+
+createDirWhenNeeded :: FilePath -> Annex () -> Annex ()
+createDirWhenNeeded f a = a `catchNonAsync` \_e -> do
+	-- Most of the time, the directory will exist, so this is only
+	-- done if writing the file fails.
+	createAnnexDirectory (parentDir f)
+	a
diff --git a/Logs/MetaData.hs b/Logs/MetaData.hs
--- a/Logs/MetaData.hs
+++ b/Logs/MetaData.hs
@@ -40,7 +40,7 @@
 import qualified Annex.Branch
 import qualified Annex
 import Logs
-import Logs.TimeStamp
+import Utility.TimeStamp
 import Logs.MetaData.Pure
 
 import qualified Data.Set as S
diff --git a/Logs/Smudge.hs b/Logs/Smudge.hs
new file mode 100644
--- /dev/null
+++ b/Logs/Smudge.hs
@@ -0,0 +1,40 @@
+{- git-annex smudge log file
+ -
+ - Copyright 2018 Joey Hess <id@joeyh.name>
+ -
+ - Licensed under the GNU AGPL version 3 or higher.
+ -}
+
+module Logs.Smudge where
+
+import Annex.Common
+import Git.FilePath
+import Logs.File
+
+-- | Log a smudged file.
+smudgeLog :: Key -> TopFilePath -> Annex ()
+smudgeLog k f = do
+	logf <- fromRepo gitAnnexSmudgeLog
+	appendLogFile logf gitAnnexSmudgeLock $ 
+		key2file k ++ " " ++ getTopFilePath f
+
+-- | Streams all smudged files, and then empties the log at the end.
+--
+-- If the action is interrupted or throws an exception, the log file is
+-- left unchanged.
+--
+-- Locking is used to prevent new items being added to the log while this
+-- is running.
+streamSmudged :: (Key -> TopFilePath -> Annex ()) -> Annex ()
+streamSmudged a = do
+	logf <- fromRepo gitAnnexSmudgeLog
+	streamLogFile logf gitAnnexSmudgeLock $ \l -> 
+		case parse l of
+			Nothing -> noop
+			Just (k, f) -> a k f
+  where
+	parse l = 
+		let (ks, f) = separate (== ' ') l
+		in do
+			k <- file2key ks
+			return (k, asTopFilePath f)
diff --git a/Logs/TimeStamp.hs b/Logs/TimeStamp.hs
deleted file mode 100644
--- a/Logs/TimeStamp.hs
+++ /dev/null
@@ -1,39 +0,0 @@
-{- log timestamp parsing
- -
- - Copyright 2015-2016 Joey Hess <id@joeyh.name>
- -
- - Licensed under the GNU GPL version 3 or higher.
- -}
-
-{-# LANGUAGE CPP #-}
-
-module Logs.TimeStamp where
-
-import Utility.PartialPrelude
-import Utility.Misc
-
-import Data.Time.Clock.POSIX
-import Data.Time
-import Data.Ratio
-#if ! MIN_VERSION_time(1,5,0)
-import System.Locale
-#endif
-
-{- Parses how POSIXTime shows itself: "1431286201.113452s"
- - Also handles the format with no fractional seconds. -}
-parsePOSIXTime :: String -> Maybe POSIXTime
-parsePOSIXTime s = do
-	let (sn, sd) = separate (== '.') s
-	n <- readi sn
-	if null sd 
-		then return (fromIntegral n)
-		else do
-			d <- readi sd
-			let r = d % (10 ^ (length sd - 1))
-			return (fromIntegral n + fromRational r)
-  where
-	readi :: String -> Maybe Integer
-	readi = readish
-
-formatPOSIXTime :: String -> POSIXTime -> String
-formatPOSIXTime fmt t = formatTime defaultTimeLocale fmt (posixSecondsToUTCTime t)
diff --git a/Logs/Transfer.hs b/Logs/Transfer.hs
--- a/Logs/Transfer.hs
+++ b/Logs/Transfer.hs
@@ -18,7 +18,7 @@
 import Utility.Percentage
 import Utility.PID
 import Annex.LockPool
-import Logs.TimeStamp
+import Utility.TimeStamp
 import Logs.File
 
 import Data.Time.Clock
diff --git a/Logs/Unused.hs b/Logs/Unused.hs
--- a/Logs/Unused.hs
+++ b/Logs/Unused.hs
@@ -33,7 +33,7 @@
 
 import Annex.Common
 import qualified Annex
-import Logs.TimeStamp
+import Utility.TimeStamp
 import Logs.File
 
 -- everything that is stored in the unused log
diff --git a/Messages.hs b/Messages.hs
--- a/Messages.hs
+++ b/Messages.hs
@@ -16,6 +16,7 @@
 	showSideAction,
 	doSideAction,
 	doQuietSideAction,
+	doQuietAction,
 	showStoringStateAction,
 	showOutput,
 	showLongNote,
@@ -111,11 +112,27 @@
 doSideAction = doSideAction' StartBlock
 
 doSideAction' :: SideActionBlock -> Annex a -> Annex a
-doSideAction' b a = do
-	o <- Annex.getState Annex.output
-	set $ o { sideActionBlock = b }
-	set o `after` a
+doSideAction' b = bracket setup cleanup . const
   where
+	setup = do
+		o <- Annex.getState Annex.output
+		set $ o { sideActionBlock = b }
+		return o
+	cleanup = set
+	set o = Annex.changeState $ \s -> s { Annex.output = o }
+
+{- Performs an action, suppressing all normal standard output,
+ - but not json output. -}
+doQuietAction :: Annex a -> Annex a
+doQuietAction = bracket setup cleanup . const
+  where
+	setup = do
+		o <- Annex.getState Annex.output
+		case outputType o of
+			NormalOutput -> set $ o { outputType = QuietOutput }
+			_ -> noop
+		return o
+	cleanup = set
 	set o = Annex.changeState $ \s -> s {  Annex.output = o }
 
 {- Make way for subsequent output of a command. -}
diff --git a/Messages/Concurrent.hs b/Messages/Concurrent.hs
--- a/Messages/Concurrent.hs
+++ b/Messages/Concurrent.hs
@@ -14,7 +14,6 @@
 import Types.Messages
 import qualified Annex
 
-#ifdef WITH_CONCURRENTOUTPUT
 import Common
 import qualified System.Console.Concurrent as Console
 import qualified System.Console.Regions as Regions
@@ -23,7 +22,6 @@
 #ifndef mingw32_HOST_OS
 import GHC.IO.Encoding
 #endif
-#endif
 
 {- Outputs a message in a concurrency safe way.
  -
@@ -33,15 +31,10 @@
  - instead.
  -}
 concurrentMessage :: MessageState -> Bool -> String -> Annex () -> Annex ()
-#ifdef WITH_CONCURRENTOUTPUT
 concurrentMessage s iserror msg fallback 
 	| concurrentOutputEnabled s =
 		go =<< consoleRegion <$> Annex.getState Annex.output
-#else
-concurrentMessage _s _iserror _msg fallback 
-#endif
 	| otherwise = fallback
-#ifdef WITH_CONCURRENTOUTPUT
   where
 	go Nothing
 		| iserror = liftIO $ Console.errorConcurrent msg
@@ -58,7 +51,6 @@
 			rl <- takeTMVar Regions.regionList
 			putTMVar Regions.regionList
 				(if r `elem` rl then rl else r:rl)
-#endif
 
 {- Runs an action in its own dedicated region of the console.
  -
@@ -70,7 +62,6 @@
  - complete.
  -}
 inOwnConsoleRegion :: MessageState -> Annex a -> Annex a
-#ifdef WITH_CONCURRENTOUTPUT
 inOwnConsoleRegion s a
 	| concurrentOutputEnabled s = do
 		r <- mkregion
@@ -85,11 +76,7 @@
 			Right ret -> do
 				rmregion r
 				return ret
-#else
-inOwnConsoleRegion _s a
-#endif
 	| otherwise = a
-#ifdef WITH_CONCURRENTOUTPUT
   where
 	-- The region is allocated here, but not displayed until 
 	-- a message is added to it. This avoids unnecessary screen
@@ -108,10 +95,8 @@
 			unless (T.null t) $
 				Console.bufferOutputSTM h t
 			Regions.closeConsoleRegion r
-#endif
 
 {- The progress region is displayed inline with the current console region. -}
-#ifdef WITH_CONCURRENTOUTPUT
 withProgressRegion :: (Regions.ConsoleRegion -> Annex a) -> Annex a
 withProgressRegion a = do
 	parent <- consoleRegion <$> Annex.getState Annex.output
@@ -119,14 +104,12 @@
 
 instance Regions.LiftRegion Annex where
 	liftRegion = liftIO . atomically
-#endif
 
 {- The concurrent-output library uses Text, which bypasses the normal use
  - of the fileSystemEncoding to roundtrip invalid characters, when in a
  - non-unicode locale. Work around that problem by avoiding using
  - concurrent output when not in a unicode locale. -}
 concurrentOutputSupported :: IO Bool
-#ifdef WITH_CONCURRENTOUTPUT
 #ifndef mingw32_HOST_OS
 concurrentOutputSupported = do
 	enc <- getLocaleEncoding
@@ -134,9 +117,6 @@
 #else
 concurrentOutputSupported = return True -- Windows is always unicode
 #endif
-#else
-concurrentOutputSupported = return False
-#endif
 
 {- Hide any currently displayed console regions while running the action,
  - so that the action can use the console itself.
@@ -144,7 +124,6 @@
  - the regions will not be hidden, but the action still runs, garbling the
  - display. -}
 hideRegionsWhile :: Annex a -> Annex a
-#ifdef WITH_CONCURRENTOUTPUT
 #if MIN_VERSION_concurrent_output(1,9,0)
 hideRegionsWhile a = bracketIO setup cleanup go
   where
@@ -153,9 +132,6 @@
 	go _ = do
 		liftIO $ hFlush stdout
 		a
-#else
-hideRegionsWhile = id
-#endif
 #else
 hideRegionsWhile = id
 #endif
diff --git a/Messages/Progress.hs b/Messages/Progress.hs
--- a/Messages/Progress.hs
+++ b/Messages/Progress.hs
@@ -5,8 +5,6 @@
  - Licensed under the GNU GPL version 3 or higher.
  -}
 
-{-# LANGUAGE CPP #-}
-
 module Messages.Progress where
 
 import Common
@@ -16,12 +14,10 @@
 import Types.Messages
 import Types.Key
 import qualified Messages.JSON as JSON
-
-#ifdef WITH_CONCURRENTOUTPUT
 import Messages.Concurrent
+
 import qualified System.Console.Regions as Regions
 import qualified System.Console.Concurrent as Console
-#endif
 
 {- Shows a progress meter while performing a transfer of a key.
  - The action is passed the meter and a callback to use to update the meter.
@@ -45,7 +41,6 @@
 		liftIO $ clearMeterHandle meter stdout
 		return r
 	go msize (MessageState { outputType = NormalOutput, concurrentOutputEnabled = True }) =
-#if WITH_CONCURRENTOUTPUT
 		withProgressRegion $ \r -> do
 			meter <- liftIO $ mkMeter msize $ \_ msize' old new ->
 				let s = bandwidthMeter msize' old new
@@ -53,9 +48,6 @@
 			m <- liftIO $ rateLimitMeterUpdate 0.2 meter $
 				updateMeter meter
 			a meter (combinemeter m)
-#else
-		nometer
-#endif
 	go msize (MessageState { outputType = JSONOutput jsonoptions })
 		| jsonProgress jsonoptions = do
 			buf <- withMessageState $ return . jsonBuffer
@@ -133,7 +125,6 @@
 mkStderrEmitter :: Annex (String -> IO ())
 mkStderrEmitter = withMessageState go
   where
-#ifdef WITH_CONCURRENTOUTPUT
-	go s | concurrentOutputEnabled s = return Console.errorConcurrent
-#endif
-	go _ = return (hPutStrLn stderr)
+	go s
+		| concurrentOutputEnabled s = return Console.errorConcurrent
+		| otherwise = return (hPutStrLn stderr)
diff --git a/NEWS b/NEWS
--- a/NEWS
+++ b/NEWS
@@ -1,3 +1,21 @@
+git-annex (7.20181031) upstream; urgency=medium
+
+  Repository version 7 is now available. v6 repositories will automatically
+  upgrade to v7. v5 repositories are still supported and will not be
+  automatically upgraded yet.
+
+  Direct mode is deprecated, and upgrading direct mode repositories to v7 is
+  encouraged, unless they need to remain usable by older versions of git-annex.
+  Just run `git annex upgrade`.
+
+  git-annex will no longer initialize new repositories on crippled filesystems
+  using direct mode, instead it uses v7.
+
+  The git-annex Android app is no longer being updated. Users of the app
+  should remove it and install using the new Termux based installation method.
+
+ -- Joey Hess <id@joeyh.name>  Wed, 31 Oct 2018 13:05:48 -0400
+
 git-annex (6.20180626) upstream; urgency=high
 
   A security fix has changed git-annex to refuse to download content from
diff --git a/P2P/IO.hs b/P2P/IO.hs
--- a/P2P/IO.hs
+++ b/P2P/IO.hs
@@ -12,6 +12,7 @@
 	, RunState(..)
 	, mkRunState
 	, P2PConnection(..)
+	, ConnIdent(..)
 	, ClosableConnection(..)
 	, stdioP2PConnection
 	, connectPeer
@@ -77,8 +78,12 @@
 	, connCheckAuth :: (AuthToken -> Bool)
 	, connIhdl :: Handle
 	, connOhdl :: Handle
+	, connIdent :: ConnIdent
 	}
 
+-- Identifier for a connection, only used for debugging.
+newtype ConnIdent = ConnIdent (Maybe String)
+
 data ClosableConnection conn
 	= OpenConnection conn
 	| ClosedConnection
@@ -90,6 +95,7 @@
 	, connCheckAuth = const False
 	, connIhdl = stdin
 	, connOhdl = stdout
+	, connIdent = ConnIdent Nothing
 	}
 
 -- Opens a connection to a peer. Does not authenticate with it.
@@ -101,6 +107,7 @@
 		, connCheckAuth = const False
 		, connIhdl = h
 		, connOhdl = h
+		, connIdent = ConnIdent Nothing
 		}
 
 closeConnection :: P2PConnection -> IO ()
@@ -166,7 +173,7 @@
 	SendMessage m next -> do
 		v <- liftIO $ tryNonAsync $ do
 			let l = unwords (formatMessage m)
-			debugMessage "P2P >" m
+			debugMessage conn "P2P >" m
 			hPutStrLn (connOhdl conn) l
 			hFlush (connOhdl conn)
 		case v of
@@ -180,7 +187,7 @@
 				ProtoFailureMessage "protocol error"
 			Right (Just l) -> case parseMessage l of
 				Just m -> do
-					liftIO $ debugMessage "P2P <" m
+					liftIO $ debugMessage conn "P2P <" m
 					runner (next (Just m))
 				Nothing -> runner (next Nothing)
 	SendBytes len b p next -> do
@@ -225,13 +232,19 @@
 		Serving _ _ tv -> tv
 		Client tv -> tv
 
-debugMessage :: String -> Message -> IO ()
-debugMessage prefix m = debugM "p2p" $
-	prefix ++ " " ++ unwords (formatMessage safem)
+debugMessage :: P2PConnection -> String -> Message -> IO ()
+debugMessage conn prefix m = do
+	tid <- myThreadId	
+	debugM "p2p" $ concat $ catMaybes $
+		[ (\ident -> "[" ++ ident ++ "] ") <$> mident
+		, Just $ "[" ++ show tid ++ "] "
+		, Just $ prefix ++ " " ++ unwords (formatMessage safem)
+		]
   where
 	safem = case m of
 		AUTH u _ -> AUTH u nullAuthToken
 		_ -> m
+	ConnIdent mident = connIdent conn
 
 -- Send exactly the specified number of bytes or returns False.
 --
diff --git a/Remote/External.hs b/Remote/External.hs
--- a/Remote/External.hs
+++ b/Remote/External.hs
@@ -689,10 +689,6 @@
 	handleRequest external (CHECKURL url) Nothing $ \req -> case req of
 		CHECKURL_CONTENTS sz f -> result $ UrlContents sz $
 			if null f then Nothing else Just $ mkSafeFilePath f
-		-- Treat a single item multi response specially to
-		-- simplify the external remote implementation.
-		CHECKURL_MULTI ((_, sz, f):[]) ->
-			result $ UrlContents sz $ Just $ mkSafeFilePath f
 		CHECKURL_MULTI l -> result $ UrlMulti $ map mkmulti l
 		CHECKURL_FAILURE errmsg -> Just $ giveup errmsg
 		UNSUPPORTED_REQUEST -> giveup "CHECKURL not implemented by external special remote"
diff --git a/Remote/Helper/Export.hs b/Remote/Helper/Export.hs
--- a/Remote/Helper/Export.hs
+++ b/Remote/Helper/Export.hs
@@ -89,23 +89,32 @@
 		}
 	isexport = do
 		db <- openDb (uuid r)
+		updateflag <- liftIO $ newTVarIO Nothing
 
-		updateflag <- liftIO newEmptyTMVarIO
-		let updateonce = liftIO $ atomically $
-			ifM (isEmptyTMVar updateflag)
-				( do
-					putTMVar updateflag ()
+		-- When multiple threads run this, all except the first
+		-- will block until the first runs doneupdateonce.
+		-- Returns True when an update should be done and False
+		-- when the update has already been done.
+		let startupdateonce = liftIO $ atomically $
+			readTVar updateflag >>= \case
+				Nothing -> do
+					writeTVar updateflag (Just True)
 					return True
-				, return False
-				)
+				Just True -> retry
+				Just False -> return False
+		let doneupdateonce = \updated ->
+			when updated $
+				liftIO $ atomically $
+					writeTVar updateflag (Just False)
 		
 		-- Get export locations for a key. Checks once
 		-- if the export log is different than the database and
 		-- updates the database, to notice when an export has been
 		-- updated from another repository.
 		let getexportlocs = \k -> do
-			whenM updateonce $
-				updateExportTreeFromLog db
+			bracket startupdateonce doneupdateonce $ \updatenow ->
+				when updatenow $
+					updateExportTreeFromLog db
 			liftIO $ getExportTree db k
 
 		return $ r
diff --git a/Remote/Helper/Ssh.hs b/Remote/Helper/Ssh.hs
--- a/Remote/Helper/Ssh.hs
+++ b/Remote/Helper/Ssh.hs
@@ -29,6 +29,7 @@
 import Control.Concurrent.STM
 import Control.Concurrent.Async
 import qualified Data.ByteString as B
+import Data.Unique
 
 toRepo :: ConsumeStdin -> Git.Repo -> RemoteGitConfig -> SshCommand -> Annex (FilePath, [CommandParam])
 toRepo cs r gc remotecmd = do
@@ -257,11 +258,16 @@
 				, std_out = CreatePipe
 				, std_err = CreatePipe
 				}
+		-- Could use getPid, but need to build with older versions
+		-- of process, so instead a unique connection number.
+		connnum <- hashUnique <$> newUnique
 		let conn = P2P.P2PConnection
 			{ P2P.connRepo = repo
 			, P2P.connCheckAuth = const False
 			, P2P.connIhdl = to
 			, P2P.connOhdl = from
+			, P2P.connIdent = P2P.ConnIdent $
+				Just $ "ssh connection " ++ show connnum
 			}
 		stderrhandlerst <- newStderrHandler err
 		runst <- P2P.mkRunState P2P.Client
diff --git a/Remote/List.hs b/Remote/List.hs
--- a/Remote/List.hs
+++ b/Remote/List.hs
@@ -93,6 +93,7 @@
 	newg <- inRepo Git.Config.reRead
 	Annex.changeState $ \s -> s 
 		{ Annex.remotes = []
+		, Annex.gitremotes = Nothing
 		, Annex.repo = newg
 		}
 	remoteList
diff --git a/RemoteDaemon/Transport/Tor.hs b/RemoteDaemon/Transport/Tor.hs
--- a/RemoteDaemon/Transport/Tor.hs
+++ b/RemoteDaemon/Transport/Tor.hs
@@ -114,6 +114,7 @@
 				, connCheckAuth = (`isAllowedAuthToken` allowed)
 				, connIhdl = h
 				, connOhdl = h
+				, connIdent = ConnIdent $ Just "tor remotedaemon"
 				}
 			-- not really Client, but we don't know their uuid yet
 			runstauth <- liftIO $ mkRunState Client
diff --git a/Test.hs b/Test.hs
--- a/Test.hs
+++ b/Test.hs
@@ -1,6 +1,6 @@
 {- git-annex test suite
  -
- - Copyright 2010-2017 Joey Hess <id@joeyh.name>
+ - Copyright 2010-2018 Joey Hess <id@joeyh.name>
  -
  - Licensed under the GNU GPL version 3 or higher.
  -}
@@ -10,6 +10,7 @@
 module Test where
 
 import Types.Test
+import Types.RepoVersion
 import Test.Framework
 import Options.Applicative.Types
 
@@ -148,10 +149,10 @@
 	map (\(d, te) -> withTestMode te initTests (unitTests d)) testmodes
   where
 	testmodes = catMaybes
-		[ Just ("v6 unlocked", (testMode opts "6") { unlockedFiles = True })
-		, unlesscrippled ("v5", testMode opts "5")
-		, unlesscrippled ("v6 locked", testMode opts "6")
-		, Just ("v5 direct", (testMode opts "5") { forceDirect = True })
+		[ Just ("v7 unlocked", (testMode opts (RepoVersion 7)) { unlockedFiles = True })
+		, unlesscrippled ("v5", testMode opts (RepoVersion 5))
+		, unlesscrippled ("v7 locked", testMode opts (RepoVersion 7))
+		, Just ("v5 direct", (testMode opts (RepoVersion 5)) { forceDirect = True })
 		]
 	unlesscrippled v
 		| crippledfilesystem = Nothing
@@ -225,7 +226,7 @@
 	, testCase "move (ssh remote)" test_move_ssh_remote
 	, testCase "copy" test_copy
 	, testCase "lock" test_lock
-	, testCase "lock (v6 --force)" test_lock_v6_force
+	, testCase "lock (v7 --force)" test_lock_v7_force
 	, testCase "edit (no pre-commit)" test_edit
 	, testCase "edit (pre-commit)" test_edit_precommit
 	, testCase "partial commit" test_partial_commit
@@ -280,7 +281,7 @@
 	ver <- annexVersion <$> getTestMode
 	if ver == Annex.Version.defaultVersion
 		then git_annex "init" [reponame] @? "init failed"
-		else git_annex "init" [reponame, "--version", ver] @? "init failed"
+		else git_annex "init" [reponame, "--version", show (fromRepoVersion ver)] @? "init failed"
 	setupTestMode
   where
 	reponame = "test repo"
@@ -289,10 +290,10 @@
 -- annexed file that later tests will use
 test_add :: Assertion
 test_add = inmainrepo $ do
-	writeFile annexedfile $ content annexedfile
+	writecontent annexedfile $ content annexedfile
 	add_annex annexedfile @? "add failed"
 	annexed_present annexedfile
-	writeFile sha1annexedfile $ content sha1annexedfile
+	writecontent sha1annexedfile $ content sha1annexedfile
 	git_annex "add" [sha1annexedfile, "--backend=SHA1"] @? "add with SHA1 failed"
 	whenM (unlockedFiles <$> getTestMode) $
 		git_annex "unlock" [sha1annexedfile] @? "unlock failed"
@@ -300,12 +301,12 @@
 	checkbackend sha1annexedfile backendSHA1
 	ifM (annexeval Config.isDirect)
 		( do
-			writeFile ingitfile $ content ingitfile
+			writecontent ingitfile $ content ingitfile
 			not <$> boolSystem "git" [Param "add", File ingitfile] @? "git add failed to fail in direct mode"
 			nukeFile ingitfile
 			git_annex "sync" [] @? "sync failed"
 		, do
-			writeFile ingitfile $ content ingitfile
+			writecontent ingitfile $ content ingitfile
 			boolSystem "git" [Param "add", File ingitfile] @? "git add failed"
 			boolSystem "git" [Param "commit", Param "-q", Param "-m", Param "commit"] @? "git commit failed"
 			git_annex "add" [ingitfile] @? "add ingitfile should be no-op"
@@ -314,14 +315,14 @@
 
 test_add_dup :: Assertion
 test_add_dup = intmpclonerepo $ do
-	writeFile annexedfiledup $ content annexedfiledup
+	writecontent annexedfiledup $ content annexedfiledup
 	add_annex annexedfiledup @? "add of second file with same content failed"
 	annexed_present annexedfiledup
 	annexed_present annexedfile
 
 test_add_extras :: Assertion
 test_add_extras = intmpclonerepo $ do
-	writeFile wormannexedfile $ content wormannexedfile
+	writecontent wormannexedfile $ content wormannexedfile
 	git_annex "add" [wormannexedfile, "--backend=WORM"] @? "add with WORM failed"
 	whenM (unlockedFiles <$> getTestMode) $
 		git_annex "unlock" [wormannexedfile] @? "unlock failed"
@@ -378,7 +379,7 @@
 	git_annex "drop" ["--force", imported1, imported2, imported5] @? "drop failed"
 	annexed_notpresent_imported imported2
 	(toimportdup, importfdup, importeddup) <- mktoimport importdir "importdup"
-	not <$> git_annex "import" ["--clean-duplicates", toimportdup] 
+	git_annex_shouldfail "import" ["--clean-duplicates", toimportdup] 
 		@? "import of missing duplicate with --clean-duplicates failed to fail"
 	checkdoesnotexist importeddup
 	checkexists importfdup
@@ -386,7 +387,7 @@
 	mktoimport importdir subdir = do
 		createDirectory (importdir </> subdir)
 		let importf = subdir </> "f"
-		writeFile (importdir </> importf) (content importf)
+		writecontent (importdir </> importf) (content importf)
 		return (importdir </> subdir, importdir </> importf, importf)
 	annexed_present_imported f = ifM (annexeval Config.crippledFileSystem)
 		( annexed_present_unlocked f
@@ -401,7 +402,7 @@
 test_reinject = intmpclonerepoInDirect $ do
 	git_annex "drop" ["--force", sha1annexedfile] @? "drop failed"
 	annexed_notpresent sha1annexedfile
-	writeFile tmp $ content sha1annexedfile
+	writecontent tmp $ content sha1annexedfile
 	key <- Key.key2file <$> getKey backendSHA1 tmp
 	git_annex "reinject" [tmp, sha1annexedfile] @? "reinject failed"
 	annexed_present sha1annexedfile
@@ -436,7 +437,7 @@
 	git_annex "get" [annexedfile] @? "get failed"
 	boolSystem "git" [Param "remote", Param "rm", Param "origin"]
 		@? "git remote rm origin failed"
-	not <$> git_annex "drop" [annexedfile] @? "drop wrongly succeeded with no known copy of file"
+	git_annex_shouldfail "drop" [annexedfile] @? "drop wrongly succeeded with no known copy of file"
 	annexed_present annexedfile
 	git_annex "drop" ["--force", annexedfile] @? "drop --force failed"
 	annexed_notpresent annexedfile
@@ -450,7 +451,7 @@
 	git_annex "get" [annexedfile] @? "get failed"
 	annexed_present annexedfile
 	git_annex "numcopies" ["2"] @? "numcopies config failed"
-	not <$> git_annex "drop" [annexedfile] @? "drop succeeded although numcopies is not satisfied"
+	git_annex_shouldfail "drop" [annexedfile] @? "drop succeeded although numcopies is not satisfied"
 	git_annex "numcopies" ["1"] @? "numcopies config failed"
 	git_annex "drop" [annexedfile] @? "drop failed though origin has copy"
 	annexed_notpresent annexedfile
@@ -464,7 +465,7 @@
 	git_annex "untrust" ["origin"] @? "untrust of origin failed"
 	git_annex "get" [annexedfile] @? "get failed"
 	annexed_present annexedfile
-	not <$> git_annex "drop" [annexedfile] @? "drop wrongly succeeded with only an untrusted copy of the file"
+	git_annex_shouldfail "drop" [annexedfile] @? "drop wrongly succeeded with only an untrusted copy of the file"
 	annexed_present annexedfile
 	inmainrepo $ annexed_present annexedfile
 
@@ -595,18 +596,18 @@
 	annexed_notpresent annexedfile
 	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"
+			( git_annex_shouldfail "lock" [annexedfile] @? "lock failed to fail with not present file"
+			, git_annex_shouldfail "unlock" [annexedfile] @? "unlock failed to fail with not present file"
 			)
 	annexed_notpresent annexedfile
 
 	-- regression test: unlock of newly added, not committed file
-	-- should fail in v5 mode. In v6 mode, this is allowed.
-	writeFile "newfile" "foo"
+	-- should fail in v5 mode. In v7 mode, this is allowed.
+	writecontent "newfile" "foo"
 	git_annex "add" ["newfile"] @? "add new file failed"
 	ifM (annexeval Annex.Version.versionSupportsUnlockedPointers)
-		( git_annex "unlock" ["newfile"] @? "unlock failed on newly added, never committed file in v6 repository"
-		, not <$> git_annex "unlock" ["newfile"] @? "unlock failed to fail on newly added, never committed file in v5 repository"
+		( git_annex "unlock" ["newfile"] @? "unlock failed on newly added, never committed file in v7 repository"
+		, git_annex_shouldfail "unlock" ["newfile"] @? "unlock failed to fail on newly added, never committed file in v5 repository"
 		)
 
 	git_annex "get" [annexedfile] @? "get of file failed"
@@ -616,10 +617,10 @@
 	-- write different content, to verify that lock
 	-- throws it away
 	changecontent annexedfile
-	writeFile annexedfile $ content annexedfile ++ "foo"
-	not <$> git_annex "lock" [annexedfile] @? "lock failed to fail without --force"
+	writecontent annexedfile $ content annexedfile ++ "foo"
+	git_annex_shouldfail "lock" [annexedfile] @? "lock failed to fail without --force"
 	git_annex "lock" ["--force", annexedfile] @? "lock --force failed"
-	-- In v6 mode, the original content of the file is not always
+	-- In v7 mode, the original content of the file is not always
 	-- preserved after modification, so re-get it.
 	git_annex "get" [annexedfile] @? "get of file failed after lock --force"
 	annexed_present_locked annexedfile
@@ -642,19 +643,20 @@
 -- Regression test: lock --force when work tree file
 -- was modified lost the (unmodified) annex object.
 -- (Only occurred when the keys database was out of sync.)
-test_lock_v6_force :: Assertion
-test_lock_v6_force = intmpclonerepoInDirect $ do
+test_lock_v7_force :: Assertion
+test_lock_v7_force = intmpclonerepoInDirect $ do
 	git_annex "upgrade" [] @? "upgrade failed"
 	whenM (annexeval Annex.Version.versionSupportsUnlockedPointers) $ do
 		git_annex "get" [annexedfile] @? "get of file failed"
-		git_annex "unlock" [annexedfile] @? "unlock failed in v6 mode"
+		git_annex "unlock" [annexedfile] @? "unlock failed in v7 mode"
 		annexeval $ do
+			Just k <- Annex.WorkTree.lookupFile annexedfile
+			Database.Keys.removeInodeCaches k
 			Database.Keys.closeDb
-			dbdir <- Annex.fromRepo Annex.Locations.gitAnnexKeysDb
-			liftIO $ renameDirectory dbdir (dbdir ++ ".old")
-		writeFile annexedfile "test_lock_v6_force content"
-		not <$> git_annex "lock" [annexedfile] @? "lock of modified file failed to fail in v6 mode"
-		git_annex "lock" ["--force", annexedfile] @? "lock --force of modified file failed in v6 mode"
+			liftIO . nukeFile =<< Annex.fromRepo Annex.Locations.gitAnnexKeysDbIndexCache
+		writecontent annexedfile "test_lock_v7_force content"
+		git_annex_shouldfail "lock" [annexedfile] @? "lock of modified file failed to fail in v7 mode"
+		git_annex "lock" ["--force", annexedfile] @? "lock --force of modified file failed in v7 mode"
 		annexed_present_locked annexedfile
 
 test_edit :: Assertion
@@ -683,7 +685,7 @@
 		)
 	c <- readFile annexedfile
 	assertEqual "content of modified file" c (changedcontent annexedfile)
-	not <$> git_annex "drop" [annexedfile] @? "drop wrongly succeeded with no known copy of modified file"
+	git_annex_shouldfail "drop" [annexedfile] @? "drop wrongly succeeded with no known copy of modified file"
 
 test_partial_commit :: Assertion
 test_partial_commit = intmpclonerepoInDirect $ do
@@ -693,7 +695,7 @@
 	changecontent annexedfile
 	ifM (annexeval Annex.Version.versionSupportsUnlockedPointers)
 		( boolSystem "git" [Param "commit", Param "-q", Param "-m", Param "test", File annexedfile]
-			@? "partial commit of unlocked file should be allowed in v6 repository"
+			@? "partial commit of unlocked file should be allowed in v7 repository"
 		, not <$> boolSystem "git" [Param "commit", Param "-q", Param "-m", Param "test", File annexedfile]
 			@? "partial commit of unlocked file not blocked by pre-commit hook"
 		)
@@ -723,7 +725,7 @@
 	git_annex "get" [annexedfile] @? "get of file failed"
 	annexed_present annexedfile
 	ifM (annexeval Annex.Version.versionSupportsUnlockedPointers)
-		( not <$> git_annex "direct" [] @? "switch to direct mode failed to fail in v6 repository"
+		( git_annex_shouldfail "direct" [] @? "switch to direct mode failed to fail in v7 repository"
 		, do
 			git_annex "direct" [] @? "switch to direct mode failed"
 			annexed_present annexedfile
@@ -769,10 +771,10 @@
 	corrupt f = do
 		git_annex "get" [f] @? "get of file failed"
 		Utility.FileMode.allowWrite f
-		writeFile f (changedcontent f)
+		writecontent f (changedcontent f)
 		ifM (annexeval Config.isDirect <||> unlockedFiles <$> getTestMode)
 			( git_annex "fsck" [] @? "fsck failed on unlocked file with changed file content"
-			, not <$> git_annex "fsck" [] @? "fsck failed to fail with corrupted file content"
+			, git_annex_shouldfail "fsck" [] @? "fsck failed to fail with corrupted file content"
 			)
 		git_annex "fsck" [] @? "fsck unexpectedly failed again; previous one did not fix problem with " ++ f
 
@@ -803,7 +805,7 @@
 	git_annex "fsck" ["--from", "origin"] @? "fsck --from origin failed"
 
 fsck_should_fail :: String -> Assertion
-fsck_should_fail m = not <$> git_annex "fsck" []
+fsck_should_fail m = git_annex_shouldfail "fsck" []
 	@? "fsck failed to fail with " ++ m
 
 test_migrate :: Assertion
@@ -875,10 +877,10 @@
 		@? "dropkey failed"
 	checkunused [sha1annexedfilekey] ("after dropkey --force " ++ Key.key2file annexedfilekey)
 
-	not <$> git_annex "dropunused" ["1"] @? "dropunused failed to fail without --force"
+	git_annex_shouldfail "dropunused" ["1"] @? "dropunused failed to fail without --force"
 	git_annex "dropunused" ["--force", "1"] @? "dropunused failed"
 	checkunused [] "after dropunused"
-	not <$> git_annex "dropunused" ["--force", "10", "501"] @? "dropunused failed to fail on bogus numbers"
+	git_annex_shouldfail "dropunused" ["--force", "10", "501"] @? "dropunused failed to fail on bogus numbers"
 
 	-- Unused used to miss renamed symlinks that were not staged
 	-- and pointed at annexed content, and think that content was unused.
@@ -886,7 +888,7 @@
 	-- unlocked, the work tree file has the content, and there's no way
 	-- to associate it with the key.
 	unlessM (unlockedFiles <$> getTestMode) $ do
-		writeFile "unusedfile" "unusedcontent"
+		writecontent "unusedfile" "unusedcontent"
 		git_annex "add" ["unusedfile"] @? "add of unusedfile failed"
 		unusedfilekey <- getKey backendSHA256E "unusedfile"
 		renameFile "unusedfile" "unusedunstagedfile"
@@ -897,7 +899,7 @@
 
 	-- unused used to miss symlinks that were deleted or modified
 	-- manually
-	writeFile "unusedfile" "unusedcontent"
+	writecontent "unusedfile" "unusedcontent"
 	git_annex "add" ["unusedfile"] @? "add of unusedfile failed"
 	boolSystem "git" [Param "add", File "unusedfile"] @? "git add failed"
 	unusedfilekey' <- getKey backendSHA256E "unusedfile"
@@ -907,7 +909,7 @@
 
 	-- unused used to false positive on symlinks that were
 	-- deleted or modified manually, but not staged as such
-	writeFile "unusedfile" "unusedcontent"
+	writecontent "unusedfile" "unusedcontent"
 	git_annex "add" ["unusedfile"] @? "add of unusedfile failed"
 	boolSystem "git" [Param "add", File "unusedfile"] @? "git add failed"
 	checkunused [] "with staged file"
@@ -919,10 +921,10 @@
 	-- found as unused.
 	whenM (unlockedFiles <$> getTestMode) $ do
 		let f = "unlockedfile"
-		writeFile f "unlockedcontent1"
+		writecontent f "unlockedcontent1"
 		boolSystem "git" [Param "add", File "unlockedfile"] @? "git add failed"
 		checkunused [] "with unlocked file before modification"
-		writeFile f "unlockedcontent2"
+		writecontent f "unlockedcontent2"
 		checkunused [] "with unlocked file after modification"
 		not <$> boolSystem "git" [Param "diff", Param "--quiet", File f] @? "git diff did not show changes to unlocked file"
 		-- still nothing unused because one version is in the index
@@ -959,7 +961,7 @@
 	{- --include=* should match files in subdirectories too,
 	 - and --exclude=* should exclude them. -}
 	createDirectory "dir"
-	writeFile "dir/subfile" "subfile"
+	writecontent "dir/subfile" "subfile"
 	git_annex "add" ["dir"] @? "add of subdir failed"
 	git_annex_expectoutput "find" ["--include", "*", "--exclude", annexedfile, "--exclude", sha1annexedfile] ["dir/subfile"]
 	git_annex_expectoutput "find" ["--exclude", "*"] []
@@ -1043,10 +1045,10 @@
 			{- Set up a conflict. -}
 			let newcontent = content annexedfile ++ rname r
 			ifM (annexeval Config.isDirect)
-				( writeFile annexedfile newcontent
+				( writecontent annexedfile newcontent
 				, do
 					git_annex "unlock" [annexedfile] @? "unlock failed"		
-					writeFile annexedfile newcontent
+					writecontent annexedfile newcontent
 				)
 		{- Sync twice in r1 so it gets the conflict resolution
 		 - update from r2 -}
@@ -1070,12 +1072,12 @@
 		withtmpclonerepo $ \r2 -> do
 			indir r1 $ do
 				disconnectOrigin
-				writeFile conflictor "conflictor1"
+				writecontent conflictor "conflictor1"
 				add_annex conflictor @? "add conflicter failed"
 				git_annex "sync" [] @? "sync failed in r1"
 			indir r2 $ do
 				disconnectOrigin
-				writeFile conflictor "conflictor2"
+				writecontent conflictor "conflictor2"
 				add_annex conflictor @? "add conflicter failed"
 				git_annex "sync" [] @? "sync failed in r2"
 			pair r1 r2
@@ -1098,20 +1100,20 @@
 
 {- Conflict resolution while in an adjusted branch. -}
 test_conflict_resolution_adjusted_branch :: Assertion
-test_conflict_resolution_adjusted_branch = whenM Annex.AdjustedBranch.isGitVersionSupported $
+test_conflict_resolution_adjusted_branch = whenM (annexeval Annex.AdjustedBranch.isSupported) $
 	withtmpclonerepo $ \r1 ->
 		withtmpclonerepo $ \r2 -> do
 			indir r1 $ do
 				disconnectOrigin
-				writeFile conflictor "conflictor1"
+				writecontent conflictor "conflictor1"
 				add_annex conflictor @? "add conflicter failed"
 				git_annex "sync" [] @? "sync failed in r1"
 			indir r2 $ do
 				disconnectOrigin
-				writeFile conflictor "conflictor2"
+				writecontent conflictor "conflictor2"
 				add_annex conflictor @? "add conflicter failed"
 				git_annex "sync" [] @? "sync failed in r2"
-				-- need v6 to use adjust
+				-- need v7 to use adjust
 				git_annex "upgrade" [] @? "upgrade failed"
 				-- We might be in an adjusted branch
 				-- already, when eg on a crippled
@@ -1146,13 +1148,13 @@
 		withtmpclonerepo $ \r2 -> do
 			indir r1 $ do
 				disconnectOrigin
-				writeFile conflictor "conflictor"
+				writecontent conflictor "conflictor"
 				add_annex conflictor @? "add conflicter failed"
 				git_annex "sync" [] @? "sync failed in r1"
 			indir r2 $ do
 				disconnectOrigin
 				createDirectory conflictor
-				writeFile subfile "subfile"
+				writecontent subfile "subfile"
 				add_annex conflictor @? "add conflicter failed"
 				git_annex "sync" [] @? "sync failed in r2"
 			pair r1 r2
@@ -1188,7 +1190,7 @@
 		withtmpclonerepo $ \r2 -> do
 			indir r1 $ do
 				disconnectOrigin
-				writeFile conflictor "conflictor"
+				writecontent conflictor "conflictor"
 				add_annex conflictor @? "add conflicter failed"
 				git_annex "sync" [] @? "sync failed in r1"
 			indir r2 $
@@ -1201,7 +1203,7 @@
 				unlessM (annexeval Config.isDirect) $ do
 					git_annex "unlock" [conflictor]
 						@? "unlock conflictor failed"
-				writeFile conflictor "newconflictor"
+				writecontent conflictor "newconflictor"
 			indir r1 $
 				nukeFile conflictor
 			let l = if inr1 then [r1, r2, r1] else [r2, r1, r2]
@@ -1237,12 +1239,12 @@
 			whenM (isInDirect r1 <&&> isInDirect r2) $ do
 				indir r1 $ do
 					disconnectOrigin
-					writeFile conflictor "conflictor"
+					writecontent conflictor "conflictor"
 					add_annex conflictor @? "add conflicter failed"
 					git_annex "sync" [] @? "sync failed in r1"
 				indir r2 $ do
 					disconnectOrigin
-					writeFile conflictor nonannexed_content
+					writecontent conflictor nonannexed_content
 					boolSystem "git"
 						[ Param "config"
 						, Param "annex.largefiles"
@@ -1294,7 +1296,7 @@
 			       <&&> isInDirect r1 <&&> isInDirect r2) $ do
 				indir r1 $ do
 					disconnectOrigin
-					writeFile conflictor "conflictor"
+					writecontent conflictor "conflictor"
 					add_annex conflictor @? "add conflicter failed"
 					git_annex "sync" [] @? "sync failed in r1"
 				indir r2 $ do
@@ -1345,12 +1347,12 @@
 			indir r1 $ do
 				disconnectOrigin
 				createDirectoryIfMissing True (parentDir remoteconflictor)
-				writeFile remoteconflictor annexedcontent
+				writecontent remoteconflictor annexedcontent
 				add_annex conflictor @? "add remoteconflicter failed"
 				git_annex "sync" [] @? "sync failed in r1"
 			indir r2 $ do
 				disconnectOrigin
-				writeFile conflictor localcontent
+				writecontent conflictor localcontent
 			pair r1 r2
 			indir r2 $ ifM (annexeval Config.isDirect)
 				( do
@@ -1366,7 +1368,7 @@
 				-- this case is intentionally not handled
 				-- in indirect mode, since the user
 				-- can recover on their own easily
-				, not <$> git_annex "sync" [] @? "sync failed to fail"
+				, git_annex_shouldfail "sync" [] @? "sync failed to fail"
 				)
 	conflictor = "conflictor"
 	localprefix = ".variant-local"
@@ -1382,18 +1384,18 @@
 		withtmpclonerepo $ \r2 ->
 			withtmpclonerepo $ \r3 -> do
 				indir r1 $ do
-					writeFile conflictor "conflictor"
+					writecontent conflictor "conflictor"
 					git_annex "add" [conflictor] @? "add conflicter failed"
 					git_annex "sync" [] @? "sync failed in r1"
 					check_is_link conflictor "r1"
 				indir r2 $ do
 					createDirectory conflictor
-					writeFile (conflictor </> "subfile") "subfile"
+					writecontent (conflictor </> "subfile") "subfile"
 					git_annex "add" [conflictor] @? "add conflicter failed"
 					git_annex "sync" [] @? "sync failed in r2"
 					check_is_link (conflictor </> "subfile") "r2"
 				indir r3 $ do
-					writeFile conflictor "conflictor"
+					writecontent conflictor "conflictor"
 					git_annex "add" [conflictor] @? "add conflicter failed"
 					git_annex "sync" [] @? "sync failed in r1"
 					check_is_link (conflictor </> "subfile") "r3"
@@ -1405,7 +1407,7 @@
 		all (\i -> Git.Types.toTreeItemType (Git.LsTree.mode i) == Just Git.Types.TreeSymlink) l
 			@? (what ++ " " ++ f ++ " lost symlink bit after merge: " ++ show l)
 
-{- A v6 unlocked file that conflicts with a locked file should be resolved
+{- A v7 unlocked file that conflicts with a locked file should be resolved
  - in favor of the unlocked file, with no variant files, as long as they
  - both point to the same key. -}
 test_mixed_lock_conflict_resolution :: Assertion
@@ -1414,12 +1416,12 @@
 		withtmpclonerepo $ \r2 -> do
 			indir r1 $ whenM shouldtest $ do
 				disconnectOrigin
-				writeFile conflictor "conflictor"
+				writecontent conflictor "conflictor"
 				git_annex "add" [conflictor] @? "add conflicter failed"
 				git_annex "sync" [] @? "sync failed in r1"
 			indir r2 $ whenM shouldtest $ do
 				disconnectOrigin
-				writeFile conflictor "conflictor"
+				writecontent conflictor "conflictor"
 				git_annex "add" [conflictor] @? "add conflicter failed"
 				git_annex "unlock" [conflictor] @? "unlock conflicter failed"
 				git_annex "sync" [] @? "sync failed in r2"
@@ -1447,7 +1449,7 @@
  - 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 $
+test_adjusted_branch_merge_regression = whenM (annexeval Annex.AdjustedBranch.isSupported) $
 	withtmpclonerepo $ \r1 ->
 		withtmpclonerepo $ \r2 -> do
 			pair r1 r2
@@ -1461,7 +1463,7 @@
 		disconnectOrigin
 		git_annex "upgrade" [] @? "upgrade failed"
 		git_annex "adjust" ["--unlock", "--force"] @? "adjust failed"
-		writeFile conflictor "conflictor"
+		writecontent conflictor "conflictor"
 		git_annex "add" [conflictor] @? "add conflicter failed"
 		git_annex "sync" [] @? "sync failed"
 	checkmerge what d = indir d $ do
@@ -1474,18 +1476,18 @@
  - a subtree to an existing tree lost files. -}
 test_adjusted_branch_subtree_regression :: Assertion
 test_adjusted_branch_subtree_regression = 
-	whenM Annex.AdjustedBranch.isGitVersionSupported $ 
+	whenM (annexeval Annex.AdjustedBranch.isSupported) $ 
 		withtmpclonerepo $ \r -> do
 			indir r $ do
 				disconnectOrigin
 				git_annex "upgrade" [] @? "upgrade failed"
 				git_annex "adjust" ["--unlock", "--force"] @? "adjust failed"
 				createDirectoryIfMissing True "a/b/c"
-				writeFile "a/b/c/d" "foo"
+				writecontent "a/b/c/d" "foo"
 				git_annex "add" ["a/b/c"] @? "add a/b/c failed"
 				git_annex "sync" [] @? "sync failed"
 				createDirectoryIfMissing True "a/b/x"
-				writeFile "a/b/x/y" "foo"
+				writecontent "a/b/x/y" "foo"
 				git_annex "add" ["a/b/x"] @? "add a/b/x failed"
 				git_annex "sync" [] @? "sync failed"
 				boolSystem "git" [Param "checkout", Param "master"] @? "git checkout master failed"
@@ -1518,7 +1520,7 @@
 test_uninit_inbranch :: Assertion
 test_uninit_inbranch = intmpclonerepoInDirect $ do
 	boolSystem "git" [Param "checkout", Param "git-annex"] @? "git checkout git-annex"
-	not <$> git_annex "uninit" [] @? "uninit failed to fail when git-annex branch was checked out"
+	git_annex_shouldfail "uninit" [] @? "uninit failed to fail when git-annex branch was checked out"
 
 test_upgrade :: Assertion
 test_upgrade = intmpclonerepo $
@@ -1529,7 +1531,7 @@
 	annexed_notpresent annexedfile
 	git_annex "whereis" [annexedfile] @? "whereis on non-present file failed"
 	git_annex "untrust" ["origin"] @? "untrust failed"
-	not <$> git_annex "whereis" [annexedfile] @? "whereis on non-present file only present in untrusted repo failed to fail"
+	git_annex_shouldfail "whereis" [annexedfile] @? "whereis on non-present file only present in untrusted repo failed to fail"
 	git_annex "get" [annexedfile] @? "get failed"
 	annexed_present annexedfile
 	git_annex "whereis" [annexedfile] @? "whereis on present file failed"
@@ -1555,7 +1557,7 @@
 	annexed_notpresent annexedfile
 	git_annex "move" [annexedfile, "--from", "foo"] @? "move --from hook remote failed"
 	annexed_present annexedfile
-	not <$> git_annex "drop" [annexedfile, "--numcopies=2"] @? "drop failed to fail"
+	git_annex_shouldfail "drop" [annexedfile, "--numcopies=2"] @? "drop failed to fail"
 	annexed_present annexedfile
   where
 	dir = "dir"
@@ -1579,7 +1581,7 @@
 	annexed_notpresent annexedfile
 	git_annex "move" [annexedfile, "--from", "foo"] @? "move --from directory remote failed"
 	annexed_present annexedfile
-	not <$> git_annex "drop" [annexedfile, "--numcopies=2"] @? "drop failed to fail"
+	git_annex_shouldfail "drop" [annexedfile, "--numcopies=2"] @? "drop failed to fail"
 	annexed_present annexedfile
 
 test_rsync_remote :: Assertion
@@ -1594,7 +1596,7 @@
 	annexed_notpresent annexedfile
 	git_annex "move" [annexedfile, "--from", "foo"] @? "move --from rsync remote failed"
 	annexed_present annexedfile
-	not <$> git_annex "drop" [annexedfile, "--numcopies=2"] @? "drop failed to fail"
+	git_annex_shouldfail "drop" [annexedfile, "--numcopies=2"] @? "drop failed to fail"
 	annexed_present annexedfile
 
 test_bup_remote :: Assertion
@@ -1658,7 +1660,7 @@
 			annexed_notpresent annexedfile
 			git_annex "move" [annexedfile, "--from", "foo"] @? "move --from encrypted remote failed"
 			annexed_present annexedfile
-			not <$> git_annex "drop" [annexedfile, "--numcopies=2"] @? "drop failed to fail"
+			git_annex_shouldfail "drop" [annexedfile, "--numcopies=2"] @? "drop failed to fail"
 			annexed_present annexedfile
 	{- Ensure the configuration complies with the encryption scheme, and
 	 - that all keys are encrypted properly for the given directory remote. -}
@@ -1695,7 +1697,7 @@
 test_add_subdirs :: Assertion
 test_add_subdirs = intmpclonerepo $ do
 	createDirectory "dir"
-	writeFile ("dir" </> "foo") $ "dir/" ++ content annexedfile
+	writecontent ("dir" </> "foo") $ "dir/" ++ content annexedfile
 	git_annex "add" ["dir"] @? "add of subdir failed"
 
 	{- Regression test for Windows bug where symlinks were not
@@ -1707,7 +1709,7 @@
 		"../.git/annex/" `isPrefixOf` l @? ("symlink from subdir to .git/annex is wrong: " ++ l)
 
 	createDirectory "dir2"
-	writeFile ("dir2" </> "foo") $ content annexedfile
+	writecontent ("dir2" </> "foo") $ content annexedfile
 	setCurrentDirectory "dir"
 	git_annex "add" [".." </> "dir2"] @? "add of ../subdir failed"
 
@@ -1717,8 +1719,8 @@
 	let filecmd c ps = git_annex c ("-cannex.security.allowed-url-schemes=file" : ps)
 	f <- absPath "myurl"
 	let url = replace "\\" "/" ("file:///" ++ dropDrive f)
-	writeFile f "foo"
-	not <$> git_annex "addurl" [url] @? "addurl failed to fail on file url"
+	writecontent f "foo"
+	git_annex_shouldfail "addurl" [url] @? "addurl failed to fail on file url"
 	filecmd "addurl" [url] @? ("addurl failed on " ++ url)
 	let dest = "addurlurldest"
 	filecmd "addurl" ["--file", dest, url] @? ("addurl failed on " ++ url ++ "  with --file")
diff --git a/Test/Framework.hs b/Test/Framework.hs
--- a/Test/Framework.hs
+++ b/Test/Framework.hs
@@ -10,6 +10,7 @@
 import Test.Tasty
 import Test.Tasty.Runners
 import Test.Tasty.HUnit
+import Control.Concurrent
 
 import Common
 import Types.Test
@@ -17,6 +18,7 @@
 import qualified Annex
 import qualified Annex.UUID
 import qualified Annex.Version
+import qualified Types.RepoVersion
 import qualified Backend
 import qualified Git.CurrentRepo
 import qualified Git.Construct
@@ -45,12 +47,22 @@
 -- This is equivilant to running git-annex, but it's all run in-process
 -- so test coverage collection works.
 git_annex :: String -> [String] -> IO Bool
-git_annex command params = do
+git_annex command params = git_annex' command params >>= \case
+	Right () -> return True
+	Left e -> do
+		hPutStrLn stderr (show e)
+		return False
+
+-- For when git-annex is expected to fail.
+git_annex_shouldfail :: String -> [String] -> IO Bool
+git_annex_shouldfail command params = git_annex' command params >>= \case
+	Right () -> return False
+	Left _ -> return True
+
+git_annex' :: String -> [String] -> IO (Either SomeException ())
+git_annex' command params = do
 	-- catch all errors, including normally fatal errors
-	r <- try run ::IO (Either SomeException ())
-	case r of
-		Right _ -> return True
-		Left _ -> return False
+	try run ::IO (Either SomeException ())
   where
 	run = GitAnnex.run dummyTestOptParser Nothing (command:"-q":params)
 	dummyTestOptParser = pure mempty
@@ -198,7 +210,7 @@
 		ver <- annexVersion <$> getTestMode
 		if ver == Annex.Version.defaultVersion
 			then git_annex "init" ["-q", new] @? "git annex init failed"
-			else git_annex "init" ["-q", new, "--version", ver] @? "git annex init failed"
+			else git_annex "init" ["-q", new, "--version", show (Types.RepoVersion.fromRepoVersion ver)] @? "git annex init failed"
 	unless (bareClone cfg) $
 		indir new $
 			setupTestMode
@@ -387,11 +399,11 @@
 data TestMode = TestMode
 	{ forceDirect :: Bool
 	, unlockedFiles :: Bool
-	, annexVersion :: Annex.Version.Version
+	, annexVersion :: Types.RepoVersion.RepoVersion
 	, keepFailures :: Bool
 	} deriving (Read, Show)
 
-testMode :: TestOptions -> Annex.Version.Version -> TestMode
+testMode :: TestOptions -> Types.RepoVersion.RepoVersion -> TestMode
 testMode opts v = TestMode
 	{ forceDirect = False
 	, unlockedFiles = False
@@ -502,8 +514,29 @@
 	| "import" `isPrefixOf` f = "imported content"
 	| otherwise = "unknown file " ++ f
 
+-- Writes new content to a file, and makes sure that it has a different
+-- mtime than it did before
+writecontent :: FilePath -> String -> IO ()
+writecontent f c = go (10000000 :: Integer)
+  where
+	go ticsleft = do
+		oldmtime <- catchMaybeIO $ getModificationTime f
+		writeFile f c
+		newmtime <- getModificationTime f
+		if Just newmtime == oldmtime
+			then do
+				threadDelay 100000
+				let ticsleft' = ticsleft - 100000
+				if ticsleft' > 0
+					then go ticsleft'
+					else do
+						hPutStrLn stderr "file mtimes do not seem to be changing (tried for 10 seconds)"
+						hFlush stderr
+						return ()
+			else return ()
+
 changecontent :: FilePath -> IO ()
-changecontent f = writeFile f $ changedcontent f
+changecontent f = writecontent f $ changedcontent f
 
 changedcontent :: FilePath -> String
 changedcontent f = content f ++ " (modified)"
diff --git a/Types/AdjustedBranch.hs b/Types/AdjustedBranch.hs
new file mode 100644
--- /dev/null
+++ b/Types/AdjustedBranch.hs
@@ -0,0 +1,53 @@
+{- adjusted branch types
+ -
+ - Copyright 2016-2018 Joey Hess <id@joeyh.name>
+ -
+ - Licensed under the GNU AGPL version 3 or higher.
+ -}
+
+module Types.AdjustedBranch where
+
+data Adjustment
+	= LinkAdjustment LinkAdjustment
+	| PresenceAdjustment PresenceAdjustment (Maybe LinkAdjustment)
+	deriving (Show, Eq)
+
+-- Doesn't make sense to combine unlock with fix.
+data LinkAdjustment
+	= UnlockAdjustment
+	| LockAdjustment
+	| FixAdjustment
+	| UnFixAdjustment
+	deriving (Show, Eq)
+
+data PresenceAdjustment
+	= HideMissingAdjustment
+	| ShowMissingAdjustment
+	deriving (Show, Eq)
+
+-- Adjustments have to be able to be reversed, so that commits made to the
+-- adjusted branch can be reversed to the commit that would have been made
+-- without the adjustment and applied to the original branch.
+class ReversableAdjustment t where
+	reverseAdjustment :: t -> t
+
+instance ReversableAdjustment Adjustment where
+	reverseAdjustment (LinkAdjustment l) = 
+		LinkAdjustment (reverseAdjustment l)
+	reverseAdjustment (PresenceAdjustment p ml) =
+		PresenceAdjustment (reverseAdjustment p) (fmap reverseAdjustment ml)
+
+instance ReversableAdjustment LinkAdjustment where
+	reverseAdjustment UnlockAdjustment = LockAdjustment
+	reverseAdjustment LockAdjustment = UnlockAdjustment
+	reverseAdjustment FixAdjustment = UnFixAdjustment
+	reverseAdjustment UnFixAdjustment = FixAdjustment
+
+instance ReversableAdjustment PresenceAdjustment where
+	reverseAdjustment HideMissingAdjustment = ShowMissingAdjustment
+	reverseAdjustment ShowMissingAdjustment = HideMissingAdjustment
+
+adjustmentHidesFiles :: Adjustment -> Bool
+adjustmentHidesFiles (PresenceAdjustment HideMissingAdjustment _) = True
+adjustmentHidesFiles _ = False
+
diff --git a/Types/DesktopNotify.hs b/Types/DesktopNotify.hs
--- a/Types/DesktopNotify.hs
+++ b/Types/DesktopNotify.hs
@@ -10,9 +10,7 @@
 module Types.DesktopNotify where
 
 import Data.Monoid
-#if MIN_VERSION_base(4,9,0)
 import qualified Data.Semigroup as Sem
-#endif
 import Prelude
 
 data DesktopNotify = DesktopNotify
@@ -21,22 +19,14 @@
 	}
 	deriving (Show)
 
-appendDesktopNotify :: DesktopNotify -> DesktopNotify -> DesktopNotify
-appendDesktopNotify (DesktopNotify s1 f1) (DesktopNotify s2 f2) =
-	DesktopNotify (s1 || s2) (f1 || f2)
-
-#if MIN_VERSION_base(4,9,0)
 instance Sem.Semigroup DesktopNotify where
-	(<>) = appendDesktopNotify
-#endif
+	(DesktopNotify s1 f1) <> (DesktopNotify s2 f2) =
+		DesktopNotify (s1 || s2) (f1 || f2)
 
 instance Monoid DesktopNotify where
 	mempty = DesktopNotify False False
-#if MIN_VERSION_base(4,11,0)
-#elif MIN_VERSION_base(4,9,0)
+#if ! MIN_VERSION_base(4,11,0)
 	mappend = (Sem.<>)
-#else
-	mappend = appendDesktopNotify
 #endif
 
 mkNotifyStart :: DesktopNotify
diff --git a/Types/Difference.hs b/Types/Difference.hs
--- a/Types/Difference.hs
+++ b/Types/Difference.hs
@@ -26,9 +26,7 @@
 import Data.Maybe
 import Data.Monoid
 import qualified Data.Set as S
-#if MIN_VERSION_base(4,9,0)
 import qualified Data.Semigroup as Sem
-#endif
 import Prelude
 
 -- Describes differences from the v5 repository format.
@@ -80,18 +78,13 @@
 	}
 appendDifferences _ _ = UnknownDifferences
 
-#if MIN_VERSION_base(4,9,0)
 instance Sem.Semigroup Differences where
 	(<>) = appendDifferences
-#endif
 
 instance Monoid Differences where
 	mempty = Differences False False False
-#if MIN_VERSION_base(4,11,0)
-#elif MIN_VERSION_base(4,9,0)
+#if ! MIN_VERSION_base(4,11,0)
 	mappend = (Sem.<>)
-#else
-	mappend = appendDifferences
 #endif
 
 readDifferences :: String -> Differences
diff --git a/Types/GitConfig.hs b/Types/GitConfig.hs
--- a/Types/GitConfig.hs
+++ b/Types/GitConfig.hs
@@ -30,6 +30,7 @@
 import Types.NumCopies
 import Types.Difference
 import Types.RefSpec
+import Types.RepoVersion
 import Config.DynamicConfig
 import Utility.HumanTime
 import Utility.Gpg (GpgCmd, mkGpgCmd)
@@ -52,7 +53,7 @@
 {- Main git-annex settings. Each setting corresponds to a git-config key
  - such as annex.foo -}
 data GitConfig = GitConfig
-	{ annexVersion :: Maybe String
+	{ annexVersion :: Maybe RepoVersion
 	, annexUUID :: UUID
 	, annexNumCopies :: Maybe NumCopies
 	, annexDiskReserve :: Integer
@@ -110,7 +111,7 @@
 
 extractGitConfig :: Git.Repo -> GitConfig
 extractGitConfig r = GitConfig
-	{ annexVersion = notempty $ getmaybe (annex "version")
+	{ annexVersion = RepoVersion <$> getmayberead (annex "version")
 	, annexUUID = maybe NoUUID toUUID $ getmaybe (annex "uuid")
 	, annexNumCopies = NumCopies <$> getmayberead (annex "numcopies")
 	, annexDiskReserve = fromMaybe onemegabyte $
diff --git a/Types/Messages.hs b/Types/Messages.hs
--- a/Types/Messages.hs
+++ b/Types/Messages.hs
@@ -5,16 +5,12 @@
  - Licensed under the GNU GPL version 3 or higher.
  -}
 
-{-# LANGUAGE CPP #-}
-
 module Types.Messages where
 
 import qualified Utility.Aeson as Aeson
 
 import Control.Concurrent
-#ifdef WITH_CONCURRENTOUTPUT
 import System.Console.Regions (ConsoleRegion)
-#endif
 
 data OutputType = NormalOutput | QuietOutput | JSONOutput JSONOptions
 	deriving (Show)
@@ -40,10 +36,8 @@
 	, concurrentOutputEnabled :: Bool
 	, sideActionBlock :: SideActionBlock
 	, implicitMessages :: Bool
-#ifdef WITH_CONCURRENTOUTPUT
 	, consoleRegion :: Maybe ConsoleRegion
 	, consoleRegionErrFlag :: Bool
-#endif
 	, jsonBuffer :: Maybe Aeson.Object
 	, promptLock :: MVar () -- left full when not prompting
 	}
@@ -56,10 +50,8 @@
 		, concurrentOutputEnabled = False
 		, sideActionBlock = NoBlock
 		, implicitMessages = True 
-#ifdef WITH_CONCURRENTOUTPUT
 		, consoleRegion = Nothing
 		, consoleRegionErrFlag = False
-#endif
 		, jsonBuffer = Nothing
 		, promptLock = promptlock
 		}
diff --git a/Types/RepoVersion.hs b/Types/RepoVersion.hs
new file mode 100644
--- /dev/null
+++ b/Types/RepoVersion.hs
@@ -0,0 +1,11 @@
+{- git-annex repository versioning
+ -
+ - Copyright 2010-2018 Joey Hess <id@joeyh.name>
+ -
+ - Licensed under the GNU AGPL version 3 or higher.
+ -}
+
+module Types.RepoVersion where
+
+newtype RepoVersion = RepoVersion { fromRepoVersion :: Int }
+	deriving (Eq, Ord, Read, Show)
diff --git a/Types/Test.hs b/Types/Test.hs
--- a/Types/Test.hs
+++ b/Types/Test.hs
@@ -11,9 +11,7 @@
 
 import Test.Tasty.Options
 import Data.Monoid
-#if MIN_VERSION_base(4,9,0)
 import qualified Data.Semigroup as Sem
-#endif
 import Prelude
 
 import Types.Command
@@ -25,25 +23,17 @@
 	, internalData :: CmdParams
 	}
 
-appendTestOptions :: TestOptions -> TestOptions -> TestOptions
-appendTestOptions a b = TestOptions
-	(tastyOptionSet a <> tastyOptionSet b)
-	(keepFailuresOption a || keepFailuresOption b)
-	(fakeSsh a || fakeSsh b)
-	(internalData a <> internalData b)
-
-#if MIN_VERSION_base(4,9,0)
 instance Sem.Semigroup TestOptions where
-	(<>) = appendTestOptions
-#endif
+	a <> b = TestOptions
+		(tastyOptionSet a <> tastyOptionSet b)
+		(keepFailuresOption a || keepFailuresOption b)
+		(fakeSsh a || fakeSsh b)
+		(internalData a <> internalData b)
 
 instance Monoid TestOptions where
 	mempty = TestOptions mempty False False mempty
-#if MIN_VERSION_base(4,11,0)
-#elif MIN_VERSION_base(4,9,0)
+#if ! MIN_VERSION_base(4,11,0)
 	mappend = (Sem.<>)
-#else
-	mappend = appendTestOptions
 #endif
 
 type TestRunner = TestOptions -> IO ()
diff --git a/Upgrade.hs b/Upgrade.hs
--- a/Upgrade.hs
+++ b/Upgrade.hs
@@ -11,6 +11,7 @@
 
 import Annex.Common
 import Annex.Version
+import Types.RepoVersion
 #ifndef mingw32_HOST_OS
 import qualified Upgrade.V0
 import qualified Upgrade.V1
@@ -19,41 +20,57 @@
 import qualified Upgrade.V3
 import qualified Upgrade.V4
 import qualified Upgrade.V5
+import qualified Upgrade.V6
 
-checkUpgrade :: Version -> Annex ()
+import qualified Data.Map as M
+
+checkUpgrade :: RepoVersion -> Annex ()
 checkUpgrade = maybe noop giveup <=< needsUpgrade
 
-needsUpgrade :: Version -> Annex (Maybe String)
+needsUpgrade :: RepoVersion -> Annex (Maybe String)
 needsUpgrade v
 	| v `elem` supportedVersions = ok
-	| v `elem` autoUpgradeableVersions = ifM (upgrade True defaultVersion)
-		( ok
-		, err "Automatic upgrade failed!"
-		)
-	| v `elem` upgradableVersions = err "Upgrade this repository: git-annex upgrade"
-	| otherwise = err "Upgrade git-annex."
+	| otherwise = case M.lookup v autoUpgradeableVersions of
+		Nothing
+			| v `elem` upgradableVersions ->
+				err "Upgrade this repository: git-annex upgrade"
+			| otherwise ->
+				err "Upgrade git-annex."
+		Just newv -> ifM (upgrade True newv)
+			( ok
+			, err "Automatic upgrade failed!"
+			)
   where
-	err msg = return $ Just $ "Repository version " ++ v ++
+	err msg = return $ Just $ "Repository version " ++
+		show (fromRepoVersion v) ++
 		" is not supported. " ++ msg
 	ok = return Nothing
 
-upgrade :: Bool -> Version -> Annex Bool
+upgrade :: Bool -> RepoVersion -> Annex Bool
 upgrade automatic destversion = do
 	upgraded <- go =<< getVersion
 	when upgraded $
 		setVersion destversion
 	return upgraded
   where
-	go (Just v) | v >= destversion = return True
+	go (Just v)
+		| v >= destversion = return True
+		| otherwise = ifM (up v)
+			( go (Just (RepoVersion (fromRepoVersion v + 1)))
+			, return False
+			)
+	go _ = return True
+
 #ifndef mingw32_HOST_OS
-	go (Just "0") = Upgrade.V0.upgrade
-	go (Just "1") = Upgrade.V1.upgrade
+	up (RepoVersion 0) = Upgrade.V0.upgrade
+	up (RepoVersion 1) = Upgrade.V1.upgrade
 #else
-	go (Just "0") = giveup "upgrade from v0 on Windows not supported"
-	go (Just "1") = giveup "upgrade from v1 on Windows not supported"
+	up (RepoVersion 0) = giveup "upgrade from v0 on Windows not supported"
+	up (RepoVersion 1) = giveup "upgrade from v1 on Windows not supported"
 #endif
-	go (Just "2") = Upgrade.V2.upgrade
-	go (Just "3") = Upgrade.V3.upgrade automatic
-	go (Just "4") = Upgrade.V4.upgrade automatic
-	go (Just "5") = Upgrade.V5.upgrade automatic
-	go _ = return True
+	up (RepoVersion 2) = Upgrade.V2.upgrade
+	up (RepoVersion 3) = Upgrade.V3.upgrade automatic
+	up (RepoVersion 4) = Upgrade.V4.upgrade automatic
+	up (RepoVersion 5) = Upgrade.V5.upgrade automatic
+	up (RepoVersion 6) = Upgrade.V6.upgrade automatic
+	up _ = return True
diff --git a/Upgrade/V5.hs b/Upgrade/V5.hs
--- a/Upgrade/V5.hs
+++ b/Upgrade/V5.hs
@@ -56,7 +56,7 @@
 		{- Create adjusted branch where all files are unlocked.
 		 - This should have the same content for each file as
 		 - have been staged in upgradeDirectWorkTree. -}
-		AdjBranch b <- adjustBranch UnlockAdjustment cur
+		AdjBranch b <- adjustBranch (LinkAdjustment UnlockAdjustment) cur
 		{- Since the work tree was already set up by
 		 - upgradeDirectWorkTree, and contains unlocked file
 		 - contents too, don't use git checkout to check out the
diff --git a/Upgrade/V6.hs b/Upgrade/V6.hs
new file mode 100644
--- /dev/null
+++ b/Upgrade/V6.hs
@@ -0,0 +1,21 @@
+{- git-annex v6 -> v7 upgrade support
+ -
+ - Copyright 2018 Joey Hess <id@joeyh.name>
+ -
+ - Licensed under the GNU AGPL version 3 or higher.
+ -}
+
+module Upgrade.V6 where
+
+import Annex.Common
+import Config
+import Annex.Hook
+
+upgrade :: Bool -> Annex Bool
+upgrade automatic = do
+	unless automatic $
+		showAction "v6 to v7"
+	unlessM isBareRepo $ do
+		hookWrite postCheckoutHook
+		hookWrite postMergeHook
+	return True
diff --git a/Utility/Batch.hs b/Utility/Batch.hs
--- a/Utility/Batch.hs
+++ b/Utility/Batch.hs
@@ -11,7 +11,7 @@
 
 import Common
 
-#if defined(linux_HOST_OS) || defined(__ANDROID__)
+#if defined(linux_HOST_OS)
 import Control.Concurrent.Async
 import System.Posix.Process
 #endif
@@ -29,7 +29,7 @@
  - systems, the action is simply ran.
  -}
 batch :: IO a -> IO a
-#if defined(linux_HOST_OS) || defined(__ANDROID__)
+#if defined(linux_HOST_OS)
 batch a = wait =<< batchthread
   where
 	batchthread = asyncBound $ do
@@ -51,11 +51,7 @@
 #ifndef mingw32_HOST_OS
 	nicers <- filterM (inPath . fst)
 		[ ("nice", [])
-#ifndef __ANDROID__
-		-- Android's ionice does not allow specifying a command,
-		-- so don't use it.
 		, ("ionice", ["-c3"])
-#endif
 		, ("nocache", [])
 		]
 	return $ \(command, params) ->
diff --git a/Utility/CopyFile.hs b/Utility/CopyFile.hs
--- a/Utility/CopyFile.hs
+++ b/Utility/CopyFile.hs
@@ -5,8 +5,6 @@
  - License: BSD-2-clause
  -}
 
-{-# LANGUAGE CPP #-}
-
 module Utility.CopyFile (
 	copyFileExternal,
 	createLinkOrCopy,
@@ -32,7 +30,6 @@
 		removeFile dest
 	boolSystem "cp" $ params ++ [File src, File dest]
   where
-#ifndef __ANDROID__
 	params = map snd $ filter fst
 		[ (BuildInfo.cp_reflink_auto, Param "--reflink=auto")
 		, (allmeta && BuildInfo.cp_a, Param "-a")
@@ -41,9 +38,6 @@
 		, (not allmeta && BuildInfo.cp_preserve_timestamps
 			, Param "--preserve=timestamps")
 		]
-#else
-	params = if allmeta then [] else []
-#endif
 	allmeta = meta == CopyAllMetaData
 
 {- Create a hard link if the filesystem allows it, and fall back to copying
diff --git a/Utility/DiskFree.hs b/Utility/DiskFree.hs
--- a/Utility/DiskFree.hs
+++ b/Utility/DiskFree.hs
@@ -13,8 +13,6 @@
 	getDiskSize
 ) where
 
-#ifndef __ANDROID__
-
 import System.DiskSpace
 import Utility.Applicative
 import Utility.Exception
@@ -24,15 +22,3 @@
 
 getDiskSize :: FilePath -> IO (Maybe Integer)
 getDiskSize = fmap diskTotal <$$> catchMaybeIO . getDiskUsage
-
-#else
-
-#warning Building without disk free space checking support
-
-getDiskFree :: FilePath -> IO (Maybe Integer)
-getDiskFree _ = return Nothing
-
-getDiskSize :: FilePath -> IO (Maybe Integer)
-getDiskSize _ = return Nothing
-
-#endif
diff --git a/Utility/Exception.hs b/Utility/Exception.hs
--- a/Utility/Exception.hs
+++ b/Utility/Exception.hs
@@ -5,7 +5,7 @@
  - License: BSD-2-clause
  -}
 
-{-# LANGUAGE CPP, ScopedTypeVariables #-}
+{-# LANGUAGE ScopedTypeVariables #-}
 {-# OPTIONS_GHC -fno-warn-tabs #-}
 
 module Utility.Exception (
@@ -29,11 +29,7 @@
 import Control.Monad.Catch as X hiding (Handler)
 import qualified Control.Monad.Catch as M
 import Control.Exception (IOException, AsyncException)
-#ifdef MIN_VERSION_GLASGOW_HASKELL
-#if MIN_VERSION_GLASGOW_HASKELL(7,10,0,0)
 import Control.Exception (SomeAsyncException)
-#endif
-#endif
 import Control.Monad
 import Control.Monad.IO.Class (liftIO, MonadIO)
 import System.IO.Error (isDoesNotExistError, ioeGetErrorType)
@@ -46,15 +42,7 @@
  - where there's a problem that the user is excpected to see in some
  - circumstances. -}
 giveup :: [Char] -> a
-#ifdef MIN_VERSION_base
-#if MIN_VERSION_base(4,9,0)
 giveup = errorWithoutStackTrace
-#else
-giveup = error
-#endif
-#else
-giveup = error
-#endif
 
 {- Catches IO errors and returns a Bool -}
 catchBoolIO :: MonadCatch m => m Bool -> m Bool
@@ -95,11 +83,7 @@
 catchNonAsync :: MonadCatch m => m a -> (SomeException -> m a) -> m a
 catchNonAsync a onerr = a `catches`
 	[ M.Handler (\ (e :: AsyncException) -> throwM e)
-#ifdef MIN_VERSION_GLASGOW_HASKELL
-#if MIN_VERSION_GLASGOW_HASKELL(7,10,0,0)
 	, M.Handler (\ (e :: SomeAsyncException) -> throwM e)
-#endif
-#endif
 	, M.Handler (\ (e :: SomeException) -> onerr e)
 	]
 
diff --git a/Utility/InodeCache.hs b/Utility/InodeCache.hs
--- a/Utility/InodeCache.hs
+++ b/Utility/InodeCache.hs
@@ -1,12 +1,13 @@
 {- Caching a file's inode, size, and modification time
  - to see when it's changed.
  -
- - Copyright 2013-2014 Joey Hess <id@joeyh.name>
+ - Copyright 2013-2018 Joey Hess <id@joeyh.name>
  -
  - License: BSD-2-clause
  -}
 
 {-# LANGUAGE CPP #-}
+{-# LANGUAGE TypeSynonymInstances #-}
 {-# OPTIONS_GHC -fno-warn-orphans #-}
 
 module Utility.InodeCache (
@@ -38,14 +39,20 @@
 ) where
 
 import Common
-import System.PosixCompat.Types
+import Utility.TimeStamp
 import Utility.QuickCheck
 
+import System.PosixCompat.Types
+import Data.Time.Clock.POSIX
+
 #ifdef mingw32_HOST_OS
 import Data.Word (Word64)
+import System.Directory
+#else
+import System.Posix.Files
 #endif
 
-data InodeCachePrim = InodeCachePrim FileID Integer EpochTime
+data InodeCachePrim = InodeCachePrim FileID FileSize MTime
 	deriving (Show, Eq, Ord)
 
 newtype InodeCache = InodeCache InodeCachePrim
@@ -65,14 +72,14 @@
  - due to some filesystems being remounted.
  -
  - The weak mtime comparison treats any mtimes that are within 2 seconds
- - of one-anther as the same. This is because FAT has only a 2 second
+ - of one-another as the same. This is because FAT has only a 2 second
  - resolution. When a FAT filesystem is used on Linux, higher resolution
- - timestamps are cached and used by Linux, but this is lost on unmount,
- - so after a remount, the timestamp can appear to have changed.
+ - timestamps maybe be are cached and used by Linux, but they are lost
+ - on unmount, so after a remount, the timestamp can appear to have changed.
  -}
 compareWeak :: InodeCache -> InodeCache -> Bool
 compareWeak (InodeCache (InodeCachePrim _ size1 mtime1)) (InodeCache (InodeCachePrim _ size2 mtime2)) =
-	size1 == size2 && (abs (mtime1 - mtime2) < 2)
+	size1 == size2 && (abs (lowResTime mtime1 - lowResTime mtime2) < 2)
 
 compareBy :: InodeComparisonType -> InodeCache -> InodeCache -> Bool
 compareBy Strongly = compareStrong
@@ -90,24 +97,67 @@
 inodeCacheToKey :: InodeComparisonType -> InodeCache -> InodeCacheKey 
 inodeCacheToKey ct (InodeCache prim) = InodeCacheKey ct prim
 
-inodeCacheToMtime :: InodeCache -> EpochTime
-inodeCacheToMtime (InodeCache (InodeCachePrim _ _ mtime)) = mtime
+inodeCacheToMtime :: InodeCache -> POSIXTime
+inodeCacheToMtime (InodeCache (InodeCachePrim _ _ mtime)) = highResTime mtime
 
+{- For backwards compatability, support low-res mtime with no
+ - fractional seconds. -}
+data MTime = MTimeLowRes EpochTime | MTimeHighRes POSIXTime
+	deriving (Show, Ord)
+
+{- A low-res time compares equal to any high-res time in the same second. -}
+instance Eq MTime where
+	MTimeLowRes a == MTimeLowRes b = a == b
+	MTimeHighRes a == MTimeHighRes b = a == b
+	MTimeHighRes a == MTimeLowRes b = lowResTime a == b
+	MTimeLowRes a == MTimeHighRes b = a == lowResTime b
+
+class MultiResTime t where
+	lowResTime :: t -> EpochTime
+	highResTime :: t -> POSIXTime
+
+instance MultiResTime EpochTime where
+	lowResTime = id
+	highResTime = realToFrac
+
+instance MultiResTime POSIXTime where
+	lowResTime = fromInteger . floor
+	highResTime = id
+
+instance MultiResTime MTime where
+	lowResTime (MTimeLowRes t) = t
+	lowResTime (MTimeHighRes t) = lowResTime t
+	highResTime (MTimeLowRes t) = highResTime t
+	highResTime (MTimeHighRes t) = t
+
 showInodeCache :: InodeCache -> String
-showInodeCache (InodeCache (InodeCachePrim inode size mtime)) = unwords
-	[ show inode
-	, show size
-	, show mtime
-	]
+showInodeCache (InodeCache (InodeCachePrim inode size (MTimeHighRes mtime))) = 
+	let (t, d) = separate (== '.') (takeWhile (/= 's') (show mtime))
+	in unwords
+		[ show inode
+		, show size
+		, t
+		, d
+		]
+showInodeCache (InodeCache (InodeCachePrim inode size (MTimeLowRes mtime))) =
+	unwords
+		[ show inode
+		, show size
+		, show mtime
+		]
 
 readInodeCache :: String -> Maybe InodeCache
 readInodeCache s = case words s of
-	(inode:size:mtime:_) ->
-		let prim = InodeCachePrim
-			<$> readish inode
-			<*> readish size
-			<*> readish mtime
-		in InodeCache <$> prim
+	(inode:size:mtime:[]) -> do
+		i <- readish inode
+		sz <- readish size
+		t <- readish mtime
+		return $ InodeCache $ InodeCachePrim i sz (MTimeLowRes t)
+	(inode:size:mtime:mtimedecimal:_) -> do
+		i <- readish inode
+		sz <- readish size
+		t <- parsePOSIXTime' mtime mtimedecimal
+		return $ InodeCache $ InodeCachePrim i sz (MTimeHighRes t)
 	_ -> Nothing
 
 genInodeCache :: FilePath -> TSDelta -> IO (Maybe InodeCache)
@@ -119,10 +169,12 @@
 	| isRegularFile s = do
 		delta <- getdelta
 		sz <- getFileSize' f s
-		return $ Just $ InodeCache $ InodeCachePrim
-			(fileID s)
-			sz
-			(modificationTime s + delta)
+#ifdef mingw32_HOST_OS
+		mtime <- MTimeHighRes . utcTimeToPOSIXSeconds <$> getModificationTime f
+#else
+ 		let mtime = (MTimeHighRes (modificationTimeHiRes s + highResTime delta))
+#endif
+		return $ Just $ InodeCache $ InodeCachePrim (fileID s) sz mtime
 	| otherwise = pure Nothing
 
 {- Some filesystem get new random inodes each time they are mounted.
@@ -194,7 +246,7 @@
 			mnew <- gennewcache
 			return $ case mnew of
 				Just (InodeCache (InodeCachePrim _ _ currmtime)) ->
-					oldmtime - currmtime
+					lowResTime oldmtime - lowResTime currmtime
 				Nothing -> 0
 #else
 		unchanged = oldinode == newinode && oldsize == newsize && oldmtime == newmtime
@@ -210,9 +262,23 @@
 		let prim = InodeCachePrim
 			<$> arbitrary
 			<*> arbitrary
-			-- timestamp cannot be negative
-			<*> (abs . fromInteger <$> arbitrary)
+			<*> arbitrary
 		in InodeCache <$> prim
+
+instance Arbitrary MTime where
+	arbitrary = frequency
+		-- timestamp is not usually negative
+                [ (50, MTimeLowRes <$> (abs . fromInteger <$> arbitrary))
+                , (50, MTimeHighRes <$> (abs <$> arbposixtime))
+		]
+	  where
+		-- include fractional part, which the usual instance does not
+		arbposixtime = do
+			t <- arbitrary
+			f <- arbitrary
+			return $ if f == 0
+				then t
+				else t + recip f
 
 #ifdef mingw32_HOST_OS
 instance Arbitrary FileID where
diff --git a/Utility/Lsof.hs b/Utility/Lsof.hs
--- a/Utility/Lsof.hs
+++ b/Utility/Lsof.hs
@@ -5,8 +5,6 @@
  - License: BSD-2-clause
  -}
 
-{-# LANGUAGE CPP #-}
-
 module Utility.Lsof where
 
 import Common
@@ -54,13 +52,6 @@
 
 type LsofParser = String -> [(FilePath, LsofOpenMode, ProcessInfo)]
 
-parse :: LsofParser
-#ifdef __ANDROID__
-parse = parseDefault
-#else
-parse = parseFormatted
-#endif
-
 {- Parsing null-delimited output like:
  -
  - pPID\0cCMDLINE\0
@@ -71,8 +62,8 @@
  - Where each new process block is started by a pid, and a process can
  - have multiple files open.
  -}
-parseFormatted :: LsofParser
-parseFormatted s = bundle $ go [] $ lines s
+parse :: LsofParser
+parse s = bundle $ go [] $ lines s
   where
 	bundle = concatMap (\(fs, p) -> map (\(f, m) -> (f, m, p)) fs)
 
@@ -110,14 +101,3 @@
 	splitnull = splitc '\0'
 
 	parsefail = error $ "failed to parse lsof output: " ++ show s
-
-{- Parses lsof's default output format. -}
-parseDefault :: LsofParser
-parseDefault = mapMaybe parseline . drop 1 . lines
-  where
-	parseline l = case words l of
-		(command : spid : _user : _fd : _type : _device : _size : _node : rest) -> 
-			case readish spid of
-				Nothing -> Nothing
-				Just pid -> Just (unwords rest, OpenUnknown, ProcessInfo pid command)
-		_ -> Nothing
diff --git a/Utility/Mounts.hs b/Utility/Mounts.hs
--- a/Utility/Mounts.hs
+++ b/Utility/Mounts.hs
@@ -5,7 +5,6 @@
  - License: BSD-2-clause
  -}
 
-{-# LANGUAGE CPP #-}
 {-# OPTIONS_GHC -fno-warn-tabs #-}
 
 module Utility.Mounts (getMounts, Mntent(..)) where
@@ -16,11 +15,7 @@
 import Utility.Exception
 
 getMounts :: IO [Mntent] 
-#ifndef __ANDROID__
 getMounts = System.MountPoints.getMounts
 	-- That will crash when the linux build is running on Android,
 	-- so fall back to this.
 	`catchNonAsync` const System.MountPoints.getProcMounts
-#else
-getMounts = System.MountPoints.getProcMounts
-#endif
diff --git a/Utility/PartialPrelude.hs b/Utility/PartialPrelude.hs
--- a/Utility/PartialPrelude.hs
+++ b/Utility/PartialPrelude.hs
@@ -38,8 +38,9 @@
 
 {- Attempts to read a value from a String.
  -
- - Unlike Text.Read.readMaybe, this ignores leading/trailing whitespace,
- - and throws away any trailing text after the part that can be read.
+ - Unlike Text.Read.readMaybe, this ignores some trailing text
+ - after the part that can be read. However, if the trailing text looks
+ - like another readable value, it fails.
  -}
 readish :: Read a => String -> Maybe a
 readish s = case reads s of
diff --git a/Utility/QuickCheck.hs b/Utility/QuickCheck.hs
--- a/Utility/QuickCheck.hs
+++ b/Utility/QuickCheck.hs
@@ -31,7 +31,7 @@
 	arbitrary = S.fromList <$> arbitrary
 #endif
 
-{- Times before the epoch are excluded. -}
+{- Times before the epoch are excluded, and no fraction is included. -}
 instance Arbitrary POSIXTime where
 	arbitrary = fromInteger <$> nonNegative arbitrarySizedIntegral
 
diff --git a/Utility/Shell.hs b/Utility/Shell.hs
--- a/Utility/Shell.hs
+++ b/Utility/Shell.hs
@@ -20,21 +20,11 @@
 import System.FilePath
 #endif
 
-shellPath_portable :: FilePath
-shellPath_portable = "/bin/sh"
-
-shellPath_local :: FilePath
-#ifndef __ANDROID__
-shellPath_local = shellPath_portable
-#else
-shellPath_local = "/system/bin/sh"
-#endif
-
-shebang_portable :: String
-shebang_portable = "#!" ++ shellPath_portable
+shellPath :: FilePath
+shellPath = "/bin/sh"
 
-shebang_local :: String
-shebang_local = "#!" ++ shellPath_local
+shebang :: String
+shebang = "#!" ++ shellPath
 
 -- | On Windows, shebang is not handled by the kernel, so to support
 -- shell scripts etc, have to look at the program being run and
diff --git a/Utility/ThreadScheduler.hs b/Utility/ThreadScheduler.hs
--- a/Utility/ThreadScheduler.hs
+++ b/Utility/ThreadScheduler.hs
@@ -18,10 +18,8 @@
 #endif
 #ifndef mingw32_HOST_OS
 import System.Posix.Signals
-#ifndef __ANDROID__
 import System.Posix.Terminal
 #endif
-#endif
 
 newtype Seconds = Seconds { fromSeconds :: Int }
 	deriving (Eq, Ord, Show)
@@ -63,10 +61,8 @@
 	let check sig = void $
 		installHandler sig (CatchOnce $ putMVar lock ()) Nothing
 	check softwareTermination
-#ifndef __ANDROID__
 	whenM (queryTerminal stdInput) $
 		check keyboardSignal
-#endif
 	takeMVar lock
 #endif
 
diff --git a/Utility/TimeStamp.hs b/Utility/TimeStamp.hs
new file mode 100644
--- /dev/null
+++ b/Utility/TimeStamp.hs
@@ -0,0 +1,45 @@
+{- timestamp parsing and formatting
+ -
+ - Copyright 2015-2016 Joey Hess <id@joeyh.name>
+ -
+ - License: BSD-2-clause
+ -}
+
+{-# LANGUAGE CPP #-}
+
+module Utility.TimeStamp where
+
+import Utility.PartialPrelude
+import Utility.Misc
+
+import Data.Time.Clock.POSIX
+import Data.Time
+import Data.Ratio
+#if ! MIN_VERSION_time(1,5,0)
+import System.Locale
+#endif
+
+{- Parses how POSIXTime shows itself: "1431286201.113452s"
+ - Also handles the format with no fractional seconds. -}
+parsePOSIXTime :: String -> Maybe POSIXTime
+parsePOSIXTime = uncurry parsePOSIXTime' . separate (== '.')
+
+{- Parses the integral and decimal part of a POSIXTime -}
+parsePOSIXTime' :: String -> String -> Maybe POSIXTime
+parsePOSIXTime' sn sd = do
+	n <- fromIntegral <$> readi sn
+	let sd' = takeWhile (/= 's') sd
+	if null sd'
+		then return n
+		else do
+			d <- readi sd'
+			let r = d % (10 ^ (length sd'))
+			return $ if n < 0
+				then n - fromRational r
+				else n + fromRational r
+  where
+	readi :: String -> Maybe Integer
+	readi = readish
+
+formatPOSIXTime :: String -> POSIXTime -> String
+formatPOSIXTime fmt t = formatTime defaultTimeLocale fmt (posixSecondsToUTCTime t)
diff --git a/Utility/Touch.hs b/Utility/Touch.hs
--- a/Utility/Touch.hs
+++ b/Utility/Touch.hs
@@ -1,6 +1,6 @@
-{- More control over touching a file.
+{- Portability shim for touching a file.
  -
- - Copyright 2011 Joey Hess <id@joeyh.name>
+ - Copyright 2011-2018 Joey Hess <id@joeyh.name>
  -
  - License: BSD-2-clause
  -}
@@ -8,45 +8,36 @@
 {-# LANGUAGE CPP #-}
 
 module Utility.Touch (
-	TimeSpec(..),
 	touchBoth,
 	touch
 ) where
 
-#if ! defined(mingw32_HOST_OS) && ! defined(__ANDROID__)
-
-#if MIN_VERSION_unix(2,7,0)
+#if ! defined(mingw32_HOST_OS)
 
 import System.Posix.Files
-import System.Posix.Types
-
-newtype TimeSpec = TimeSpec EpochTime
+import Data.Time.Clock.POSIX
 
 {- Changes the access and modification times of an existing file.
-   Can follow symlinks, or not. Throws IO error on failure. -}
-touchBoth :: FilePath -> TimeSpec -> TimeSpec -> Bool -> IO ()
-touchBoth file (TimeSpec atime) (TimeSpec mtime) follow
-	| follow = setFileTimes file atime mtime
-	| otherwise = setSymbolicLinkTimesHiRes file (realToFrac atime) (realToFrac mtime)
+   Can follow symlinks, or not. -}
+touchBoth :: FilePath -> POSIXTime -> POSIXTime -> Bool -> IO ()
+touchBoth file atime mtime follow
+	| follow = setFileTimesHiRes file atime mtime
+	| otherwise = setSymbolicLinkTimesHiRes file atime mtime
 
-touch :: FilePath -> TimeSpec -> Bool -> IO ()
+{- Changes the access and modification times of an existing file
+ - to the same value. Can follow symlinks, or not. -}
+touch :: FilePath -> POSIXTime -> Bool -> IO ()
 touch file mtime = touchBoth file mtime mtime
 
 #else
-import Utility.Touch.Old
-#endif
 
-#else
-
-import System.PosixCompat
-
-newtype TimeSpec = TimeSpec EpochTime
+import Data.Time.Clock.POSIX
 
 {- Noop for Windows -}
-touchBoth :: FilePath -> TimeSpec -> TimeSpec -> Bool -> IO ()
+touchBoth :: FilePath -> POSIXTime -> POSIXTime -> Bool -> IO ()
 touchBoth _ _ _ _ = return ()
 
-touch :: FilePath -> TimeSpec -> Bool -> IO ()
+touch :: FilePath -> POSIXTime -> Bool -> IO ()
 touch _ _ _ = return ()
 
 #endif
diff --git a/Utility/Touch/Old.hsc b/Utility/Touch/Old.hsc
deleted file mode 100644
--- a/Utility/Touch/Old.hsc
+++ /dev/null
@@ -1,123 +0,0 @@
-{- Compatability interface for old version of unix, to be removed eventally.
- -
- - Copyright 2011 Joey Hess <id@joeyh.name>
- -
- - License: BSD-2-clause
- -}
-
-{-# LANGUAGE ForeignFunctionInterface, CPP #-}
-
-module Utility.Touch.Old (
-	TimeSpec(..),
-	touchBoth,
-	touch
-) where
-
-#include <sys/types.h>
-#include <sys/stat.h>
-#include <fcntl.h>
-#include <sys/time.h>
-
-#ifndef _BSD_SOURCE
-#define _BSD_SOURCE
-#endif
-
-#if (defined UTIME_OMIT && defined UTIME_NOW && defined AT_FDCWD && defined AT_SYMLINK_NOFOLLOW)
-#define use_utimensat 1
-
-import Utility.FileSystemEncoding
-
-import Control.Monad (when)
-import Foreign
-#endif
-
-import Foreign.C
-
-newtype TimeSpec = TimeSpec CTime
-
-touchBoth :: FilePath -> TimeSpec -> TimeSpec -> Bool -> IO ()
-
-touch :: FilePath -> TimeSpec -> Bool -> IO ()
-touch file mtime = touchBoth file mtime mtime
-
-#ifdef use_utimensat
-
-at_fdcwd :: CInt
-at_fdcwd = #const AT_FDCWD
-
-at_symlink_nofollow :: CInt
-at_symlink_nofollow = #const AT_SYMLINK_NOFOLLOW
-
-instance Storable TimeSpec where
-	-- use the larger alignment of the two types in the struct
-	alignment _ = max sec_alignment nsec_alignment
-	  where
-		sec_alignment = alignment (1::CTime)
-		nsec_alignment = alignment (1::CLong)
-	sizeOf _ = #{size struct timespec}
-	peek ptr = do
-		sec <- #{peek struct timespec, tv_sec} ptr
-		return $ TimeSpec sec
-	poke ptr (TimeSpec sec) = do
-		#{poke struct timespec, tv_sec} ptr sec
-		#{poke struct timespec, tv_nsec} ptr (0 :: CLong)
-
-{- While its interface is beastly, utimensat is in recent
-   POSIX standards, unlike lutimes. -}
-foreign import ccall "utimensat" 
-	c_utimensat :: CInt -> CString -> Ptr TimeSpec -> CInt -> IO CInt
-
-touchBoth file atime mtime follow = 
-	allocaArray 2 $ \ptr ->
-	withFilePath file $ \f -> do
-		pokeArray ptr [atime, mtime]
-		r <- c_utimensat at_fdcwd f ptr flags
-		when (r /= 0) $ throwErrno "touchBoth"
-  where
-	flags
-       		| follow = 0
-		| otherwise = at_symlink_nofollow 
-
-#else
-#if 0
-{- Using lutimes is needed for BSD.
- - 
- - TODO: test if lutimes is available. May have to do it in configure.
- - TODO: TimeSpec uses a CTime, while tv_sec is a CLong. It is implementation
- - dependent whether these are the same; need to find a cast that works.
- - (Without the cast it works on linux i386, but
- - maybe not elsewhere.)
- -}
-
-instance Storable TimeSpec where
-	alignment _ = alignment (1::CLong)
-	sizeOf _ = #{size struct timeval}
-	peek ptr = do
-		sec <- #{peek struct timeval, tv_sec} ptr
-		return $ TimeSpec sec
-	poke ptr (TimeSpec sec) = do
-		#{poke struct timeval, tv_sec} ptr sec
-		#{poke struct timeval, tv_usec} ptr (0 :: CLong) 
-
-foreign import ccall "utimes" 
-	c_utimes :: CString -> Ptr TimeSpec -> IO CInt
-foreign import ccall "lutimes" 
-	c_lutimes :: CString -> Ptr TimeSpec -> IO CInt
-
-touchBoth file atime mtime follow = 
-	allocaArray 2 $ \ptr ->
-	withFilePath file $ \f -> do
-		pokeArray ptr [atime, mtime]
-		r <- syscall f ptr
-		when (r /= 0) $
-			throwErrno "touchBoth"
-  where
-	syscall
-       		| follow = c_lutimes
-		| otherwise = c_utimes
-
-#else
-#warning "utimensat and lutimes not available; building without symlink timestamp preservation support"
-touchBoth _ _ _ _ = return ()
-#endif
-#endif
diff --git a/Utility/UserInfo.hs b/Utility/UserInfo.hs
--- a/Utility/UserInfo.hs
+++ b/Utility/UserInfo.hs
@@ -47,8 +47,8 @@
 #endif
 
 myUserGecos :: IO (Maybe String)
--- userGecos crashes on Android and is not available on Windows.
-#if defined(__ANDROID__) || defined(mingw32_HOST_OS)
+-- userGecos is not available on Windows.
+#if defined(mingw32_HOST_OS)
 myUserGecos = return Nothing
 #else
 myUserGecos = eitherToMaybe <$> myVal [] userGecos
diff --git a/Utility/WebApp.hs b/Utility/WebApp.hs
--- a/Utility/WebApp.hs
+++ b/Utility/WebApp.hs
@@ -30,9 +30,6 @@
 import Blaze.ByteString.Builder (Builder)
 import Control.Arrow ((***))
 import Control.Concurrent
-#ifdef __ANDROID__
-import Data.Endian
-#endif
 
 localhost :: HostName
 localhost = "localhost"
@@ -42,11 +39,6 @@
 #ifdef darwin_HOST_OS
 browserProc url = proc "open" [url]
 #else
-#ifdef __ANDROID__
--- Warning: The `am` command does not work very reliably on Android.
-browserProc url = proc "am"
-	["start", "-a", "android.intent.action.VIEW", "-d", url]
-#else
 #ifdef mingw32_HOST_OS
 -- Warning: On Windows, no quoting or escaping of the url seems possible,
 -- so spaces in it will cause problems. One approach is to make the url
@@ -57,7 +49,6 @@
 browserProc url = proc "xdg-open" [url]
 #endif
 #endif
-#endif
 
 {- Binds to a socket on localhost, or possibly a different specified
  - hostname or address, and runs a webapp on it.
@@ -69,18 +60,10 @@
 runWebApp tlssettings h app observer = withSocketsDo $ do
 	sock <- getSocket h
 	void $ forkIO $ go webAppSettings sock app	
-	sockaddr <- fixSockAddr <$> getSocketName sock
+	sockaddr <- getSocketName sock
 	observer sockaddr
   where
 	go = (maybe runSettingsSocket (\ts -> runTLSSocket ts) tlssettings)
-
-fixSockAddr :: SockAddr -> SockAddr
-#ifdef __ANDROID__
-{- On Android, the port is currently incorrectly returned in network
- - byte order, which is wrong on little endian systems. -}
-fixSockAddr (SockAddrInet (PortNum port) addr) = SockAddrInet (PortNum $ swapEndian port) addr
-#endif
-fixSockAddr addr = addr
 
 -- disable buggy sloworis attack prevention code
 webAppSettings :: Settings
diff --git a/Utility/Yesod.hs b/Utility/Yesod.hs
--- a/Utility/Yesod.hs
+++ b/Utility/Yesod.hs
@@ -1,7 +1,6 @@
 {- Yesod stuff, that's typically found in the scaffolded site.
  -
- - Also a bit of a compatability layer to make it easier to support yesod
- - 1.1-1.4 in the same code base.
+ - Also a bit of a compatability layer for older versions of yesod.
  -
  - Copyright 2012-2014 Joey Hess <id@joeyh.name>
  -
@@ -13,28 +12,17 @@
 module Utility.Yesod 
 	( module Y
 	, liftH
-#ifndef __NO_TH__
 	, widgetFile
 	, hamletTemplate
-#endif
-#if ! MIN_VERSION_yesod_core(1,2,20)
-	, withUrlRenderer
-#endif
 	) where
 
 import Yesod as Y
 import Yesod.Form.Bootstrap3 as Y hiding (bfs)
-#ifndef __NO_TH__
 import Yesod.Default.Util
 import Language.Haskell.TH.Syntax (Q, Exp)
 import Data.Default (def)
 import Text.Hamlet hiding (Html)
-#endif
-#if ! MIN_VERSION_yesod(1,4,0)
-import Data.Text (Text)
-#endif
 
-#ifndef __NO_TH__
 widgetFile :: String -> Q Exp
 widgetFile = widgetFileNoReload $ def
 	{ wfsHamletSettings = defaultHamletSettings
@@ -44,7 +32,6 @@
 
 hamletTemplate :: FilePath -> FilePath
 hamletTemplate f = globFile "hamlet" f
-#endif
 
 {- Lift Handler to Widget -}
 #if MIN_VERSION_yesod_core(1,6,0)
@@ -53,8 +40,3 @@
 liftH :: Monad m => HandlerT site m a -> WidgetT site m a
 #endif
 liftH = handlerToWidget
-
-#if ! MIN_VERSION_yesod_core(1,2,20)
-withUrlRenderer :: MonadHandler m => ((Route (HandlerSite m) -> [(Text, Text)] -> Text) -> output) -> m output
-withUrlRenderer = giveUrlRenderer
-#endif
diff --git a/doc/git-annex-add.mdwn b/doc/git-annex-add.mdwn
--- a/doc/git-annex-add.mdwn
+++ b/doc/git-annex-add.mdwn
@@ -24,7 +24,7 @@
 (This is not the case however when a repository is in a filesystem not
 supporting symlinks, or is in direct mode.)
 To add a file to the annex in unlocked form, `git add` can be used instead 
-(that only works when the repository has annex.version 6 or higher).
+(that only works in repository v7 or higher).
 
 This command can also be used to add symbolic links, both symlinks to
 annexed content, and other symlinks.
diff --git a/doc/git-annex-adjust.mdwn b/doc/git-annex-adjust.mdwn
--- a/doc/git-annex-adjust.mdwn
+++ b/doc/git-annex-adjust.mdwn
@@ -4,7 +4,7 @@
 
 # SYNOPSIS
 
-git annex adjust `--unlock|--fix`
+git annex adjust `--unlock|--fix|--hide-missing [--unlock|--fix]`
 
 # DESCRIPTION
 
@@ -20,10 +20,15 @@
 usual. Any commits that you make will initially only be made to the
 adjusted branch. 
 
-To propagate changes from the adjusted branch back to the original branch,
+To propagate commits from the adjusted branch back to the original branch,
 and to other repositories, as well as to merge in changes from other
-repositories, use `git annex sync`.
+repositories, run `git annex sync`.
 
+Re-running this command with the same options
+while inside the adjusted branch will update the adjusted branch
+as necessary (eg for `--hide-missing`), and will also propagate commits
+back to the original branch.
+
 This command can only be used in a v6 git-annex repository.
 
 # OPTIONS
@@ -39,6 +44,26 @@
   object directory. This can be useful if a repository is checked out in an
   unusual way that prevents the symlinks committed to git from pointing at
   the annex objects.
+
+* `--hide-missing`
+
+  Only include annexed files in the adjusted branch when their content
+  is present.
+
+  The adjusted branch is not immediately changed when content availability
+  changes, so if you `git annex drop` files, they will become broken
+  links in the usual way. And when files that were missing are copied into the
+  repository from elsewhere, they won't immediatly become visible in the
+  branch.
+  
+  To update the adjusted branch to reflect changes to content availability, 
+  run `git annex adjust --hide-missing` again.
+
+  Despite missing files being hidden, `git annex sync --content` will
+  still operate on them, and can be used to download missing
+  files from remotes.
+
+  This option can be combined with --unlock or --fix.
 
 # SEE ALSO
 
diff --git a/doc/git-annex-pre-commit.mdwn b/doc/git-annex-pre-commit.mdwn
--- a/doc/git-annex-pre-commit.mdwn
+++ b/doc/git-annex-pre-commit.mdwn
@@ -17,7 +17,7 @@
 When in a view, updates metadata to reflect changes
 made to files in the view.
 
-When in a repository that has not been upgraded to annex.version 6, 
+When in a repository that has not been upgraded to v7, 
 also handles injecting changes to unlocked files into the annex. 
 
 # SEE ALSO
diff --git a/doc/git-annex-smudge.mdwn b/doc/git-annex-smudge.mdwn
--- a/doc/git-annex-smudge.mdwn
+++ b/doc/git-annex-smudge.mdwn
@@ -6,11 +6,13 @@
 
 git annex smudge [--clean] file
 
+git annex smudge --update
+
 # DESCRIPTION
 
 This command lets git-annex be used as a git filter driver which lets
-annexed files in the git repository to be unlocked at all times, instead
-of being symlinks.
+annexed files in the git repository to be unlocked, instead
+of being symlinks, and lets `git add` store files in the annex.
 
 When adding a file with `git add`, the annex.largefiles config is
 consulted to decide if a given file should be added to git as-is,
@@ -31,6 +33,16 @@
 
 	* filter=annex
 	.* !filter
+
+The smudge filter does not provide git with the content of annexed files,
+because that would be slow and triggers memory leaks in git. Instead,
+it records which worktree files need to be updated, and 
+`git annex smudge --update` later updates the work tree to contain
+the content. That is run by several git hooks, including post-checkout
+and post-merge. However, a few git commands, notably `git stash` and
+`git cherry-pick`, do not run any hooks, so after using those commands
+you can manually run `git annex smudge --update` to update the working
+tree.
 
 # SEE ALSO
 
diff --git a/doc/git-annex-sync.mdwn b/doc/git-annex-sync.mdwn
--- a/doc/git-annex-sync.mdwn
+++ b/doc/git-annex-sync.mdwn
@@ -70,15 +70,15 @@
 * `--content`, `--no-content`
 
   Normally, syncing does not transfer the contents of annexed files.
-  The --content option causes the content of files in the work tree
+  The --content option causes the content of annexed files
   to also be uploaded and downloaded as necessary.
 
   The `annex.synccontent` configuration can be set to true to make content
   be synced by default.
 
-  Normally this tries to get each annexed file in the work tree
-  that the local repository  does not yet have, and then copies each
-  file in the work tree to every remote that it is syncing with.
+  Normally this tries to get each annexed file that the local repository
+  does not yet have, and then copies each file to every remote that it
+  is syncing with.
   This behavior can be overridden by configuring the preferred content
   of a repository. See [[git-annex-preferred-content]](1).
 
@@ -88,7 +88,7 @@
 
 * `--content-of=path` `-C path`
 
-  While --content operates on all annexed files in the work tree,
+  While --content operates on all annexed files,
   --content-of allows limiting the transferred files to ones in a given
   location.
 
diff --git a/doc/git-annex-unlock.mdwn b/doc/git-annex-unlock.mdwn
--- a/doc/git-annex-unlock.mdwn
+++ b/doc/git-annex-unlock.mdwn
@@ -14,10 +14,10 @@
 You can then modify it and `git annex add` (or `git commit`) to save your
 changes.
 
-In repositories with annex.version 5 or earlier, unlocking a file is local
-to the repository, and is temporary. With version 6, unlocking a file
+In v5 repositories, unlocking a file is local
+to the repository, and is temporary. In v7 repositories, unlocking a file
 changes how it is stored in the git repository (from a symlink to a pointer
-file), so you can commit it like any other change. Also in version 6, you
+file), so you can commit it like any other change. Also in v7, you
 can use `git add` to add a file to the annex in unlocked form. This allows
 workflows where a file starts out unlocked, is modified as necessary, and
 is locked once it reaches its final version.
@@ -26,7 +26,7 @@
 so that its original content is preserved, while the copy can be modified.
 To use less space, annex.thin can be set to true; this makes a hard link
 to the content be made instead of a copy. (Only when supported by the file
-system, and only in repository version 6.) While this can save considerable
+system, and only in v7 and higher.) While this can save considerable
 disk space, any modification made to a file will cause the old version of the
 file to be lost from the local repository. So, enable annex.thin with care.
 
diff --git a/doc/git-annex.mdwn b/doc/git-annex.mdwn
--- a/doc/git-annex.mdwn
+++ b/doc/git-annex.mdwn
@@ -901,7 +901,7 @@
 
   Set to true to make commands like `git-annex add` that add files to the
   repository add them in unlocked form. The default is to add files in
-  locked form. This only has effect in version 6 repositories.
+  locked form. This only has effect in v7 repositories.
 
   When a repository has core.symlinks set to false, it implicitly
   sets annex.addunlocked to true.
@@ -1024,18 +1024,16 @@
 * `annex.thin`
 
   Set this to `true` to make unlocked files be a hard link to their content
-  in the annex, rather than a second copy. (Only when supported by the file
-  system, and only in repository version 6.) This can save considerable
+  in the annex, rather than a second copy. This can save considerable
   disk space, but when a modification is made to a file, you will lose the
   local (and possibly only) copy of the old version. So, enable with care.
 
   After setting (or unsetting) this, you should run `git annex fix` to
   fix up the annexed files in the work tree to be hard links (or copies).
-
-  Note that `annex.thin` is not honored when git updates an annexed file
-  in the working tree. So when `git checkout` or `git merge` updates the
-  working tree, a second copy of annexed files will result. You can run
-  `git-annex fix` to fix up the hard links after running such git commands.
+ 
+  Note that this has no effect when the filesystem does not support hard links.
+  And when multiple files in the work tree have the same content, only
+  one of them gets hard linked to the annex.
 
 * `annex.delayadd`
 
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: 6.20181011
+Version: 7.20181031
 Cabal-Version: >= 1.8
 License: GPL-3
 Maintainer: Joey Hess <id@joeyh.name>
@@ -218,7 +218,6 @@
   templates/configurators/ssh/add.hamlet
   templates/configurators/ssh/setupmodal.hamlet
   templates/configurators/ssh/confirm.hamlet
-  templates/configurators/upgrade/android.hamlet
   templates/configurators/enableia.hamlet
   templates/configurators/fsck.hamlet
   templates/configurators/addrepository/archive.hamlet
@@ -270,23 +269,12 @@
 Flag Production
   Description: Enable production build (slower build; faster binary)
 
-Flag Android
-  Description: Cross building for Android
-  Default: False
-
-Flag AndroidSplice
-  Description: Building to get TH splices for Android
-  Default: False
-
 Flag TorrentParser
   Description: Use haskell torrent library to parse torrent files
 
 Flag MagicMime
   Description: Use libmagic to determine file MIME types
 
-Flag ConcurrentOutput
-  Description: Use concurrent-output library
-
 Flag Benchmark
   Description: Enable benchmarking
   Default: False
@@ -299,18 +287,18 @@
   location: git://git-annex.branchable.com/
 
 custom-setup
-  Setup-Depends: base (>= 4.6), hslogger, split, unix-compat, process,
+  Setup-Depends: base (>= 4.9), hslogger, split, unix-compat, process,
     filepath, exceptions, bytestring, directory, IfElse, data-default,
     utf8-string, transformers, Cabal
 
 Executable git-annex
   Main-Is: git-annex.hs
   Build-Depends:
-   base (>= 4.6 && < 5.0),
+   base (>= 4.9 && < 5.0),
    network (>= 2.6.3.0),
    network-uri (>= 2.6),
    optparse-applicative (>= 0.11.0), 
-   containers (>= 0.5.0.0),
+   containers (>= 0.5.7.1),
    exceptions (>= 0.6),
    stm (>= 2.3),
    mtl (>= 2),
@@ -324,6 +312,7 @@
    SafeSemaphore,
    async,
    directory (>= 1.2),
+   disk-free-space,
    filepath,
    IfElse,
    hslogger,
@@ -347,9 +336,10 @@
    time,
    old-locale,
    esqueleto,
-   persistent-sqlite, 
+   persistent-sqlite (>= 2.1.3), 
    persistent,
    persistent-template,
+   microlens,
    aeson,
    vector,
    tagsoup,
@@ -365,6 +355,7 @@
    memory,
    split,
    attoparsec,
+   concurrent-output (>= 1.6),
    QuickCheck (>= 2.1),
    tasty (>= 0.7),
    tasty-hunit,
@@ -381,11 +372,8 @@
   if flag(Production)
     -- Lower memory systems can run out of memory with -O2, so
     -- optimise slightly less.
-    -- This needs -O1 before the -optlo, due to this bug:
-    -- https://ghc.haskell.org/trac/ghc/ticket/14821
-    -- But unfortunately, hackage currently refuses to accept -O1
     if arch(arm)
-      GHC-Options: -optlo-O2
+      GHC-Options: -O2 -optlo-O2
     else
       GHC-Options: -O2
 
@@ -401,9 +389,7 @@
       setenv,
       process (>= 1.6.2.0)
   else
-    Build-Depends: unix
-    if impl(ghc <= 7.6.3)
-      Other-Modules: Utility.Touch.Old
+    Build-Depends: unix (>= 2.7.2)
 
   if flag(S3)
     Build-Depends: aws (>= 0.9.2)
@@ -501,7 +487,7 @@
       Utility.Mounts
       Utility.OSX
 
-    if os(linux) || flag(Android)
+    if os(linux)
       Build-Depends: hinotify
       CPP-Options: -DWITH_INOTIFY
       Other-Modules: Utility.DirWatcher.INotify
@@ -529,30 +515,21 @@
       CPP-Options: -DWITH_DBUS -DWITH_DESKTOP_NOTIFY -DWITH_DBUS_NOTIFICATIONS
       Other-Modules: Utility.DBus
 
-  if flag(Android)
-    Build-Depends: data-endian
-    CPP-Options: -D__ANDROID__ -DANDROID_SPLICES -D__NO_TH__
-  else
-    Build-Depends: disk-free-space
-
-  if flag(AndroidSplice)
-    CPP-Options: -DANDROID_SPLICES
-
   if flag(Webapp)
     Build-Depends:
-     yesod (>= 1.2.6), 
-     yesod-static (>= 1.2.4),
-     yesod-form (>= 1.3.15),
-     yesod-core (>= 1.2.19),
-     path-pieces (>= 0.1.4),
-     warp (>= 3.0.0.5),
-     warp-tls (>= 1.4),
+     yesod (>= 1.4.3), 
+     yesod-static (>= 1.5.1),
+     yesod-form (>= 1.4.8),
+     yesod-core (>= 1.4.25),
+     path-pieces (>= 0.2.1),
+     warp (>= 3.2.8),
+     warp-tls (>= 3.2.2),
      wai,
      wai-extra,
      blaze-builder,
      clientsession,
      template-haskell,
-     shakespeare (>= 2.0.0)
+     shakespeare (>= 2.0.11)
     CPP-Options: -DWITH_WEBAPP
     Other-Modules:
       Command.WebApp
@@ -605,10 +582,6 @@
       Build-Depends: magic
       CPP-Options: -DWITH_MAGICMIME
 
-  if flag(ConcurrentOutput)
-    Build-Depends: concurrent-output (>= 1.6)
-    CPP-Options: -DWITH_CONCURRENTOUTPUT
-
   if flag(Benchmark)
     Build-Depends: criterion, deepseq
     CPP-Options: -DWITH_BENCHMARK
@@ -618,6 +591,7 @@
     Annex
     Annex.Action
     Annex.AdjustedBranch
+    Annex.AdjustedBranch.Name
     Annex.AutoMerge
     Annex.BloomFilter
     Annex.Branch
@@ -633,6 +607,7 @@
     Annex.Content.Direct
     Annex.Content.LowLevel
     Annex.Content.PointerFile
+    Annex.CurrentBranch
     Annex.Difference
     Annex.DirHashes
     Annex.Direct
@@ -901,7 +876,7 @@
     Logs.Schedule
     Logs.SingleValue
     Logs.SingleValue.Pure
-    Logs.TimeStamp
+    Logs.Smudge
     Logs.Transfer
     Logs.Transitions
     Logs.Trust
@@ -965,6 +940,7 @@
     Test.Framework
     Types
     Types.ActionItem
+    Types.AdjustedBranch
     Types.Availability
     Types.Backend
     Types.BranchState
@@ -989,6 +965,7 @@
     Types.NumCopies
     Types.RefSpec
     Types.Remote
+    Types.RepoVersion
     Types.ScheduledActivity
     Types.StandardGroups
     Types.StoreRetrieve
@@ -1005,6 +982,7 @@
     Upgrade.V3
     Upgrade.V4
     Upgrade.V5
+    Upgrade.V6
     Utility.Aeson
     Utility.Android
     Utility.Applicative
@@ -1081,6 +1059,7 @@
     Utility.SshHost
     Utility.Su
     Utility.SystemDirectory
+    Utility.TimeStamp
     Utility.TList
     Utility.Tense
     Utility.ThreadLock
diff --git a/stack.yaml b/stack.yaml
--- a/stack.yaml
+++ b/stack.yaml
@@ -1,6 +1,5 @@
 flags:
   git-annex:
-    concurrentoutput: true
     production: true
     assistant: true
     pairing: true
@@ -10,8 +9,6 @@
     webapp: true
     magicmime: false
     dbus: false
-    android: false
-    androidsplice: false
 packages:
 - '.'
 extra-deps:
diff --git a/templates/configurators/upgrade/android.hamlet b/templates/configurators/upgrade/android.hamlet
deleted file mode 100644
--- a/templates/configurators/upgrade/android.hamlet
+++ /dev/null
@@ -1,10 +0,0 @@
-<div .col-sm-9>
-  <div .content-box>
-    <h2>
-      Upgrading git-annex
-    <p>
-      To start the upgrade #
-      <a .btn .btn-primary href="#{url}">
-        Download #{takeFileName url}
-    <p>
-      Once the download is complete, open the file to upgrade git-annex.
diff --git a/templates/page.hamlet b/templates/page.hamlet
--- a/templates/page.hamlet
+++ b/templates/page.hamlet
@@ -16,9 +16,8 @@
               #{name}
       $maybe reldir <- relDir webapp
         <ul .nav .navbar-nav .navbar-right>
-          $if hasFileBrowser
-            <li>
-              ^{actionButton FileBrowserR (Just "Files") (Just "Click to open a file browser") "" "glyphicon-folder-open icon-white"}
+          <li>
+            ^{actionButton FileBrowserR (Just "Files") (Just "Click to open a file browser") "" "glyphicon-folder-open icon-white"}
           <li .dropdown #menu1>
             <a .dropdown-toggle data-toggle="dropdown" href="#menu1">
               Repository: #{reldir}