diff --git a/Command/Add.hs b/Command/Add.hs
index 73edb5eaaf..7fa7cb3a86 100644
--- a/Command/Add.hs
+++ b/Command/Add.hs
@@ -32,20 +32,20 @@ seek = [withFilesNotInGit start, withFilesUnlocked start]
  - to its content. -}
 start :: FilePath -> CommandStart
 start file = notBareRepo $ ifAnnexed file fixup add
-	where
-		add = do
-			s <- liftIO $ getSymbolicLinkStatus file
-			if isSymbolicLink s || not (isRegularFile s)
-				then stop
-				else do
-					showStart "add" file
-					next $ perform file
-		fixup (key, _) = do
-			-- fixup from an interrupted add; the symlink
-			-- is present but not yet added to git
-			showStart "add" file
-			liftIO $ removeFile file
-			next $ next $ cleanup file key =<< inAnnex key
+  where
+	add = do
+		s <- liftIO $ getSymbolicLinkStatus file
+		if isSymbolicLink s || not (isRegularFile s)
+			then stop
+			else do
+				showStart "add" file
+				next $ perform file
+	fixup (key, _) = do
+		-- fixup from an interrupted add; the symlink
+		-- is present but not yet added to git
+		showStart "add" file
+		liftIO $ removeFile file
+		next $ next $ cleanup file key =<< inAnnex key
 
 {- The file that's being added is locked down before a key is generated,
  - to prevent it from being modified in between. It's hard linked into a
@@ -67,15 +67,15 @@ ingest :: KeySource -> Annex (Maybe Key)
 ingest source = do
 	backend <- chooseBackend $ keyFilename source
 	genKey source backend >>= go
-	where
-		go Nothing = do
-			liftIO $ nukeFile $ contentLocation source
-			return Nothing
-		go (Just (key, _)) = do
-			handle (undo (keyFilename source) key) $
-				moveAnnex key $ contentLocation source
-			liftIO $ nukeFile $ keyFilename source
-			return $ Just key
+  where
+	go Nothing = do
+		liftIO $ nukeFile $ contentLocation source
+		return Nothing
+	go (Just (key, _)) = do
+		handle (undo (keyFilename source) key) $
+			moveAnnex key $ contentLocation source
+		liftIO $ nukeFile $ keyFilename source
+		return $ Just key
 
 perform :: FilePath -> CommandPerform
 perform file = 
@@ -91,12 +91,12 @@ undo file key e = do
 		handle tryharder $ fromAnnex key file
 		logStatus key InfoMissing
 	throw e
-	where
-		-- fromAnnex could fail if the file ownership is weird
-		tryharder :: IOException -> Annex ()
-		tryharder _ = do
-			src <- inRepo $ gitAnnexLocation key
-			liftIO $ moveFile src file
+  where
+	-- fromAnnex could fail if the file ownership is weird
+	tryharder :: IOException -> Annex ()
+	tryharder _ = do
+		src <- inRepo $ gitAnnexLocation key
+		liftIO $ moveFile src file
 
 {- Creates the symlink to the annexed content, returns the link target. -}
 link :: FilePath -> Key -> Bool -> Annex String
diff --git a/Command/AddUnused.hs b/Command/AddUnused.hs
index f705003545..519c67e1b2 100644
--- a/Command/AddUnused.hs
+++ b/Command/AddUnused.hs
@@ -25,8 +25,8 @@ start = startUnused "addunused" perform (performOther "bad") (performOther "tmp"
 
 perform :: Key -> CommandPerform
 perform key = next $ Command.Add.cleanup file key True
-	where
-		file = "unused." ++ key2file key
+  where
+	file = "unused." ++ key2file key
 
 {- The content is not in the annex, but in another directory, and
  - it seems better to error out, rather than moving bad/tmp content into
diff --git a/Command/AddUrl.hs b/Command/AddUrl.hs
index bef1d68752..0003237ebf 100644
--- a/Command/AddUrl.hs
+++ b/Command/AddUrl.hs
@@ -40,31 +40,31 @@ seek = [withField fileOption return $ \f ->
 
 start :: Maybe FilePath -> Maybe Int -> String -> CommandStart
 start optfile pathdepth s = notBareRepo $ go $ fromMaybe bad $ parseURI s
-	where
-		bad = fromMaybe (error $ "bad url " ++ s) $
-			parseURI $ escapeURIString isUnescapedInURI s
-		go url = do
-			let file = fromMaybe (url2file url pathdepth) optfile
-			showStart "addurl" file
-			next $ perform s file
+  where
+	bad = fromMaybe (error $ "bad url " ++ s) $
+		parseURI $ escapeURIString isUnescapedInURI s
+	go url = do
+		let file = fromMaybe (url2file url pathdepth) optfile
+		showStart "addurl" file
+		next $ perform s file
 
 perform :: String -> FilePath -> CommandPerform
 perform url file = ifAnnexed file addurl geturl
-	where
-		geturl = do
-			liftIO $ createDirectoryIfMissing True (parentDir file)
-			ifM (Annex.getState Annex.fast)
-				( nodownload url file , download url file )
-		addurl (key, _backend) = do
-			headers <- getHttpHeaders
-			ifM (liftIO $ Url.check url headers $ keySize key)
-				( do
-					setUrlPresent key url
-					next $ return True
-				, do
-					warning $ "failed to verify url: " ++ url
-					stop
-				)
+  where
+	geturl = do
+		liftIO $ createDirectoryIfMissing True (parentDir file)
+		ifM (Annex.getState Annex.fast)
+			( nodownload url file , download url file )
+	addurl (key, _backend) = do
+		headers <- getHttpHeaders
+		ifM (liftIO $ Url.check url headers $ keySize key)
+			( do
+				setUrlPresent key url
+				next $ return True
+			, do
+				warning $ "failed to verify url: " ++ url
+				stop
+			)
 
 download :: String -> FilePath -> CommandPerform
 download url file = do
@@ -103,10 +103,10 @@ url2file url pathdepth = case pathdepth of
 		| depth > 0 -> frombits $ drop depth
 		| depth < 0 -> frombits $ reverse . take (negate depth) . reverse
 		| otherwise -> error "bad --pathdepth"
-	where
-		fullurl = uriRegName auth ++ uriPath url ++ uriQuery url
-		frombits a = join "/" $ a urlbits
-		urlbits = map (filesize . escape) $ filter (not . null) $ split "/" fullurl
-		auth = fromMaybe (error $ "bad url " ++ show url) $ uriAuthority url
-		filesize = take 255
-		escape = replace "/" "_" . replace "?" "_"
+  where
+	fullurl = uriRegName auth ++ uriPath url ++ uriQuery url
+	frombits a = join "/" $ a urlbits
+	urlbits = map (filesize . escape) $ filter (not . null) $ split "/" fullurl
+	auth = fromMaybe (error $ "bad url " ++ show url) $ uriAuthority url
+	filesize = take 255
+	escape = replace "/" "_" . replace "?" "_"
diff --git a/Command/Assistant.hs b/Command/Assistant.hs
index b039e27310..ea8a87a3d8 100644
--- a/Command/Assistant.hs
+++ b/Command/Assistant.hs
@@ -65,7 +65,7 @@ autoStart = do
 					)
 		, nothing
 		)
-	where
-		go program dir = do
-			changeWorkingDirectory dir
-			boolSystem program [Param "assistant"]
+  where
+	go program dir = do
+		changeWorkingDirectory dir
+		boolSystem program [Param "assistant"]
diff --git a/Command/Commit.hs b/Command/Commit.hs
index d3ce3d7bb1..1659061394 100644
--- a/Command/Commit.hs
+++ b/Command/Commit.hs
@@ -24,6 +24,6 @@ start = next $ next $ do
 	Annex.Branch.commit "update"
 	_ <- runhook <=< inRepo $ Git.hookPath "annex-content"
 	return True
-	where
-		runhook (Just hook) = liftIO $ boolSystem hook []
-		runhook Nothing = return True
+  where
+	runhook (Just hook) = liftIO $ boolSystem hook []
+	runhook Nothing = return True
diff --git a/Command/Copy.hs b/Command/Copy.hs
index 4352aaa31b..dd55992649 100644
--- a/Command/Copy.hs
+++ b/Command/Copy.hs
@@ -29,7 +29,7 @@ start :: Maybe Remote -> Maybe Remote -> FilePath -> (Key, Backend) -> CommandSt
 start to from file (key, backend) = autoCopies file key (<) $
 	stopUnless shouldCopy $ 
 		Command.Move.start to from False file (key, backend)
-	where
-		shouldCopy = case to of
-			Nothing -> checkAuto $ wantGet (Just file)
-			Just r -> checkAuto $ wantSend (Just file) (Remote.uuid r)
+  where
+	shouldCopy = case to of
+		Nothing -> checkAuto $ wantGet (Just file)
+		Just r -> checkAuto $ wantSend (Just file) (Remote.uuid r)
diff --git a/Command/Drop.hs b/Command/Drop.hs
index 9e58701dbd..6c210b1e1e 100644
--- a/Command/Drop.hs
+++ b/Command/Drop.hs
@@ -76,8 +76,8 @@ performRemote key numcopies remote = lockContent key $ do
 	stopUnless (canDropKey key numcopies have tocheck [uuid]) $ do
 		ok <- Remote.removeKey remote key
 		next $ cleanupRemote key remote ok
-	where
-		uuid = Remote.uuid remote
+ where
+	uuid = Remote.uuid remote
 
 cleanupLocal :: Key -> CommandCleanup
 cleanupLocal key = do
@@ -106,20 +106,20 @@ canDropKey key numcopiesM have check skip = do
 
 findCopies :: Key -> Int -> [UUID] -> [UUID] -> [Remote] -> Annex Bool
 findCopies key need skip = helper []
-	where
-		helper bad have []
-			| length have >= need = return True
-			| otherwise = notEnoughCopies key need have skip bad
-		helper bad have (r:rs)
-			| length have >= need = return True
-			| otherwise = do
-				let u = Remote.uuid r
-				let duplicate = u `elem` have
-				haskey <- Remote.hasKey r key
-				case (duplicate, haskey) of
-					(False, Right True) -> helper bad (u:have) rs
-					(False, Left _)     -> helper (r:bad) have rs
-					_                   -> helper bad have rs
+  where
+	helper bad have []
+		| length have >= need = return True
+		| otherwise = notEnoughCopies key need have skip bad
+	helper bad have (r:rs)
+		| length have >= need = return True
+		| otherwise = do
+			let u = Remote.uuid r
+			let duplicate = u `elem` have
+			haskey <- Remote.hasKey r key
+			case (duplicate, haskey) of
+				(False, Right True) -> helper bad (u:have) rs
+				(False, Left _)     -> helper (r:bad) have rs
+				_                   -> helper bad have rs
 
 notEnoughCopies :: Key -> Int -> [UUID] -> [UUID] -> [Remote] -> Annex Bool
 notEnoughCopies key need have skip bad = do
@@ -132,6 +132,6 @@ notEnoughCopies key need have skip bad = do
 	Remote.showLocations key (have++skip)
 	hint
 	return False
-	where
-		unsafe = showNote "unsafe"
-		hint = showLongNote "(Use --force to override this check, or adjust annex.numcopies.)"
+  where
+	unsafe = showNote "unsafe"
+	hint = showLongNote "(Use --force to override this check, or adjust annex.numcopies.)"
diff --git a/Command/DropUnused.hs b/Command/DropUnused.hs
index 597a4eec07..00c0eec129 100644
--- a/Command/DropUnused.hs
+++ b/Command/DropUnused.hs
@@ -29,13 +29,13 @@ start = startUnused "dropunused" perform (performOther gitAnnexBadLocation) (per
 
 perform :: Key -> CommandPerform
 perform key = maybe droplocal dropremote =<< Remote.byName =<< from
-	where
-		dropremote r = do
-			showAction $ "from " ++ Remote.name r
-			ok <- Remote.removeKey r key
-			next $ Command.Drop.cleanupRemote key r ok
-		droplocal = Command.Drop.performLocal key (Just 0) -- force drop
-		from = Annex.getField $ Option.name Command.Drop.fromOption
+  where
+	dropremote r = do
+		showAction $ "from " ++ Remote.name r
+		ok <- Remote.removeKey r key
+		next $ Command.Drop.cleanupRemote key r ok
+	droplocal = Command.Drop.performLocal key (Just 0) -- force drop
+	from = Annex.getField $ Option.name Command.Drop.fromOption
 
 performOther :: (Key -> Git.Repo -> FilePath) -> Key -> CommandPerform
 performOther filespec key = do
diff --git a/Command/Find.hs b/Command/Find.hs
index 177b794cd0..1e509d1dd1 100644
--- a/Command/Find.hs
+++ b/Command/Find.hs
@@ -29,14 +29,14 @@ formatOption = Option.field [] "format" paramFormat "control format of output"
 print0Option :: Option
 print0Option = Option.Option [] ["print0"] (Option.NoArg set)
 	"terminate output with null"
-	where
-		set = Annex.setField (Option.name formatOption) "${file}\0"
+  where
+	set = Annex.setField (Option.name formatOption) "${file}\0"
 
 seek :: [CommandSeek]
 seek = [withField formatOption formatconverter $ \f ->
 		withFilesInGit $ whenAnnexed $ start f]
-	where
-		formatconverter = return . fmap Utility.Format.gen
+  where
+	formatconverter = return . fmap Utility.Format.gen
 
 start :: Maybe Utility.Format.Format -> FilePath -> (Key, Backend) -> CommandStart
 start format file (key, _) = do
@@ -50,12 +50,12 @@ start format file (key, _) = do
 					Utility.Format.format formatter $
 						M.fromList vars
 	stop
-	where
-		vars =
-			[ ("file", file)
-			, ("key", key2file key)
-			, ("backend", keyBackendName key)
-			, ("bytesize", size show)
-			, ("humansize", size $ roughSize storageUnits True)
-			]
-		size c = maybe "unknown" c $ keySize key
+  where
+	vars =
+		[ ("file", file)
+		, ("key", key2file key)
+		, ("backend", keyBackendName key)
+		, ("bytesize", size show)
+		, ("humansize", size $ roughSize storageUnits True)
+		]
+	size c = maybe "unknown" c $ keySize key
diff --git a/Command/Fsck.hs b/Command/Fsck.hs
index 5e130c9487..deb3a5c818 100644
--- a/Command/Fsck.hs
+++ b/Command/Fsck.hs
@@ -78,22 +78,22 @@ withIncremental = withValue $ do
 		(True, _, _) ->
 			maybe startIncremental (return . ContIncremental . Just)
 				=<< getStartTime
-	where
-		startIncremental = do
-			recordStartTime
-			return StartIncremental
+  where
+	startIncremental = do
+		recordStartTime
+		return StartIncremental
 
-		checkschedule Nothing = error "bad --incremental-schedule value"
-		checkschedule (Just delta) = do
-			Annex.addCleanup "" $ do
-				v <- getStartTime
-				case v of
-					Nothing -> noop
-					Just started -> do
-						now <- liftIO getPOSIXTime
-						when (now - realToFrac started >= delta) $
-							resetStartTime
-			return True
+	checkschedule Nothing = error "bad --incremental-schedule value"
+	checkschedule (Just delta) = do
+		Annex.addCleanup "" $ do
+			v <- getStartTime
+			case v of
+				Nothing -> noop
+				Just started -> do
+					now <- liftIO getPOSIXTime
+					when (now - realToFrac started >= delta) $
+						resetStartTime
+		return True
 
 start :: Maybe Remote -> Incremental -> FilePath -> (Key, Backend) -> CommandStart
 start from inc file (key, backend) = do
@@ -101,8 +101,8 @@ start from inc file (key, backend) = do
 	case from of
 		Nothing -> go $ perform key file backend numcopies
 		Just r -> go $ performRemote key file backend numcopies r
-	where
-		go = runFsck inc file key
+  where
+	go = runFsck inc file key
 
 perform :: Key -> FilePath -> Backend -> Maybe Int -> Annex Bool
 perform key file backend numcopies = check
@@ -119,48 +119,48 @@ perform key file backend numcopies = check
 performRemote :: Key -> FilePath -> Backend -> Maybe Int -> Remote -> Annex Bool
 performRemote key file backend numcopies remote =
 	dispatch =<< Remote.hasKey remote key
-	where
-		dispatch (Left err) = do
-			showNote err
-			return False
-		dispatch (Right True) = withtmp $ \tmpfile ->
-			ifM (getfile tmpfile)
-				( go True (Just tmpfile)
-				, go True Nothing
-				)
-		dispatch (Right False) = go False Nothing
-		go present localcopy = check
-			[ verifyLocationLogRemote key file remote present
-			, checkKeySizeRemote key remote localcopy
-			, checkBackendRemote backend key remote localcopy
-			, checkKeyNumCopies key file numcopies
-			]
-		withtmp a = do
-			pid <- liftIO getProcessID
-			t <- fromRepo gitAnnexTmpDir
-			createAnnexDirectory t
-			let tmp = t </> "fsck" ++ show pid ++ "." ++ keyFile key
-			let cleanup = liftIO $ catchIO (removeFile tmp) (const noop)
-			cleanup
-			cleanup `after` a tmp
-		getfile tmp =
-			ifM (Remote.retrieveKeyFileCheap remote key tmp)
-				( return True
-				, ifM (Annex.getState Annex.fast)
-					( return False
-					, Remote.retrieveKeyFile remote key Nothing tmp
-					)
+  where
+	dispatch (Left err) = do
+		showNote err
+		return False
+	dispatch (Right True) = withtmp $ \tmpfile ->
+		ifM (getfile tmpfile)
+			( go True (Just tmpfile)
+			, go True Nothing
+			)
+	dispatch (Right False) = go False Nothing
+	go present localcopy = check
+		[ verifyLocationLogRemote key file remote present
+		, checkKeySizeRemote key remote localcopy
+		, checkBackendRemote backend key remote localcopy
+		, checkKeyNumCopies key file numcopies
+		]
+	withtmp a = do
+		pid <- liftIO getProcessID
+		t <- fromRepo gitAnnexTmpDir
+		createAnnexDirectory t
+		let tmp = t </> "fsck" ++ show pid ++ "." ++ keyFile key
+		let cleanup = liftIO $ catchIO (removeFile tmp) (const noop)
+		cleanup
+		cleanup `after` a tmp
+	getfile tmp =
+		ifM (Remote.retrieveKeyFileCheap remote key tmp)
+			( return True
+			, ifM (Annex.getState Annex.fast)
+				( return False
+				, Remote.retrieveKeyFile remote key Nothing tmp
 				)
+			)
 
 {- To fsck a bare repository, fsck each key in the location log. -}
 withBarePresentKeys :: (Key -> CommandStart) -> CommandSeek
 withBarePresentKeys a params = isBareRepo >>= go
-	where
-		go False = return []
-		go True = do
-			unless (null params) $
-				error "fsck should be run without parameters in a bare repository"
-			map a <$> loggedKeys
+  where
+	go False = return []
+	go True = do
+		unless (null params) $
+			error "fsck should be run without parameters in a bare repository"
+		map a <$> loggedKeys
 
 startBare :: Incremental -> Key -> CommandStart
 startBare inc key = case Backend.maybeLookupBackendName (Types.Key.keyBackendName key) of
@@ -242,10 +242,10 @@ verifyLocationLog' key desc present u bad = do
 					"but its content is missing."
 				return False
 		_ -> return True
-	where
-		fix s = do
-			showNote "fixing location log"
-			bad s
+  where
+	fix s = do
+		showNote "fixing location log"
+		bad s
 
 {- The size of the data for a key is checked against the size encoded in
  - the key's metadata, if available. -}
@@ -269,19 +269,19 @@ checkKeySizeOr bad key file = case Types.Key.keySize key of
 		size' <- fromIntegral . fileSize
 			<$> liftIO (getFileStatus file)
 		comparesizes size size'
-	where
-		comparesizes a b = do
-			let same = a == b
-			unless same $ badsize a b
-			return same
-		badsize a b = do
-			msg <- bad key
-			warning $ concat
-				[ "Bad file size ("
-				, compareSizes storageUnits True a b
-				, "); "
-				, msg
-				]
+  where
+	comparesizes a b = do
+		let same = a == b
+		unless same $ badsize a b
+		return same
+	badsize a b = do
+		msg <- bad key
+		warning $ concat
+			[ "Bad file size ("
+			, compareSizes storageUnits True a b
+			, "); "
+			, msg
+			]
 
 checkBackend :: Backend -> Key -> Annex Bool
 checkBackend backend key = do
@@ -290,8 +290,8 @@ checkBackend backend key = do
 
 checkBackendRemote :: Backend -> Key -> Remote -> Maybe FilePath -> Annex Bool
 checkBackendRemote backend key remote = maybe (return True) go
-	where
-		go = checkBackendOr (badContentRemote remote) backend key
+  where
+	go = checkBackendOr (badContentRemote remote) backend key
 
 checkBackendOr :: (Key -> Annex String) -> Backend -> Key -> FilePath -> Annex Bool
 checkBackendOr bad backend key file =
@@ -414,9 +414,9 @@ recordStartTime = do
 		t <- modificationTime <$> getFileStatus f
 		hPutStr h $ showTime $ realToFrac t
 		hClose h
-	where
-		showTime :: POSIXTime -> String
-		showTime = show
+  where
+	showTime :: POSIXTime -> String
+	showTime = show
 
 resetStartTime :: Annex ()
 resetStartTime = liftIO . nukeFile =<< fromRepo gitAnnexFsckState
@@ -431,7 +431,7 @@ getStartTime = do
 		return $ if Just (realToFrac timestamp) == t
 			then Just timestamp
 			else Nothing
-	where
-		readishTime :: String -> Maybe POSIXTime
-		readishTime s = utcTimeToPOSIXSeconds <$>
-			parseTime defaultTimeLocale "%s%Qs" s
+  where
+	readishTime :: String -> Maybe POSIXTime
+	readishTime s = utcTimeToPOSIXSeconds <$>
+		parseTime defaultTimeLocale "%s%Qs" s
diff --git a/Command/Get.hs b/Command/Get.hs
index c95e4eb94d..7f02e79353 100644
--- a/Command/Get.hs
+++ b/Command/Get.hs
@@ -32,10 +32,10 @@ start from file (key, _) = stopUnless ((not <$> inAnnex key) <&&> checkAuto (wan
 				-- get --from = copy --from
 				stopUnless (Command.Move.fromOk src key) $
 					go $ Command.Move.fromPerform src False key file
-	where
-		go a = do
-			showStart "get" file
-			next a
+  where
+	go a = do
+		showStart "get" file
+		next a
 
 perform :: Key -> FilePath -> CommandPerform
 perform key file = stopUnless (getViaTmp key $ getKeyFile key file) $
@@ -45,29 +45,29 @@ perform key file = stopUnless (getViaTmp key $ getKeyFile key file) $
  - and copy it to here. -}
 getKeyFile :: Key -> FilePath -> FilePath -> Annex Bool
 getKeyFile key file dest = dispatch =<< Remote.keyPossibilities key
-	where
-		dispatch [] = do
-			showNote "not available"
-			Remote.showLocations key []
-			return False
-		dispatch remotes = trycopy remotes remotes
-		trycopy full [] = do
-			Remote.showTriedRemotes full
-			Remote.showLocations key []
-			return False
-		trycopy full (r:rs) =
-			ifM (probablyPresent r)
-				( docopy r (trycopy full rs)
-				, trycopy full rs
-				)
-		-- This check is to avoid an ugly message if a remote is a
-		-- drive that is not mounted.
-		probablyPresent r
-			| Remote.hasKeyCheap r =
-				either (const False) id <$> Remote.hasKey r key
-			| otherwise = return True
-		docopy r continue = do
-			ok <- download (Remote.uuid r) key (Just file) noRetry $ do
-				showAction $ "from " ++ Remote.name r
-				Remote.retrieveKeyFile r key (Just file) dest
-			if ok then return ok else continue
+  where
+	dispatch [] = do
+		showNote "not available"
+		Remote.showLocations key []
+		return False
+	dispatch remotes = trycopy remotes remotes
+	trycopy full [] = do
+		Remote.showTriedRemotes full
+		Remote.showLocations key []
+		return False
+	trycopy full (r:rs) =
+		ifM (probablyPresent r)
+			( docopy r (trycopy full rs)
+			, trycopy full rs
+			)
+	-- This check is to avoid an ugly message if a remote is a
+	-- drive that is not mounted.
+	probablyPresent r
+		| Remote.hasKeyCheap r =
+			either (const False) id <$> Remote.hasKey r key
+		| otherwise = return True
+	docopy r continue = do
+		ok <- download (Remote.uuid r) key (Just file) noRetry $ do
+			showAction $ "from " ++ Remote.name r
+			Remote.retrieveKeyFile r key (Just file) dest
+		if ok then return ok else continue
diff --git a/Command/Help.hs b/Command/Help.hs
index 80a7b95207..95033eb7f4 100644
--- a/Command/Help.hs
+++ b/Command/Help.hs
@@ -47,5 +47,5 @@ showHelp = liftIO $ putStrLn $ unlines
 		]
 	, "Run git-annex without any options for a complete command and option list."
 	]
-	where
-		cmdline c = "\t" ++ cmdname c ++ "\t" ++ cmddesc c
+  where
+	cmdline c = "\t" ++ cmdname c ++ "\t" ++ cmddesc c
diff --git a/Command/InAnnex.hs b/Command/InAnnex.hs
index ac4af8d0bc..cd4bff2c69 100644
--- a/Command/InAnnex.hs
+++ b/Command/InAnnex.hs
@@ -20,8 +20,8 @@ seek = [withKeys start]
 
 start :: Key -> CommandStart
 start key = inAnnexSafe key >>= dispatch
-	where
-		dispatch (Just True) = stop
-		dispatch (Just False) = exit 1
-		dispatch Nothing = exit 100
-		exit n = liftIO $ exitWith $ ExitFailure n
+  where
+	dispatch (Just True) = stop
+	dispatch (Just False) = exit 1
+	dispatch Nothing = exit 100
+	exit n = liftIO $ exitWith $ ExitFailure n
diff --git a/Command/Init.hs b/Command/Init.hs
index bbabdc4c25..342ef84e15 100644
--- a/Command/Init.hs
+++ b/Command/Init.hs
@@ -22,8 +22,8 @@ start :: [String] -> CommandStart
 start ws = do
 	showStart "init" description
 	next $ perform description
-	where
-		description = unwords ws
+  where
+	description = unwords ws
 
 perform :: String -> CommandPerform
 perform description = do
diff --git a/Command/InitRemote.hs b/Command/InitRemote.hs
index ad93529cc2..720fdddf5d 100644
--- a/Command/InitRemote.hs
+++ b/Command/InitRemote.hs
@@ -40,8 +40,8 @@ start (name:ws) = do
 	showStart "initremote" name
 	next $ perform t u name $ M.union config c
 
-	where
-		config = Logs.Remote.keyValToConfig ws
+  where
+	config = Logs.Remote.keyValToConfig ws
 
 perform :: RemoteType -> UUID -> String -> R.RemoteConfig -> CommandPerform
 perform t u name c = do
@@ -59,19 +59,19 @@ findByName :: String -> Annex (UUID, R.RemoteConfig)
 findByName name = do
 	m <- Logs.Remote.readRemoteLog
 	maybe generate return $ findByName' name m
-	where
-		generate = do
-			uuid <- liftIO genUUID
-			return (uuid, M.insert nameKey name M.empty)
+  where
+	generate = do
+		uuid <- liftIO genUUID
+		return (uuid, M.insert nameKey name M.empty)
 
 findByName' :: String ->  M.Map UUID R.RemoteConfig -> Maybe (UUID, R.RemoteConfig)
 findByName' n = headMaybe . filter (matching . snd) . M.toList
-	where
-		matching c = case M.lookup nameKey c of
-			Nothing -> False
-			Just n'
-				| n' == n -> True
-				| otherwise -> False
+  where
+	matching c = case M.lookup nameKey c of
+		Nothing -> False
+		Just n'
+			| n' == n -> True
+			| otherwise -> False
 
 remoteNames :: Annex [String]
 remoteNames = do
@@ -81,12 +81,12 @@ remoteNames = do
 {- find the specified remote type -}
 findType :: R.RemoteConfig -> Annex RemoteType
 findType config = maybe unspecified specified $ M.lookup typeKey config
-	where
-		unspecified = error "Specify the type of remote with type="
-		specified s = case filter (findtype s) Remote.remoteTypes of
-			[] -> error $ "Unknown remote type " ++ s
-			(t:_) -> return t
-		findtype s i = R.typename i == s
+  where
+	unspecified = error "Specify the type of remote with type="
+	specified s = case filter (findtype s) Remote.remoteTypes of
+		[] -> error $ "Unknown remote type " ++ s
+		(t:_) -> return t
+	findtype s i = R.typename i == s
 
 {- The name of a configured remote is stored in its config using this key. -}
 nameKey :: String
diff --git a/Command/Log.hs b/Command/Log.hs
index 90d3d94906..6608a99065 100644
--- a/Command/Log.hs
+++ b/Command/Log.hs
@@ -47,9 +47,8 @@ passthruOptions = map odate ["since", "after", "until", "before"] ++
 	[ Option.field ['n'] "max-count" paramNumber
 		"limit number of logs displayed"
 	]
-	where
-		odate n = Option.field [] n paramDate $
-			"show log " ++ n ++ " date"
+  where
+	odate n = Option.field [] n paramDate $ "show log " ++ n ++ " date"
 
 gourceOption :: Option
 gourceOption = Option.flag [] "gource" "format output for gource"
@@ -60,10 +59,10 @@ seek = [withValue Remote.uuidDescriptions $ \m ->
 	withValue (concat <$> mapM getoption passthruOptions) $ \os ->
 	withFlag gourceOption $ \gource ->
 	withFilesInGit $ whenAnnexed $ start m zone os gource]
-	where
-		getoption o = maybe [] (use o) <$>
-			Annex.getField (Option.name o)
-		use o v = [Param ("--" ++ Option.name o), Param v]
+  where
+	getoption o = maybe [] (use o) <$>
+		Annex.getField (Option.name o)
+	use o v = [Param ("--" ++ Option.name o), Param v]
 
 start :: M.Map UUID String -> TimeZone -> [CommandParam] -> Bool ->
 	FilePath -> (Key, Backend) -> CommandStart
@@ -72,41 +71,41 @@ start m zone os gource file (key, _) = do
 	-- getLog produces a zombie; reap it
 	liftIO reapZombies
 	stop
-	where
-		output
-			| gource = gourceOutput lookupdescription file
-			| otherwise = normalOutput lookupdescription file zone
-		lookupdescription u = fromMaybe (fromUUID u) $ M.lookup u m
+  where
+	output
+		| gource = gourceOutput lookupdescription file
+		| otherwise = normalOutput lookupdescription file zone
+	lookupdescription u = fromMaybe (fromUUID u) $ M.lookup u m
 
 showLog :: Outputter -> [RefChange] -> Annex ()
 showLog outputter ps = do
 	sets <- mapM (getset newref) ps
 	previous <- maybe (return genesis) (getset oldref) (lastMaybe ps)
 	sequence_ $ compareChanges outputter $ sets ++ [previous]
-	where
-		genesis = (0, S.empty)
-		getset select change = do
-			s <- S.fromList <$> get (select change)
-			return (changetime change, s)
-		get ref = map toUUID . Logs.Presence.getLog . L.unpack <$>
-			catObject ref
+  where
+	genesis = (0, S.empty)
+	getset select change = do
+		s <- S.fromList <$> get (select change)
+		return (changetime change, s)
+	get ref = map toUUID . Logs.Presence.getLog . L.unpack <$>
+		catObject ref
 
 normalOutput :: (UUID -> String) -> FilePath -> TimeZone -> Outputter
 normalOutput lookupdescription file zone present ts us =
 	liftIO $ mapM_ (putStrLn . format) us
-	where
-		time = showTimeStamp zone ts
-		addel = if present then "+" else "-"
-		format u = unwords [ addel, time, file, "|", 
-			fromUUID u ++ " -- " ++ lookupdescription u ]
+  where
+	time = showTimeStamp zone ts
+	addel = if present then "+" else "-"
+	format u = unwords [ addel, time, file, "|", 
+		fromUUID u ++ " -- " ++ lookupdescription u ]
 
 gourceOutput :: (UUID -> String) -> FilePath -> Outputter
 gourceOutput lookupdescription file present ts us =
 	liftIO $ mapM_ (putStrLn . intercalate "|" . format) us
-	where
-		time = takeWhile isDigit $ show ts
-		addel = if present then "A" else "M"
-		format u = [ time, lookupdescription u, addel, file ]
+  where
+	time = takeWhile isDigit $ show ts
+	addel = if present then "A" else "M"
+	format u = [ time, lookupdescription u, addel, file ]
 
 {- Generates a display of the changes (which are ordered with newest first),
  - by comparing each change with the previous change.
@@ -114,12 +113,12 @@ gourceOutput lookupdescription file present ts us =
  - removed. -}
 compareChanges :: Ord a => (Bool -> POSIXTime -> [a] -> b) -> [(POSIXTime, S.Set a)] -> [b]
 compareChanges format changes = concatMap diff $ zip changes (drop 1 changes)
-	where
-		diff ((ts, new), (_, old)) =
-			[format True ts added, format False ts removed]
-			where
-				added = S.toList $ S.difference new old
-				removed = S.toList $ S.difference old new
+  where
+	diff ((ts, new), (_, old)) =
+		[format True ts added, format False ts removed]
+	  where
+		added = S.toList $ S.difference new old
+		removed = S.toList $ S.difference old new
 
 {- Gets the git log for a given location log file.
  -
@@ -148,21 +147,21 @@ getLog key os = do
 
 readLog :: [String] -> [RefChange]
 readLog = mapMaybe (parse . lines)
-	where
-		parse (ts:raw:[]) = let (old, new) = parseRaw raw in
-			Just RefChange
-				{ changetime = parseTimeStamp ts
-				, oldref = old
-				, newref = new
-				}
-		parse _ = Nothing
+  where
+	parse (ts:raw:[]) = let (old, new) = parseRaw raw in
+		Just RefChange
+			{ changetime = parseTimeStamp ts
+			, oldref = old
+			, newref = new
+			}
+	parse _ = Nothing
 
 -- Parses something like ":100644 100644 oldsha newsha M"
 parseRaw :: String -> (Git.Ref, Git.Ref)
 parseRaw l = go $ words l
-	where
-		go (_:_:oldsha:newsha:_) = (Git.Ref oldsha, Git.Ref newsha)
-		go _ = error $ "unable to parse git log output: " ++ l
+  where
+	go (_:_:oldsha:newsha:_) = (Git.Ref oldsha, Git.Ref newsha)
+	go _ = error $ "unable to parse git log output: " ++ l
 
 parseTimeStamp :: String -> POSIXTime
 parseTimeStamp = utcTimeToPOSIXSeconds . fromMaybe (error "bad timestamp") .
diff --git a/Command/Map.hs b/Command/Map.hs
index 3dbdadbd6c..94b1289dc0 100644
--- a/Command/Map.hs
+++ b/Command/Map.hs
@@ -63,14 +63,13 @@ start = do
  -}
 drawMap :: [Git.Repo] -> M.Map UUID String -> [UUID] -> String
 drawMap rs umap ts = Dot.graph $ repos ++ trusted ++ others
-	where
-		repos = map (node umap rs) rs
-		ruuids = ts ++ map getUncachedUUID rs
-		others = map (unreachable . uuidnode) $
-			filter (`notElem` ruuids) (M.keys umap)
-		trusted = map (trustworthy . uuidnode) ts
-		uuidnode u = Dot.graphNode (fromUUID u) $
-			M.findWithDefault "" u umap
+  where
+	repos = map (node umap rs) rs
+	ruuids = ts ++ map getUncachedUUID rs
+	others = map (unreachable . uuidnode) $
+		filter (`notElem` ruuids) (M.keys umap)
+	trusted = map (trustworthy . uuidnode) ts
+	uuidnode u = Dot.graphNode (fromUUID u) $ M.findWithDefault "" u umap
 
 hostname :: Git.Repo -> String
 hostname r
@@ -86,9 +85,9 @@ repoName :: M.Map UUID String -> Git.Repo -> String
 repoName umap r
 	| repouuid == NoUUID = fallback
 	| otherwise = M.findWithDefault fallback repouuid umap
-	where
-		repouuid = getUncachedUUID r
-		fallback = fromMaybe "unknown" $ Git.remoteName r
+  where
+	repouuid = getUncachedUUID r
+	fallback = fromMaybe "unknown" $ Git.remoteName r
 
 {- A unique id for the node for a repo. Uses the annex.uuid if available. -}
 nodeId :: Git.Repo -> String
@@ -100,32 +99,32 @@ nodeId r =
 {- A node representing a repo. -}
 node :: M.Map UUID String -> [Git.Repo] -> Git.Repo -> String
 node umap fullinfo r = unlines $ n:edges
-	where
-		n = Dot.subGraph (hostname r) (basehostname r) "lightblue" $
-			decorate $ Dot.graphNode (nodeId r) (repoName umap r)
-		edges = map (edge umap fullinfo r) (Git.remotes r)
-		decorate
-			| Git.config r == M.empty = unreachable
-			| otherwise = reachable
+  where
+	n = Dot.subGraph (hostname r) (basehostname r) "lightblue" $
+		decorate $ Dot.graphNode (nodeId r) (repoName umap r)
+	edges = map (edge umap fullinfo r) (Git.remotes r)
+	decorate
+		| Git.config r == M.empty = unreachable
+		| otherwise = reachable
 
 {- An edge between two repos. The second repo is a remote of the first. -}
 edge :: M.Map UUID String -> [Git.Repo] -> Git.Repo -> Git.Repo -> String	
 edge umap fullinfo from to =
 	Dot.graphEdge (nodeId from) (nodeId fullto) edgename
-	where
-		-- get the full info for the remote, to get its UUID
-		fullto = findfullinfo to
-		findfullinfo n =
-			case filter (same n) fullinfo of
-				[] -> n
-				(n':_) -> n'
-		{- Only name an edge if the name is different than the name
-		 - that will be used for the destination node, and is
-		 - different from its hostname. (This reduces visual clutter.) -}
-		edgename = maybe Nothing calcname $ Git.remoteName to
-		calcname n
-			| n `elem` [repoName umap fullto, hostname fullto] = Nothing
-			| otherwise = Just n
+  where
+	-- get the full info for the remote, to get its UUID
+	fullto = findfullinfo to
+	findfullinfo n =
+		case filter (same n) fullinfo of
+			[] -> n
+			(n':_) -> n'
+	{- Only name an edge if the name is different than the name
+	 - that will be used for the destination node, and is
+	 - different from its hostname. (This reduces visual clutter.) -}
+	edgename = maybe Nothing calcname $ Git.remoteName to
+	calcname n
+		| n `elem` [repoName umap fullto, hostname fullto] = Nothing
+		| otherwise = Just n
 
 unreachable :: String -> String
 unreachable = Dot.fillColor "red"
@@ -165,11 +164,10 @@ same a b
 	| both Git.repoIsUrl && neither Git.repoIsSsh = matching show
 	| neither Git.repoIsSsh = matching Git.repoPath
 	| otherwise = False
-		
-	where
-		matching t = t a == t b
-		both t = t a && t b
-		neither t = not (t a) && not (t b)
+  where
+	matching t = t a == t b
+	both t = t a && t b
+	neither t = not (t a) && not (t b)
 
 {- reads the config of a remote, with progress display -}
 scan :: Git.Repo -> Annex Git.Repo
@@ -192,50 +190,49 @@ tryScan r
 	| Git.repoIsSsh r = sshscan
 	| Git.repoIsUrl r = return Nothing
 	| otherwise = safely $ Git.Config.read r
-	where
-		safely a = do
-			result <- liftIO (try a :: IO (Either SomeException Git.Repo))
-			case result of
-				Left _ -> return Nothing
-				Right r' -> return $ Just r'
-		pipedconfig cmd params = safely $
-			withHandle StdoutHandle createProcessSuccess p $
-				Git.Config.hRead r
-			where
-				p = proc cmd $ toCommand params
+  where
+	safely a = do
+		result <- liftIO (try a :: IO (Either SomeException Git.Repo))
+		case result of
+			Left _ -> return Nothing
+			Right r' -> return $ Just r'
+	pipedconfig cmd params = safely $
+		withHandle StdoutHandle createProcessSuccess p $
+			Git.Config.hRead r
+	  where
+		p = proc cmd $ toCommand params
 
-		configlist =
-			onRemote r (pipedconfig, Nothing) "configlist" [] []
-		manualconfiglist = do
-			sshparams <- sshToRepo r [Param sshcmd]
-			liftIO $ pipedconfig "ssh" sshparams
-			where
-				sshcmd = cddir ++ " && " ++
-					"git config --null --list"
-				dir = Git.repoPath r
-				cddir
-					| "/~" `isPrefixOf` dir =
-						let (userhome, reldir) = span (/= '/') (drop 1 dir)
-						in "cd " ++ userhome ++ " && cd " ++ shellEscape (drop 1 reldir)
-					| otherwise = "cd " ++ shellEscape dir
+	configlist = onRemote r (pipedconfig, Nothing) "configlist" [] []
+	manualconfiglist = do
+		sshparams <- sshToRepo r [Param sshcmd]
+		liftIO $ pipedconfig "ssh" sshparams
+	  where
+		sshcmd = cddir ++ " && " ++
+			"git config --null --list"
+		dir = Git.repoPath r
+		cddir
+			| "/~" `isPrefixOf` dir =
+				let (userhome, reldir) = span (/= '/') (drop 1 dir)
+				in "cd " ++ userhome ++ " && cd " ++ shellEscape (drop 1 reldir)
+			| otherwise = "cd " ++ shellEscape dir
 
-		-- First, try sshing and running git config manually,
-		-- only fall back to git-annex-shell configlist if that
-		-- fails.
-		-- 
-		-- This is done for two reasons, first I'd like this
-		-- subcommand to be usable on non-git-annex repos.
-		-- Secondly, configlist doesn't include information about
-		-- the remote's remotes.
-		sshscan = do
-			sshnote
-			v <- manualconfiglist
-			case v of
-				Nothing -> do
-					sshnote
-					configlist
-				ok -> return ok
+	-- First, try sshing and running git config manually,
+	-- only fall back to git-annex-shell configlist if that
+	-- fails.
+	-- 
+	-- This is done for two reasons, first I'd like this
+	-- subcommand to be usable on non-git-annex repos.
+	-- Secondly, configlist doesn't include information about
+	-- the remote's remotes.
+	sshscan = do
+		sshnote
+		v <- manualconfiglist
+		case v of
+			Nothing -> do
+				sshnote
+				configlist
+			ok -> return ok
 
-		sshnote = do
-			showAction "sshing"
-			showOutput
+	sshnote = do
+		showAction "sshing"
+		showOutput
diff --git a/Command/Migrate.hs b/Command/Migrate.hs
index d3b29eecaa..0b23c2a400 100644
--- a/Command/Migrate.hs
+++ b/Command/Migrate.hs
@@ -31,9 +31,9 @@ start file (key, oldbackend) = do
 			showStart "migrate" file
 			next $ perform file key oldbackend newbackend
 		else stop
-	where
-		choosebackend Nothing = Prelude.head <$> orderedList
-		choosebackend (Just backend) = return backend
+  where
+	choosebackend Nothing = Prelude.head <$> orderedList
+	choosebackend (Just backend) = return backend
 
 {- Checks if a key is upgradable to a newer representation. -}
 {- Ideally, all keys have file size metadata. Old keys may not. -}
@@ -49,10 +49,10 @@ perform file oldkey oldbackend newbackend = do
 		( maybe stop go =<< genkey
 		, stop
 		)
-	where
-		go newkey = stopUnless (Command.ReKey.linkKey oldkey newkey) $
-			next $ Command.ReKey.cleanup file oldkey newkey
-		genkey = do
-			content <- inRepo $ gitAnnexLocation oldkey
-			let source = KeySource { keyFilename = file, contentLocation = content }
-			liftM fst <$> genKey source (Just newbackend)
+  where
+	go newkey = stopUnless (Command.ReKey.linkKey oldkey newkey) $
+		next $ Command.ReKey.cleanup file oldkey newkey
+	genkey = do
+		content <- inRepo $ gitAnnexLocation oldkey
+		let source = KeySource { keyFilename = file, contentLocation = content }
+		liftM fst <$> genKey source (Just newbackend)
diff --git a/Command/Move.hs b/Command/Move.hs
index 41daab4b26..316e4192ee 100644
--- a/Command/Move.hs
+++ b/Command/Move.hs
@@ -44,9 +44,9 @@ start to from move file (key, _) = do
 		(Nothing, Just dest) -> toStart dest move file key
 		(Just src, Nothing) -> fromStart src move file key
 		(_ ,  _) -> error "only one of --from or --to can be specified"
-	where
-		noAuto = when move $ whenM (Annex.getState Annex.auto) $ error
-			"--auto is not supported for move"
+  where
+	noAuto = when move $ whenM (Annex.getState Annex.auto) $ error
+		"--auto is not supported for move"
 
 showMoveAction :: Bool -> FilePath -> Annex ()
 showMoveAction True file = showStart "move" file
@@ -98,15 +98,15 @@ toPerform dest move key file = moveLock move key $ do
 						warning "This could have failed because --fast is enabled."
 					stop
 		Right True -> finish False
-	where
-		finish remotechanged = do
-			when remotechanged $
-				Remote.logStatus dest key InfoPresent
-			if move
-				then do
-					whenM (inAnnex key) $ removeAnnex key
-					next $ Command.Drop.cleanupLocal key
-				else next $ return True
+  where
+	finish remotechanged = do
+		when remotechanged $
+			Remote.logStatus dest key InfoPresent
+		if move
+			then do
+				whenM (inAnnex key) $ removeAnnex key
+				next $ Command.Drop.cleanupLocal key
+			else next $ return True
 
 {- Moves (or copies) the content of an annexed file from a remote
  - to the current repository.
@@ -118,35 +118,37 @@ fromStart :: Remote -> Bool -> FilePath -> Key -> CommandStart
 fromStart src move file key
 	| move = go
 	| otherwise = stopUnless (not <$> inAnnex key) go
-	where
-		go = stopUnless (fromOk src key) $ do
-			showMoveAction move file
-			next $ fromPerform src move key file
+  where
+	go = stopUnless (fromOk src key) $ do
+		showMoveAction move file
+		next $ fromPerform src move key file
+
 fromOk :: Remote -> Key -> Annex Bool
 fromOk src key
 	| Remote.hasKeyCheap src =
 		either (const expensive) return =<< Remote.hasKey src key
 	| otherwise = expensive
-	where
-		expensive = do
-			u <- getUUID
-			remotes <- Remote.keyPossibilities key
-			return $ u /= Remote.uuid src && elem src remotes
+  where
+	expensive = do
+		u <- getUUID
+		remotes <- Remote.keyPossibilities key
+		return $ u /= Remote.uuid src && elem src remotes
+
 fromPerform :: Remote -> Bool -> Key -> FilePath -> CommandPerform
 fromPerform src move key file = moveLock move key $
 	ifM (inAnnex key)
 		( handle move True
 		, handle move =<< go
 		)
-	where
-		go = download (Remote.uuid src) key (Just file) noRetry $ do
-			showAction $ "from " ++ Remote.name src
-			getViaTmp key $ Remote.retrieveKeyFile src key (Just file)
-		handle _ False = stop -- failed
-		handle False True = next $ return True -- copy complete
-		handle True True = do -- finish moving
-			ok <- Remote.removeKey src key
-			next $ Command.Drop.cleanupRemote key src ok
+  where
+	go = download (Remote.uuid src) key (Just file) noRetry $ do
+		showAction $ "from " ++ Remote.name src
+		getViaTmp key $ Remote.retrieveKeyFile src key (Just file)
+	handle _ False = stop -- failed
+	handle False True = next $ return True -- copy complete
+	handle True True = do -- finish moving
+		ok <- Remote.removeKey src key
+		next $ Command.Drop.cleanupRemote key src ok
 
 {- Locks a key in order for it to be moved.
  - No lock is needed when a key is being copied. -}
diff --git a/Command/ReKey.hs b/Command/ReKey.hs
index 5bd419ca31..ea06873c46 100644
--- a/Command/ReKey.hs
+++ b/Command/ReKey.hs
@@ -25,13 +25,13 @@ seek = [withPairs start]
 
 start :: (FilePath, String) -> CommandStart
 start (file, keyname) = ifAnnexed file go stop
-	where
-		newkey = fromMaybe (error "bad key") $ file2key keyname
-		go (oldkey, _)
-			| oldkey == newkey = stop
-			| otherwise = do
-				showStart "rekey" file
-				next $ perform file oldkey newkey
+  where
+	newkey = fromMaybe (error "bad key") $ file2key keyname
+	go (oldkey, _)
+		| oldkey == newkey = stop
+		| otherwise = do
+			showStart "rekey" file
+			next $ perform file oldkey newkey
 
 perform :: FilePath -> Key -> Key -> CommandPerform
 perform file oldkey newkey = do
diff --git a/Command/Reinject.hs b/Command/Reinject.hs
index 112b7fadfe..d346925fa6 100644
--- a/Command/Reinject.hs
+++ b/Command/Reinject.hs
@@ -27,10 +27,10 @@ start (src:dest:[])
 		ifAnnexed src
 			(error $ "cannot used annexed file as src: " ++ src)
 			go
-	where
-		go = do
-			showStart "reinject" dest
-			next $ whenAnnexed (perform src) dest
+  where
+	go = do
+		showStart "reinject" dest
+		next $ whenAnnexed (perform src) dest
 start _ = error "specify a src file and a dest file"
 
 perform :: FilePath -> FilePath -> (Key, Backend) -> CommandPerform
@@ -43,14 +43,14 @@ perform src _dest (key, backend) = do
 			next $ cleanup key
 		, error "not reinjecting"
 		)
-	where
-		-- the file might be on a different filesystem,
-		-- so mv is used rather than simply calling
-		-- moveToObjectDir; disk space is also
-		-- checked this way.
-		move = getViaTmp key $ \tmp ->
-			liftIO $ boolSystem "mv" [File src, File tmp]
-		reject = const $ return "wrong file?"
+  where
+	-- the file might be on a different filesystem,
+	-- so mv is used rather than simply calling
+	-- moveToObjectDir; disk space is also
+	-- checked this way.
+	move = getViaTmp key $ \tmp ->
+		liftIO $ boolSystem "mv" [File src, File tmp]
+	reject = const $ return "wrong file?"
 
 cleanup :: Key -> CommandCleanup
 cleanup key = do
diff --git a/Command/Status.hs b/Command/Status.hs
index a16e143172..593e8a025f 100644
--- a/Command/Status.hs
+++ b/Command/Status.hs
@@ -114,10 +114,10 @@ nojson a _ = a
 
 showStat :: Stat -> StatState ()
 showStat s = maybe noop calc =<< s
-	where
-		calc (desc, a) = do
-			(lift . showHeader) desc
-			lift . showRaw =<< a
+  where
+	calc (desc, a) = do
+		(lift . showHeader) desc
+		lift . showRaw =<< a
 
 supported_backends :: Stat
 supported_backends = stat "supported backends" $ json unwords $
@@ -133,8 +133,8 @@ remote_list level = stat n $ nojson $ lift $ do
 	rs <- fst <$> trustPartition level us
 	s <- prettyPrintUUIDs n rs
 	return $ if null s then "0" else show (length rs) ++ "\n" ++ beginning s
-	where
-		n = showTrustLevel level ++ " repositories"
+  where
+	n = showTrustLevel level ++ " repositories"
 	
 local_annex_size :: Stat
 local_annex_size = stat "local annex size" $ json id $
@@ -182,42 +182,42 @@ transfer_list = stat "transfers in progress" $ nojson $ lift $ do
 		then return "none"
 		else return $ multiLine $
 			map (\(t, i) -> line uuidmap t i) $ sort ts
-	where
-		line uuidmap t i = unwords
-			[ showLcDirection (transferDirection t) ++ "ing"
-			, fromMaybe (key2file $ transferKey t) (associatedFile i)
-			, if transferDirection t == Upload then "to" else "from"
-			, maybe (fromUUID $ transferUUID t) Remote.name $
-				M.lookup (transferUUID t) uuidmap
-			]
+  where
+	line uuidmap t i = unwords
+		[ showLcDirection (transferDirection t) ++ "ing"
+		, fromMaybe (key2file $ transferKey t) (associatedFile i)
+		, if transferDirection t == Upload then "to" else "from"
+		, maybe (fromUUID $ transferUUID t) Remote.name $
+			M.lookup (transferUUID t) uuidmap
+		]
 
 disk_size :: Stat
 disk_size = stat "available local disk space" $ json id $ lift $
 	calcfree
 		<$> getDiskReserve
 		<*> inRepo (getDiskFree . gitAnnexDir)
-	where
-		calcfree reserve (Just have) = unwords
-			[ roughSize storageUnits False $ nonneg $ have - reserve
-			, "(+" ++ roughSize storageUnits False reserve
-			, "reserved)"
-			]
-			
-		calcfree _ _ = "unknown"
-		nonneg x
-			| x >= 0 = x
-			| otherwise = 0
+  where
+	calcfree reserve (Just have) = unwords
+		[ roughSize storageUnits False $ nonneg $ have - reserve
+		, "(+" ++ roughSize storageUnits False reserve
+		, "reserved)"
+		]			
+	calcfree _ _ = "unknown"
+
+	nonneg x
+		| x >= 0 = x
+		| otherwise = 0
 
 backend_usage :: Stat
 backend_usage = stat "backend usage" $ nojson $
 	calc
 		<$> (backendsKeys <$> cachedReferencedData)
 		<*> (backendsKeys <$> cachedPresentData)
-	where
-		calc x y = multiLine $
-			map (\(n, b) -> b ++ ": " ++ show n) $
-			reverse $ sort $ map swap $ M.toList $
-			M.unionWith (+) x y
+  where
+	calc x y = multiLine $
+		map (\(n, b) -> b ++ ": " ++ show n) $
+		reverse $ sort $ map swap $ M.toList $
+		M.unionWith (+) x y
 
 cachedPresentData :: StatState KeyData
 cachedPresentData = do
@@ -249,39 +249,38 @@ foldKeys = foldl' (flip addKey) emptyKeyData
 addKey :: Key -> KeyData -> KeyData
 addKey key (KeyData count size unknownsize backends) =
 	KeyData count' size' unknownsize' backends'
-	where
-		{- All calculations strict to avoid thunks when repeatedly
-		 - applied to many keys. -}
-		!count' = count + 1
-		!backends' = M.insertWith' (+) (keyBackendName key) 1 backends
-		!size' = maybe size (+ size) ks
-		!unknownsize' = maybe (unknownsize + 1) (const unknownsize) ks
-		ks = keySize key
+  where
+	{- All calculations strict to avoid thunks when repeatedly
+	 - applied to many keys. -}
+	!count' = count + 1
+	!backends' = M.insertWith' (+) (keyBackendName key) 1 backends
+	!size' = maybe size (+ size) ks
+	!unknownsize' = maybe (unknownsize + 1) (const unknownsize) ks
+	ks = keySize key
 
 showSizeKeys :: KeyData -> String
 showSizeKeys d = total ++ missingnote
-	where
-		total = roughSize storageUnits False $ sizeKeys d
-		missingnote
-			| unknownSizeKeys d == 0 = ""
-			| otherwise = aside $
-				"+ " ++ show (unknownSizeKeys d) ++
-				" keys of unknown size"
+  where
+	total = roughSize storageUnits False $ sizeKeys d
+	missingnote
+		| unknownSizeKeys d == 0 = ""
+		| otherwise = aside $
+			"+ " ++ show (unknownSizeKeys d) ++
+			" keys of unknown size"
 
 staleSize :: String -> (Git.Repo -> FilePath) -> Stat
 staleSize label dirspec = go =<< lift (Command.Unused.staleKeys dirspec)
-	where
-		go [] = nostat
-		go keys = onsize =<< sum <$> keysizes keys
-		onsize 0 = nostat
-		onsize size = stat label $
-			json (++ aside "clean up with git-annex unused") $
-				return $ roughSize storageUnits False size
-		keysizes keys = map (fromIntegral . fileSize) <$> stats keys
-		stats keys = do
-			dir <- lift $ fromRepo dirspec
-			liftIO $ forM keys $ \k ->
-				getFileStatus (dir </> keyFile k)
+  where
+	go [] = nostat
+	go keys = onsize =<< sum <$> keysizes keys
+	onsize 0 = nostat
+	onsize size = stat label $
+		json (++ aside "clean up with git-annex unused") $
+			return $ roughSize storageUnits False size
+	keysizes keys = map (fromIntegral . fileSize) <$> stats keys
+	stats keys = do
+		dir <- lift $ fromRepo dirspec
+		liftIO $ forM keys $ \k -> getFileStatus (dir </> keyFile k)
 
 aside :: String -> String
 aside s = " (" ++ s ++ ")"
diff --git a/Command/Sync.hs b/Command/Sync.hs
index 1795a61049..f7410112e8 100644
--- a/Command/Sync.hs
+++ b/Command/Sync.hs
@@ -48,8 +48,8 @@ seek rs = do
 		, [ pushLocal branch ]
 		, [ pushRemote remote branch | remote <- remotes ]
 		]
-	where
-		nobranch = error "no branch is checked out"
+  where
+	nobranch = error "no branch is checked out"
 
 syncBranch :: Git.Ref -> Git.Ref
 syncBranch = Git.Ref.under "refs/heads/synced/"
@@ -59,23 +59,23 @@ remoteBranch remote = Git.Ref.under $ "refs/remotes/" ++ Remote.name remote
 
 syncRemotes :: [String] -> Annex [Remote]
 syncRemotes rs = ifM (Annex.getState Annex.fast) ( nub <$> pickfast , wanted )
-	where
-		pickfast = (++) <$> listed <*> (good =<< fastest <$> available)
-		wanted
-			| null rs = good =<< concat . Remote.byCost <$> available
-			| otherwise = listed
-		listed = do
-			l <- catMaybes <$> mapM (Remote.byName . Just) rs
-			let s = filter Remote.specialRemote l
-			unless (null s) $
-				error $ "cannot sync special remotes: " ++
-					unwords (map Types.Remote.name s)
-			return l
-		available = filter (not . Remote.specialRemote)
-			<$> (filterM (repoSyncable . Types.Remote.repo)
-				=<< Remote.enabledRemoteList)
-		good = filterM $ Remote.Git.repoAvail . Types.Remote.repo
-		fastest = fromMaybe [] . headMaybe . Remote.byCost
+  where
+	pickfast = (++) <$> listed <*> (good =<< fastest <$> available)
+	wanted
+		| null rs = good =<< concat . Remote.byCost <$> available
+		| otherwise = listed
+	listed = do
+		l <- catMaybes <$> mapM (Remote.byName . Just) rs
+		let s = filter Remote.specialRemote l
+		unless (null s) $
+			error $ "cannot sync special remotes: " ++
+				unwords (map Types.Remote.name s)
+		return l
+	available = filter (not . Remote.specialRemote)
+		<$> (filterM (repoSyncable . Types.Remote.repo)
+			=<< Remote.enabledRemoteList)
+	good = filterM $ Remote.Git.repoAvail . Types.Remote.repo
+	fastest = fromMaybe [] . headMaybe . Remote.byCost
 
 commit :: CommandStart
 commit = do
@@ -90,16 +90,16 @@ commit = do
 
 mergeLocal :: Git.Ref -> CommandStart
 mergeLocal branch = go =<< needmerge
-	where
-		syncbranch = syncBranch branch
-		needmerge = do
-			unlessM (inRepo $ Git.Ref.exists syncbranch) $
-				inRepo $ updateBranch syncbranch
-			inRepo $ Git.Branch.changed branch syncbranch
-		go False = stop
-		go True = do
-			showStart "merge" $ Git.Ref.describe syncbranch
-			next $ next $ mergeFrom syncbranch
+  where
+	syncbranch = syncBranch branch
+	needmerge = do
+		unlessM (inRepo $ Git.Ref.exists syncbranch) $
+			inRepo $ updateBranch syncbranch
+		inRepo $ Git.Branch.changed branch syncbranch
+	go False = stop
+	go True = do
+		showStart "merge" $ Git.Ref.describe syncbranch
+		next $ next $ mergeFrom syncbranch
 
 pushLocal :: Git.Ref -> CommandStart
 pushLocal branch = do
@@ -109,11 +109,11 @@ pushLocal branch = do
 updateBranch :: Git.Ref -> Git.Repo -> IO ()
 updateBranch syncbranch g = 
 	unlessM go $ error $ "failed to update " ++ show syncbranch
-	where
-		go = Git.Command.runBool "branch"
-			[ Param "-f"
-			, Param $ show $ Git.Ref.base syncbranch
-			] g
+  where
+	go = Git.Command.runBool "branch"
+		[ Param "-f"
+		, Param $ show $ Git.Ref.base syncbranch
+		] g
 
 pullRemote :: Remote -> Git.Ref -> CommandStart
 pullRemote remote branch = do
@@ -122,9 +122,9 @@ pullRemote remote branch = do
 		showOutput
 		stopUnless fetch $
 			next $ mergeRemote remote (Just branch)
-	where
-		fetch = inRepo $ Git.Command.runBool "fetch"
-			[Param $ Remote.name remote]
+  where
+	fetch = inRepo $ Git.Command.runBool "fetch"
+		[Param $ Remote.name remote]
 
 {- The remote probably has both a master and a synced/master branch.
  - Which to merge from? Well, the master has whatever latest changes
@@ -136,22 +136,22 @@ mergeRemote remote b = case b of
 		branch <- inRepo Git.Branch.currentUnsafe
 		all id <$> (mapM merge $ branchlist branch)
 	Just _ -> all id <$> (mapM merge =<< tomerge (branchlist b))
-	where
-		merge = mergeFrom . remoteBranch remote
-		tomerge branches = filterM (changed remote) branches
-		branchlist Nothing = []
-		branchlist (Just branch) = [branch, syncBranch branch]
+  where
+	merge = mergeFrom . remoteBranch remote
+	tomerge branches = filterM (changed remote) branches
+	branchlist Nothing = []
+	branchlist (Just branch) = [branch, syncBranch branch]
 
 pushRemote :: Remote -> Git.Ref -> CommandStart
 pushRemote remote branch = go =<< needpush
-	where
-		needpush = anyM (newer remote) [syncBranch branch, Annex.Branch.name]
-		go False = stop
-		go True = do
-			showStart "push" (Remote.name remote)
-			next $ next $ do
-				showOutput
-				inRepo $ pushBranch remote branch
+  where
+	needpush = anyM (newer remote) [syncBranch branch, Annex.Branch.name]
+	go False = stop
+	go True = do
+		showStart "push" (Remote.name remote)
+		next $ next $ do
+			showOutput
+			inRepo $ pushBranch remote branch
 
 pushBranch :: Remote -> Git.Ref -> Git.Repo -> IO Bool
 pushBranch remote branch g =
@@ -160,12 +160,12 @@ pushBranch remote branch g =
 		, Param $ refspec Annex.Branch.name
 		, Param $ refspec branch
 		] g
-	where
-		refspec b = concat 
-			[ show $ Git.Ref.base b
-			,  ":"
-			, show $ Git.Ref.base $ syncBranch b
-			]
+  where
+	refspec b = concat 
+		[ show $ Git.Ref.base b
+		,  ":"
+		, show $ Git.Ref.base $ syncBranch b
+		]
 
 mergeAnnex :: CommandStart
 mergeAnnex = do
@@ -213,37 +213,37 @@ resolveMerge' u
 		withKey LsFiles.valUs $ \keyUs ->
 		withKey LsFiles.valThem $ \keyThem -> go keyUs keyThem
 	| otherwise = return False
-	where
-		go keyUs keyThem
-			| keyUs == keyThem = do
-				makelink keyUs
-				return True
-			| otherwise = do
-				liftIO $ nukeFile file
-				Annex.Queue.addCommand "rm" [Params "--quiet -f --"] [file]
-				makelink keyUs
-				makelink keyThem
-				return True
-		file = LsFiles.unmergedFile u
-		issymlink select = any (select (LsFiles.unmergedBlobType u) ==)
-			[Just SymlinkBlob, Nothing]
-		makelink (Just key) = do
-			let dest = mergeFile file key
-			l <- calcGitLink dest key
-			liftIO $ do
-				nukeFile dest
-				createSymbolicLink l dest
-			Annex.Queue.addCommand "add" [Param "--force", Param "--"] [dest]
-		makelink _ = noop
-		withKey select a = do
-			let msha = select $ LsFiles.unmergedSha u
-			case msha of
-				Nothing -> a Nothing
-				Just sha -> do
-					key <- fileKey . takeFileName
-						. encodeW8 . L.unpack 
-						<$> catObject sha
-					maybe (return False) (a . Just) key
+  where
+	go keyUs keyThem
+		| keyUs == keyThem = do
+			makelink keyUs
+			return True
+		| otherwise = do
+			liftIO $ nukeFile file
+			Annex.Queue.addCommand "rm" [Params "--quiet -f --"] [file]
+			makelink keyUs
+			makelink keyThem
+			return True
+	file = LsFiles.unmergedFile u
+	issymlink select = any (select (LsFiles.unmergedBlobType u) ==)
+		[Just SymlinkBlob, Nothing]
+	makelink (Just key) = do
+		let dest = mergeFile file key
+		l <- calcGitLink dest key
+		liftIO $ do
+			nukeFile dest
+			createSymbolicLink l dest
+		Annex.Queue.addCommand "add" [Param "--force", Param "--"] [dest]
+	makelink _ = noop
+	withKey select a = do
+		let msha = select $ LsFiles.unmergedSha u
+		case msha of
+			Nothing -> a Nothing
+			Just sha -> do
+				key <- fileKey . takeFileName
+					. encodeW8 . L.unpack 
+					<$> catObject sha
+				maybe (return False) (a . Just) key
 
 {- The filename to use when resolving a conflicted merge of a file,
  - that points to a key.
@@ -262,13 +262,13 @@ mergeFile :: FilePath -> Key -> FilePath
 mergeFile file key
 	| doubleconflict = go $ key2file key
 	| otherwise = go $ shortHash $ key2file key
-	where
-		varmarker = ".variant-"
-		doubleconflict = varmarker `isSuffixOf` (dropExtension file)
-		go v = takeDirectory file
-			</> dropExtension (takeFileName file)
-			++ varmarker ++ v
-			++ takeExtension file
+  where
+	varmarker = ".variant-"
+	doubleconflict = varmarker `isSuffixOf` (dropExtension file)
+	go v = takeDirectory file
+		</> dropExtension (takeFileName file)
+		++ varmarker ++ v
+		++ takeExtension file
 		
 shortHash :: String -> String
 shortHash = take 4 . md5s . md5FilePath
diff --git a/Command/Uninit.hs b/Command/Uninit.hs
index 8b653da7d9..b365e8c20c 100644
--- a/Command/Uninit.hs
+++ b/Command/Uninit.hs
@@ -30,10 +30,10 @@ check = do
 	cwd <- liftIO getCurrentDirectory
 	whenM ((/=) <$> liftIO (absPath top) <*> liftIO (absPath cwd)) $
 		error "can only run uninit from the top of the git repository"
-	where
-		current_branch = Git.Ref . Prelude.head . lines <$> revhead
-		revhead = inRepo $ Git.Command.pipeReadStrict
-			[Params "rev-parse --abbrev-ref HEAD"]
+  where
+	current_branch = Git.Ref . Prelude.head . lines <$> revhead
+	revhead = inRepo $ Git.Command.pipeReadStrict
+		[Params "rev-parse --abbrev-ref HEAD"]
 
 seek :: [CommandSeek]
 seek = [
diff --git a/Command/Unlock.hs b/Command/Unlock.hs
index f3ffd31ba6..6489fc333a 100644
--- a/Command/Unlock.hs
+++ b/Command/Unlock.hs
@@ -17,8 +17,8 @@ def =
 	[ c "unlock" "unlock files for modification"
 	, c "edit" "same as unlock"
 	]
-	where
-		c n = command n paramPaths seek
+  where
+	c n = command n paramPaths seek
 
 seek :: [CommandSeek]
 seek = [withFilesInGit $ whenAnnexed start]
diff --git a/Command/Unused.hs b/Command/Unused.hs
index 79285f7d1b..c0551ddeaf 100644
--- a/Command/Unused.hs
+++ b/Command/Unused.hs
@@ -64,27 +64,26 @@ checkUnused = chain 0
 	, check "bad" staleBadMsg $ staleKeysPrune gitAnnexBadDir
 	, check "tmp" staleTmpMsg $ staleKeysPrune gitAnnexTmpDir
 	]
-	where
-		findunused True = do
-			showNote "fast mode enabled; only finding stale files"
-			return []
-		findunused False = do
-			showAction "checking for unused data"
-			excludeReferenced =<< getKeysPresent
-		chain _ [] = next $ return True
-		chain v (a:as) = do
-			v' <- a v
-			chain v' as
+  where
+	findunused True = do
+		showNote "fast mode enabled; only finding stale files"
+		return []
+	findunused False = do
+		showAction "checking for unused data"
+		excludeReferenced =<< getKeysPresent
+	chain _ [] = next $ return True
+	chain v (a:as) = do
+		v' <- a v
+		chain v' as
 
 checkRemoteUnused :: String -> CommandPerform
 checkRemoteUnused name = go =<< fromJust <$> Remote.byName (Just name)
-	where
-		go r = do
-			showAction "checking for unused data"
-			_ <- check "" (remoteUnusedMsg r) (remoteunused r) 0
-			next $ return True
-		remoteunused r =
-			excludeReferenced <=< loggedKeysFor $ Remote.uuid r
+  where
+	go r = do
+		showAction "checking for unused data"
+		_ <- check "" (remoteUnusedMsg r) (remoteunused r) 0
+		next $ return True
+	remoteunused r = excludeReferenced <=< loggedKeysFor $ Remote.uuid r
 
 check :: FilePath -> ([(Int, Key)] -> String) -> Annex [Key] -> Int -> Annex Int
 check file msg a c = do
@@ -100,9 +99,9 @@ number n (x:xs) = (n+1, x) : number (n+1) xs
 
 table :: [(Int, Key)] -> [String]
 table l = "  NUMBER  KEY" : map cols l
-	where
-		cols (n,k) = "  " ++ pad 6 (show n) ++ "  " ++ key2file k
-		pad n s = s ++ replicate (n - length s) ' '
+  where
+	cols (n,k) = "  " ++ pad 6 (show n) ++ "  " ++ key2file k
+	pad n s = s ++ replicate (n - length s) ' '
 
 staleTmpMsg :: [(Int, Key)] -> String
 staleTmpMsg t = unlines $ 
@@ -129,8 +128,8 @@ remoteUnusedMsg :: Remote -> [(Int, Key)] -> String
 remoteUnusedMsg r u = unusedMsg' u
 	["Some annexed data on " ++ name ++ " is not used by any files:"]
 	[dropMsg $ Just r]
-	where
-		name = Remote.name r 
+  where
+	name = Remote.name r 
 
 dropMsg :: Maybe Remote -> String
 dropMsg Nothing = dropMsg' ""
@@ -159,11 +158,11 @@ dropMsg' s = "\nTo remove unwanted data: git-annex dropunused" ++ s ++ " NUMBER\
  -}
 excludeReferenced :: [Key] -> Annex [Key]
 excludeReferenced ks = runfilter firstlevel ks >>= runfilter secondlevel
-	where
-		runfilter _ [] = return [] -- optimisation
-		runfilter a l = bloomFilter show l <$> genBloomFilter show a
-		firstlevel = withKeysReferencedM
-		secondlevel = withKeysReferencedInGit
+  where
+	runfilter _ [] = return [] -- optimisation
+	runfilter a l = bloomFilter show l <$> genBloomFilter show a
+	firstlevel = withKeysReferencedM
+	secondlevel = withKeysReferencedInGit
 
 {- Finds items in the first, smaller list, that are not
  - present in the second, larger list.
@@ -174,8 +173,8 @@ excludeReferenced ks = runfilter firstlevel ks >>= runfilter secondlevel
 exclude :: Ord a => [a] -> [a] -> [a]
 exclude [] _ = [] -- optimisation
 exclude smaller larger = S.toList $ remove larger $ S.fromList smaller
-	where
-		remove a b = foldl (flip S.delete) b a
+  where
+	remove a b = foldl (flip S.delete) b a
 
 {- A bloom filter capable of holding half a million keys with a
  - false positive rate of 1 in 1000 uses around 8 mb of memory,
@@ -208,8 +207,8 @@ genBloomFilter convert populate = do
 	bloom <- lift $ newMB (cheapHashes numhashes) numbits
 	_ <- populate $ \v -> lift $ insertMB bloom (convert v)
 	lift $ unsafeFreezeMB bloom
-	where
-		lift = liftIO . stToIO
+  where
+	lift = liftIO . stToIO
 
 bloomFilter :: Hashable t => (v -> t) -> [v] -> Bloom t -> [v]
 bloomFilter convert l bloom = filter (\k -> convert k `notElemB` bloom) l
@@ -218,14 +217,14 @@ bloomFilter convert l bloom = filter (\k -> convert k `notElemB` bloom) l
  - symlinks in the git repo. -}
 withKeysReferenced :: v -> (Key -> v -> v) -> Annex v
 withKeysReferenced initial a = withKeysReferenced' initial folda
-	where
-		folda k v = return $ a k v
+  where
+	folda k v = return $ a k v
 
 {- Runs an action on each referenced key in the git repo. -}
 withKeysReferencedM :: (Key -> Annex ()) -> Annex ()
 withKeysReferencedM a = withKeysReferenced' () calla
-	where
-		calla k _ = a k
+  where
+	calla k _ = a k
 
 withKeysReferenced' :: v -> (Key -> v -> Annex v) -> Annex v
 withKeysReferenced' initial a = do
@@ -233,54 +232,53 @@ withKeysReferenced' initial a = do
 	r <- go initial files
 	liftIO $ void clean
 	return r
-	where
-		getfiles = ifM isBareRepo
-			( return ([], return True)
-			, do
-				top <- fromRepo Git.repoPath
-				inRepo $ LsFiles.inRepo [top]
-			)
-		go v [] = return v
-		go v (f:fs) = do
-			x <- Backend.lookupFile f
-			case x of
-				Nothing -> go v fs
-				Just (k, _) -> do
-					!v' <- a k v
-					go v' fs
-
+  where
+	getfiles = ifM isBareRepo
+		( return ([], return True)
+		, do
+			top <- fromRepo Git.repoPath
+			inRepo $ LsFiles.inRepo [top]
+		)
+	go v [] = return v
+	go v (f:fs) = do
+		x <- Backend.lookupFile f
+		case x of
+			Nothing -> go v fs
+			Just (k, _) -> do
+				!v' <- a k v
+				go v' fs
 
 withKeysReferencedInGit :: (Key -> Annex ()) -> Annex ()
 withKeysReferencedInGit a = do
 	rs <- relevantrefs <$> showref
 	forM_ rs (withKeysReferencedInGitRef a)
-	where
-		showref = inRepo $ Git.Command.pipeReadStrict [Param "show-ref"]
-		relevantrefs = map (Git.Ref .  snd) .
-			nubBy uniqref .
-			filter ourbranches .
-			map (separate (== ' ')) . lines
-		uniqref (x, _) (y, _) = x == y
-		ourbranchend = '/' : show Annex.Branch.name
-		ourbranches (_, b) = not (ourbranchend `isSuffixOf` b)
-			&& not ("refs/synced/" `isPrefixOf` b)
+  where
+	showref = inRepo $ Git.Command.pipeReadStrict [Param "show-ref"]
+	relevantrefs = map (Git.Ref .  snd) .
+		nubBy uniqref .
+		filter ourbranches .
+		map (separate (== ' ')) . lines
+	uniqref (x, _) (y, _) = x == y
+	ourbranchend = '/' : show Annex.Branch.name
+	ourbranches (_, b) = not (ourbranchend `isSuffixOf` b)
+		&& not ("refs/synced/" `isPrefixOf` b)
 
 withKeysReferencedInGitRef :: (Key -> Annex ()) -> Git.Ref -> Annex ()
 withKeysReferencedInGitRef a ref = do
 	showAction $ "checking " ++ Git.Ref.describe ref
 	go <=< inRepo $ LsTree.lsTree ref
-	where
-		go [] = noop
-		go (l:ls)
-			| isSymLink (LsTree.mode l) = do
-				content <- encodeW8 . L.unpack
-					<$> catFile ref (LsTree.file l)
-				case fileKey (takeFileName content) of
-					Nothing -> go ls
-					Just k -> do
-						a k
-						go ls
-			| otherwise = go ls
+  where
+	go [] = noop
+	go (l:ls)
+		| isSymLink (LsTree.mode l) = do
+			content <- encodeW8 . L.unpack
+				<$> catFile ref (LsTree.file l)
+			case fileKey (takeFileName content) of
+				Nothing -> go ls
+				Just k -> do
+					a k
+					go ls
+		| otherwise = go ls
 
 {- Looks in the specified directory for bad/tmp keys, and returns a list
  - of those that might still have value, or might be stale and removable.
diff --git a/Command/Version.hs b/Command/Version.hs
index 4cc5cb4aec..907811e750 100644
--- a/Command/Version.hs
+++ b/Command/Version.hs
@@ -29,8 +29,8 @@ start = do
 		putStrLn $ "supported repository versions: " ++ vs supportedVersions
 		putStrLn $ "upgrade supported from repository versions: " ++ vs upgradableVersions
 	stop
-	where
-		vs = join " "
+  where
+	vs = join " "
 
 showPackageVersion :: IO ()
 showPackageVersion = putStrLn $ "git-annex version: " ++ SysConfig.packageversion
diff --git a/Command/Vicfg.hs b/Command/Vicfg.hs
index 0466c0c31a..cfe051c4e3 100644
--- a/Command/Vicfg.hs
+++ b/Command/Vicfg.hs
@@ -75,119 +75,116 @@ setCfg curcfg newcfg = do
 
 diffCfg :: Cfg -> Cfg -> (TrustMap, M.Map UUID (S.Set Group), M.Map UUID String)
 diffCfg curcfg newcfg = (diff cfgTrustMap, diff cfgGroupMap, diff cfgPreferredContentMap)
-	where
-		diff f = M.differenceWith (\x y -> if x == y then Nothing else Just x)
-			(f newcfg) (f curcfg)
+  where
+	diff f = M.differenceWith (\x y -> if x == y then Nothing else Just x)
+		(f newcfg) (f curcfg)
 
 genCfg :: Cfg -> M.Map UUID String -> String
 genCfg cfg descs = unlines $ concat [intro, trust, groups, preferredcontent]
-	where
-		intro =
-			[ com "git-annex configuration"
-			, com ""
-			, com "Changes saved to this file will be recorded in the git-annex branch."
-			, com ""
-			, com "Lines in this file have the format:"
-			, com "  setting uuid = value"
-			]
+  where
+	intro =
+		[ com "git-annex configuration"
+		, com ""
+		, com "Changes saved to this file will be recorded in the git-annex branch."
+		, com ""
+		, com "Lines in this file have the format:"
+		, com "  setting uuid = value"
+		]
 
-		trust = settings cfgTrustMap
-			[ ""
-			, com "Repository trust configuration"
-			, com "(Valid trust levels: " ++
-			  unwords (map showTrustLevel [Trusted .. DeadTrusted]) ++
-			  ")"
-			]
-			(\(t, u) -> line "trust" u $ showTrustLevel t)
-			(\u -> lcom $ line "trust" u $ showTrustLevel SemiTrusted)
+	trust = settings cfgTrustMap
+		[ ""
+		, com "Repository trust configuration"
+		, com "(Valid trust levels: " ++
+		  unwords (map showTrustLevel [Trusted .. DeadTrusted]) ++
+		  ")"
+		]
+		(\(t, u) -> line "trust" u $ showTrustLevel t)
+		(\u -> lcom $ line "trust" u $ showTrustLevel SemiTrusted)
 
-		groups = settings cfgGroupMap
-			[ ""
-			, com "Repository groups"
-			, com "(Separate group names with spaces)"
-			]
-			(\(s, u) -> line "group" u $ unwords $ S.toList s)
-			(\u -> lcom $ line "group" u "")
+	groups = settings cfgGroupMap
+		[ ""
+		, com "Repository groups"
+		, com "(Separate group names with spaces)"
+		]
+		(\(s, u) -> line "group" u $ unwords $ S.toList s)
+		(\u -> lcom $ line "group" u "")
 
-		preferredcontent = settings cfgPreferredContentMap
-			[ ""
-			, com "Repository preferred contents"
-			]
-			(\(s, u) -> line "preferred-content" u s)
-			(\u -> line "preferred-content" u "")
+	preferredcontent = settings cfgPreferredContentMap
+		[ ""
+		, com "Repository preferred contents"
+		]
+		(\(s, u) -> line "preferred-content" u s)
+		(\u -> line "preferred-content" u "")
 
-		settings field desc showvals showdefaults = concat
-			[ desc
-			, concatMap showvals $
-				sort $ map swap $ M.toList $ field cfg
-			, concatMap (\u -> lcom $ showdefaults u) $
-				missing field
-			]
+	settings field desc showvals showdefaults = concat
+		[ desc
+		, concatMap showvals $ sort $ map swap $ M.toList $ field cfg
+		, concatMap (\u -> lcom $ showdefaults u) $ missing field
+		]
 
-		line setting u value =
-			[ com $ "(for " ++ (fromMaybe "" $ M.lookup u descs) ++ ")"
-			, unwords [setting, fromUUID u, "=", value]
-			]
-		lcom = map (\l -> if "#" `isPrefixOf` l then l else "#" ++ l)
-		missing field = S.toList $ M.keysSet descs `S.difference` M.keysSet (field cfg)
+	line setting u value =
+		[ com $ "(for " ++ (fromMaybe "" $ M.lookup u descs) ++ ")"
+		, unwords [setting, fromUUID u, "=", value]
+		]
+	lcom = map (\l -> if "#" `isPrefixOf` l then l else "#" ++ l)
+	missing field = S.toList $ M.keysSet descs `S.difference` M.keysSet (field cfg)
 
 {- If there's a parse error, returns a new version of the file,
  - with the problem lines noted. -}
 parseCfg :: Cfg -> String -> Either String Cfg
 parseCfg curcfg = go [] curcfg . lines
-	where
-		go c cfg []
-			| null (catMaybes $ map fst c) = Right cfg
-			| otherwise = Left $ unlines $
-				badheader ++ concatMap showerr (reverse c)
-		go c cfg (l:ls) = case parse (dropWhile isSpace l) cfg of
-			Left msg -> go ((Just msg, l):c) cfg ls
-			Right cfg' -> go ((Nothing, l):c) cfg' ls
+  where
+	go c cfg []
+		| null (catMaybes $ map fst c) = Right cfg
+		| otherwise = Left $ unlines $
+			badheader ++ concatMap showerr (reverse c)
+	go c cfg (l:ls) = case parse (dropWhile isSpace l) cfg of
+		Left msg -> go ((Just msg, l):c) cfg ls
+		Right cfg' -> go ((Nothing, l):c) cfg' ls
 
-		parse l cfg
-			| null l = Right cfg
-			| "#" `isPrefixOf` l = Right cfg
-			| null setting || null u = Left "missing repository uuid"
-			| otherwise = handle cfg (toUUID u) setting value'
-			where
-				(setting, rest) = separate isSpace l
-				(r, value) = separate (== '=') rest
-				value' = trimspace value
-				u = reverse $ trimspace $
-					reverse $ trimspace r
-				trimspace = dropWhile isSpace
+	parse l cfg
+		| null l = Right cfg
+		| "#" `isPrefixOf` l = Right cfg
+		| null setting || null u = Left "missing repository uuid"
+		| otherwise = handle cfg (toUUID u) setting value'
+	  where
+		(setting, rest) = separate isSpace l
+		(r, value) = separate (== '=') rest
+		value' = trimspace value
+		u = reverse $ trimspace $ reverse $ trimspace r
+		trimspace = dropWhile isSpace
 
-		handle cfg u setting value
-			| setting == "trust" = case readTrustLevel value of
-				Nothing -> badval "trust value" value
-				Just t ->
-					let m = M.insert u t (cfgTrustMap cfg)
-					in Right $ cfg { cfgTrustMap = m }
-			| setting == "group" =
-				let m = M.insert u (S.fromList $ words value) (cfgGroupMap cfg)
-				in Right $ cfg { cfgGroupMap = m }
-			| setting == "preferred-content" = 
-				case checkPreferredContentExpression value of
-					Just e -> Left e
-					Nothing ->
-						let m = M.insert u value (cfgPreferredContentMap cfg)
-						in Right $ cfg { cfgPreferredContentMap = m }
-			| otherwise = badval "setting" setting
+	handle cfg u setting value
+		| setting == "trust" = case readTrustLevel value of
+			Nothing -> badval "trust value" value
+			Just t ->
+				let m = M.insert u t (cfgTrustMap cfg)
+				in Right $ cfg { cfgTrustMap = m }
+		| setting == "group" =
+			let m = M.insert u (S.fromList $ words value) (cfgGroupMap cfg)
+			in Right $ cfg { cfgGroupMap = m }
+		| setting == "preferred-content" = 
+			case checkPreferredContentExpression value of
+				Just e -> Left e
+				Nothing ->
+					let m = M.insert u value (cfgPreferredContentMap cfg)
+					in Right $ cfg { cfgPreferredContentMap = m }
+		| otherwise = badval "setting" setting
 
-		showerr (Just msg, l) = [parseerr ++ msg, l]
-		showerr (Nothing, l)
-			-- filter out the header and parse error lines
-			-- from any previous parse failure
-			| any (`isPrefixOf` l) (parseerr:badheader) = []
-			| otherwise = [l]
+	showerr (Just msg, l) = [parseerr ++ msg, l]
+	showerr (Nothing, l)
+		-- filter out the header and parse error lines
+		-- from any previous parse failure
+		| any (`isPrefixOf` l) (parseerr:badheader) = []
+		| otherwise = [l]
 
-		badval desc val = Left $ "unknown " ++ desc ++ " \"" ++ val ++ "\""
-		badheader = 
-			[ com "There was a problem parsing your input."
-			, com "Search for \"Parse error\" to find the bad lines."
-			, com "Either fix the bad lines, or delete them (to discard your changes)."
-			]
-		parseerr = com "Parse error in next line: "
+	badval desc val = Left $ "unknown " ++ desc ++ " \"" ++ val ++ "\""
+	badheader = 
+		[ com "There was a problem parsing your input."
+		, com "Search for \"Parse error\" to find the bad lines."
+		, com "Either fix the bad lines, or delete them (to discard your changes)."
+		]
+	parseerr = com "Parse error in next line: "
 
 com :: String -> String
 com s = "# " ++ s
diff --git a/Command/WebApp.hs b/Command/WebApp.hs
index 43b090fc88..a0bd2e7f7e 100644
--- a/Command/WebApp.hs
+++ b/Command/WebApp.hs
@@ -43,24 +43,24 @@ start' allowauto = notBareRepo $ do
 	liftIO $ ensureInstalled
 	ifM isInitialized ( go , auto )
 	stop
-	where
-		go = do
-			browser <- fromRepo webBrowser
-			f <- liftIO . absPath =<< fromRepo gitAnnexHtmlShim
-			ifM (checkpid <&&> checkshim f)
-				( liftIO $ openBrowser browser f 
-				, startDaemon True True $ Just $
-					const $ openBrowser browser
-				)
-		auto
-			| allowauto = liftIO startNoRepo
-			| otherwise = do
-				d <- liftIO getCurrentDirectory
-				error $ "no git repository in " ++ d
-		checkpid = do
-			pidfile <- fromRepo gitAnnexPidFile
-			liftIO $ isJust <$> checkDaemon pidfile
-		checkshim f = liftIO $ doesFileExist f
+  where
+	go = do
+		browser <- fromRepo webBrowser
+		f <- liftIO . absPath =<< fromRepo gitAnnexHtmlShim
+		ifM (checkpid <&&> checkshim f)
+			( liftIO $ openBrowser browser f 
+			, startDaemon True True $ Just $
+				const $ openBrowser browser
+			)
+	auto
+		| allowauto = liftIO startNoRepo
+		| otherwise = do
+			d <- liftIO getCurrentDirectory
+			error $ "no git repository in " ++ d
+	checkpid = do
+		pidfile <- fromRepo gitAnnexPidFile
+		liftIO $ isJust <$> checkDaemon pidfile
+	checkshim f = liftIO $ doesFileExist f
 
 {- When run without a repo, see if there is an autoStartFile,
  - and if so, start the first available listed repository.
@@ -111,35 +111,35 @@ firstRun = do
 		webAppThread d urlrenderer True 
 			(callback signaler)
 			(callback mainthread)
-	where
-		signaler v = do
-			putMVar v ""
-			takeMVar v
-		mainthread v _url htmlshim = do
-			browser <- maybe Nothing webBrowser <$> Git.Config.global
-			openBrowser browser htmlshim
+  where
+	signaler v = do
+		putMVar v ""
+		takeMVar v
+	mainthread v _url htmlshim = do
+		browser <- maybe Nothing webBrowser <$> Git.Config.global
+		openBrowser browser htmlshim
 
-			_wait <- takeMVar v
+		_wait <- takeMVar v
 
-			state <- Annex.new =<< Git.CurrentRepo.get
-			Annex.eval state $ do
-				dummydaemonize
-				startAssistant True id $ Just $ sendurlback v
-		sendurlback v url _htmlshim = putMVar v url
-		{- Set up the pid file in the new repo. -}
-		dummydaemonize =
-			liftIO . lockPidFile =<< fromRepo gitAnnexPidFile
+		state <- Annex.new =<< Git.CurrentRepo.get
+		Annex.eval state $ do
+			dummydaemonize
+			startAssistant True id $ Just $ sendurlback v
+	sendurlback v url _htmlshim = putMVar v url
+
+	{- Set up the pid file in the new repo. -}
+	dummydaemonize = liftIO . lockPidFile =<< fromRepo gitAnnexPidFile
 
 openBrowser :: Maybe FilePath -> FilePath -> IO ()
 openBrowser cmd htmlshim = go $ maybe runBrowser runCustomBrowser cmd
-	where
-		url = fileUrl htmlshim
-		go a = do
-			putStrLn ""
-			putStrLn $ "Launching web browser on " ++ url
-			unlessM (a url) $
-				error $ "failed to start web browser"
-		runCustomBrowser c u = boolSystem c [Param u]
+  where
+	url = fileUrl htmlshim
+	go a = do
+		putStrLn ""
+		putStrLn $ "Launching web browser on " ++ url
+		unlessM (a url) $
+			error $ "failed to start web browser"
+	runCustomBrowser c u = boolSystem c [Param u]
 
 {- web.browser is a generic git config setting for a web browser program -}
 webBrowser :: Git.Repo -> Maybe FilePath
diff --git a/Command/Whereis.hs b/Command/Whereis.hs
index c77b3a02ca..251c4ec7aa 100644
--- a/Command/Whereis.hs
+++ b/Command/Whereis.hs
@@ -40,15 +40,15 @@ perform remotemap key = do
 	forM_ (mapMaybe (`M.lookup` remotemap) locations) $
 		performRemote key
 	if null safelocations then stop else next $ return True
-	where
-		copiesplural 1 = "copy"
-		copiesplural _ = "copies"
-		untrustedheader = "The following untrusted locations may also have copies:\n"
+  where
+	copiesplural 1 = "copy"
+	copiesplural _ = "copies"
+	untrustedheader = "The following untrusted locations may also have copies:\n"
 
 performRemote :: Key -> Remote -> Annex () 
 performRemote key remote = maybe noop go $ whereisKey remote
-	where
-		go a = do
-			ls <- a key
-			unless (null ls) $ showLongNote $ unlines $
-				map (\l -> name remote ++ ": " ++ l) ls
+  where
+	go a = do
+		ls <- a key
+		unless (null ls) $ showLongNote $ unlines $
+			map (\l -> name remote ++ ": " ++ l) ls