diff --git a/Annex.hs b/Annex.hs
--- a/Annex.hs
+++ b/Annex.hs
@@ -5,6 +5,8 @@
  - Licensed under the GNU GPL version 3 or higher.
  -}
 
+{-# LANGUAGE GeneralizedNewtypeDeriving #-}
+
 module Annex (
 	Annex,
 	AnnexState(..),
@@ -17,6 +19,7 @@
 ) where
 
 import Control.Monad.State
+import Control.Monad.IO.Control
 
 import qualified Git
 import Git.Queue
@@ -28,7 +31,14 @@
 import Types.UUID
 
 -- git-annex's monad
-type Annex = StateT AnnexState IO
+newtype Annex a = Annex { runAnnex :: StateT AnnexState IO a }
+	deriving (
+		Functor,
+		Monad,
+		MonadIO,
+		MonadControlIO,
+		MonadState AnnexState
+	)
 
 -- internal state storage
 data AnnexState = AnnexState
@@ -74,13 +84,13 @@
 
 {- Create and returns an Annex state object for the specified git repo. -}
 new :: Git.Repo -> IO AnnexState
-new gitrepo = newState `liftM` (liftIO . Git.configRead) gitrepo
+new gitrepo = newState `liftM` Git.configRead gitrepo
 
 {- performs an action in the Annex monad -}
 run :: AnnexState -> Annex a -> IO (a, AnnexState)
-run = flip runStateT
+run s a = runStateT (runAnnex a) s
 eval :: AnnexState -> Annex a -> IO a
-eval = flip evalStateT
+eval s a = evalStateT (runAnnex a) s
 
 {- Gets a value from the internal state, selected by the passed value
  - constructor. -}
diff --git a/AnnexQueue.hs b/AnnexQueue.hs
--- a/AnnexQueue.hs
+++ b/AnnexQueue.hs
@@ -21,10 +21,10 @@
 
 {- Adds a git command to the queue, possibly running previously queued
  - actions if enough have accumulated. -}
-add :: String -> [CommandParam] -> FilePath -> Annex ()
-add command params file = do
+add :: String -> [CommandParam] -> [FilePath] -> Annex ()
+add command params files = do
 	q <- getState repoqueue
-	store $ Git.Queue.add q command params file
+	store $ Git.Queue.add q command params files
 
 {- Runs the queue if it is full. Should be called periodically. -}
 flushWhenFull :: Annex ()
@@ -38,7 +38,7 @@
 	q <- getState repoqueue
 	unless (0 == Git.Queue.size q) $ do
 		unless silent $
-			showSideAction "Recording state in git..."
+			showSideAction "Recording state in git"
 		g <- gitRepo
 		q' <- liftIO $ Git.Queue.flush g q
 		store q'
diff --git a/Backend.hs b/Backend.hs
--- a/Backend.hs
+++ b/Backend.hs
@@ -19,6 +19,7 @@
 import System.IO.Error (try)
 import System.FilePath
 import System.Posix.Files
+import Data.Maybe
 
 import Locations
 import qualified Git
@@ -31,12 +32,10 @@
 -- When adding a new backend, import it here and add it to the list.
 import qualified Backend.WORM
 import qualified Backend.SHA
+import qualified Backend.URL
 
 list :: [Backend Annex]
-list = concat 
-	[ Backend.WORM.backends
-	, Backend.SHA.backends
-	]
+list = Backend.WORM.backends ++ Backend.SHA.backends ++ Backend.URL.backends
 
 {- List of backends in the order to try them when storing a new key. -}
 orderedList :: Annex [Backend Annex]
@@ -54,7 +53,7 @@
 		handle Nothing s = return s
 		handle (Just "") s = return s
 		handle (Just name) s = do
-			let l' = (lookupBackendName name):s
+			let l' = lookupBackendName name : s
 			Annex.changeState $ \state -> state { Annex.backends = l' }
 			return l'
 		getstandard = do
@@ -67,7 +66,7 @@
 genKey :: FilePath -> Maybe (Backend Annex) -> Annex (Maybe (Key, Backend Annex))
 genKey file trybackend = do
 	bs <- orderedList
-	let bs' = maybe bs (:bs) trybackend
+	let bs' = maybe bs (: bs) trybackend
 	genKey' bs' file
 genKey' :: [Backend Annex] -> FilePath -> Annex (Maybe (Key, Backend Annex))
 genKey' [] _ = return Nothing
@@ -119,7 +118,7 @@
 
 {- Looks up a backend by name. May fail if unknown. -}
 lookupBackendName :: String -> Backend Annex
-lookupBackendName s = maybe unknown id $ maybeLookupBackendName s
+lookupBackendName s = fromMaybe unknown $ maybeLookupBackendName s
 	where
 		unknown = error $ "unknown backend " ++ s
 maybeLookupBackendName :: String -> Maybe (Backend Annex)
diff --git a/Backend/SHA.hs b/Backend/SHA.hs
--- a/Backend/SHA.hs
+++ b/Backend/SHA.hs
@@ -32,7 +32,7 @@
 sizes = [1, 256, 512, 224, 384]
 
 backends :: [Backend Annex]
--- order is slightly significant; want sha1 first ,and more general
+-- order is slightly significant; want sha1 first, and more general
 -- sizes earlier
 backends = catMaybes $ map genBackend sizes ++ map genBackendE sizes
 
@@ -72,7 +72,7 @@
 
 shaN :: SHASize -> FilePath -> Annex String
 shaN size file = do
-	showNote "checksum..."
+	showAction "checksum"
 	liftIO $ pOpen ReadFromPipe command (toCommand [File file]) $ \h -> do
 		line <- hGetLine h
 		let bits = split " " line
@@ -107,14 +107,14 @@
 				then "" -- probably not really an extension
 				else naiveextension
 
--- A key's checksum is checked during fsck.
+{- A key's checksum is checked during fsck. -}
 checkKeyChecksum :: SHASize -> Key -> Annex Bool
 checkKeyChecksum size key = do
 	g <- Annex.gitRepo
 	fast <- Annex.getState Annex.fast
 	let file = gitAnnexLocation g key
 	present <- liftIO $ doesFileExist file
-	if (not present || fast)
+	if not present || fast
 		then return True
 		else do
 			s <- shaN size file
diff --git a/Backend/URL.hs b/Backend/URL.hs
new file mode 100644
--- /dev/null
+++ b/Backend/URL.hs
@@ -0,0 +1,28 @@
+{- git-annex "URL" backend -- keys whose content is available from urls.
+ -
+ - Copyright 2011 Joey Hess <joey@kitenet.net>
+ -
+ - Licensed under the GNU GPL version 3 or higher.
+ -}
+
+module Backend.URL (
+	backends,
+	fromUrl
+) where
+
+import Types.Backend
+import Types.Key
+import Types
+
+backends :: [Backend Annex]
+backends = [backend]
+
+backend :: Backend Annex
+backend = Types.Backend.Backend {
+	name = "URL",
+	getKey = const (return Nothing),
+	fsckKey = const (return True)
+}
+
+fromUrl :: String -> Key
+fromUrl url = stubKey { keyName = url, keyBackendName = "URL" }
diff --git a/Backend/WORM.hs b/Backend/WORM.hs
--- a/Backend/WORM.hs
+++ b/Backend/WORM.hs
@@ -35,7 +35,7 @@
 keyValue :: FilePath -> Annex (Maybe Key)
 keyValue file = do
 	stat <- liftIO $ getFileStatus file
-	return $ Just $ Key {
+	return $ Just Key {
 		keyName = takeFileName file,
 		keyBackendName = name backend,
 		keySize = Just $ fromIntegral $ fileSize stat,
diff --git a/Branch.hs b/Branch.hs
--- a/Branch.hs
+++ b/Branch.hs
@@ -14,6 +14,7 @@
 	files,
 	refExists,
 	hasOrigin,
+	hasSomeBranch,
 	name	
 ) where
 
@@ -87,7 +88,7 @@
 
 	e <- liftIO $ doesFileExist f
 	unless e $ do
-		unless bootstrapping $ create
+		unless bootstrapping create
 		liftIO $ createDirectoryIfMissing True $ takeDirectory f
 		liftIO $ unless bootstrapping $ genIndex g
 
@@ -124,7 +125,7 @@
 
 {- Creates the branch, if it does not already exist. -}
 create :: Annex ()
-create = unlessM (refExists fullname) $ do
+create = unlessM hasBranch $ do
 	g <- Annex.gitRepo
 	e <- hasOrigin
 	if e
@@ -154,19 +155,14 @@
 		 -}
 		staged <- stageJournalFiles
 
-		g <- Annex.gitRepo
-		r <- liftIO $ Git.pipeRead g [Param "show-ref", Param name]
-		let refs = map (last . words) (lines r)
+		refs <- siblingBranches
 		updated <- catMaybes `liftM` mapM updateRef refs
+		g <- Annex.gitRepo
 		unless (null updated && not staged) $ liftIO $
 			Git.commit g "update" fullname (fullname:updated)
 		Annex.changeState $ \s -> s { Annex.branchstate = state { branchUpdated = True } }
 		invalidateCache
 
-{- Does origin/git-annex exist? -}
-hasOrigin :: Annex Bool
-hasOrigin = refExists originname
-
 {- Checks if a git ref exists. -}
 refExists :: GitRef -> Annex Bool
 refExists ref = do
@@ -174,6 +170,26 @@
 	liftIO $ Git.runBool g "show-ref"
 		[Param "--verify", Param "-q", Param ref]
 
+{- Does the main git-annex branch exist? -}
+hasBranch :: Annex Bool
+hasBranch = refExists fullname
+
+{- Does origin/git-annex exist? -}
+hasOrigin :: Annex Bool
+hasOrigin = refExists originname
+
+{- Does the git-annex branch or a foo/git-annex branch exist? -}
+hasSomeBranch :: Annex Bool
+hasSomeBranch = liftM (not . null) siblingBranches
+
+{- List of all git-annex branches, including the main one and any
+ - from remotes. -}
+siblingBranches :: Annex [String]
+siblingBranches = do
+	g <- Annex.gitRepo
+	r <- liftIO $ Git.pipeRead g [Param "show-ref", Param name]
+	return $ map (last . words) (lines r)
+
 {- Ensures that a given ref has been merged into the index. -}
 updateRef :: GitRef -> Annex (Maybe String)
 updateRef ref
@@ -187,10 +203,10 @@
 			Param (name++".."++ref),
 			Params "--oneline -n1"
 			]
-		if (null diffs)
+		if null diffs
 			then return Nothing
 			else do
-				showSideAction $ "merging " ++ shortref ref ++ " into " ++ name ++ "..."
+				showSideAction $ "merging " ++ shortref ref ++ " into " ++ name
 				-- By passing only one ref, it is actually
 				-- merged into the index, preserving any
 				-- changes that may already be staged.
@@ -305,7 +321,7 @@
 
 {- List of journal files. -}
 getJournalFiles :: Annex [FilePath]
-getJournalFiles = getJournalFilesRaw >>= return . map fileJournal
+getJournalFiles = fmap (map fileJournal) getJournalFilesRaw
 
 getJournalFilesRaw :: Annex [FilePath]
 getJournalFilesRaw = do
diff --git a/CHANGELOG b/CHANGELOG
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -1,3 +1,34 @@
+git-annex (3.20110819) unstable; urgency=low
+
+  * Now "git annex init" only has to be run once, when a git repository
+    is first being created. Clones will automatically notice that git-annex
+    is in use and automatically perform a basic initalization. It's
+    still recommended to run "git annex init" in any clones, to describe them.
+  * Added annex-cost-command configuration, which can be used to vary the
+    cost of a remote based on the output of a shell command.
+  * Fix broken upgrade from V1 repository. Closes: #638584
+
+ -- Joey Hess <joeyh@debian.org>  Fri, 19 Aug 2011 20:34:09 -0400
+
+git-annex (3.20110817) unstable; urgency=low
+
+  * Fix shell escaping in rsync special remote.
+  * addurl: --fast can be used to avoid immediately downloading the url.
+  * Added support for getting content from git remotes using http (and https).
+  * Added curl to Debian package dependencies.
+
+ -- Joey Hess <joeyh@debian.org>  Wed, 17 Aug 2011 01:29:02 -0400
+
+git-annex (3.20110719) unstable; urgency=low
+
+  * add: Be even more robust to avoid ever leaving the file seemingly deleted.
+    Closes: #634233
+  * Bugfix: Make add ../ work.
+  * Support the standard git -c name=value
+  * unannex: Clean up use of git commit -a.
+
+ -- Joey Hess <joeyh@debian.org>  Tue, 19 Jul 2011 23:39:53 -0400
+
 git-annex (3.20110707) unstable; urgency=low
 
   * Fix sign bug in disk free space checking.
diff --git a/CmdLine.hs b/CmdLine.hs
--- a/CmdLine.hs
+++ b/CmdLine.hs
@@ -22,10 +22,9 @@
 import Content
 import Types
 import Command
-import Version
 import Options
 import Messages
-import UUID
+import Init
 
 {- Runs the passed command line. -}
 dispatch :: [String] -> [Command] -> [Option] -> String -> Git.Repo -> IO ()
@@ -39,14 +38,13 @@
  - list of actions to be run in the Annex monad. -}
 parseCmd :: [String] -> String -> [Command] -> [Option] -> Annex [Annex Bool]
 parseCmd argv header cmds options = do
-	(flags, params) <- liftIO $ getopt
+	(flags, params) <- liftIO getopt
 	when (null params) $ error $ "missing command" ++ usagemsg
 	case lookupCmd (head params) of
 		[] -> error $ "unknown command" ++ usagemsg
 		[command] -> do
 			_ <- sequence flags
-			when (cmdusesrepo command) $
-				checkVersion
+			checkCmdEnviron command
 			prepCommand command (drop 1 params)
 		_ -> error "internal error: multiple matching commands"
 	where
@@ -58,6 +56,10 @@
 		lookupCmd cmd = filter (\c -> cmd  == cmdname c) cmds
 		usagemsg = "\n\n" ++ usage header cmds options
 
+{- Checks that the command can be run in the current environment. -}
+checkCmdEnviron :: Command -> Annex ()
+checkCmdEnviron command = when (cmdusesrepo command) ensureInitialized
+
 {- Usage message with lists of commands and options. -}
 usage :: String -> [Command] -> [Option] -> String
 usage header cmds options =
@@ -78,9 +80,9 @@
  - (but explicitly thrown errors terminate the whole command).
  -}
 tryRun :: Annex.AnnexState -> [Annex Bool] -> IO ()
-tryRun state actions = tryRun' state 0 actions
-tryRun' :: Annex.AnnexState -> Integer -> [Annex Bool] -> IO ()
-tryRun' state errnum (a:as) = do
+tryRun = tryRun' 0
+tryRun' :: Integer -> Annex.AnnexState -> [Annex Bool] -> IO ()
+tryRun' errnum state (a:as) = do
 	result <- try $ Annex.run state $ do
 		AnnexQueue.flushWhenFull
 		a
@@ -89,21 +91,18 @@
 			Annex.eval state $ do
 				showEndFail
 				showErr err
-			tryRun' state (errnum + 1) as
-		Right (True,state') -> tryRun' state' errnum as
-		Right (False,state') -> tryRun' state' (errnum + 1) as
-tryRun' _ errnum [] = do
-	when (errnum > 0) $ error $ show errnum ++ " failed"
+			tryRun' (errnum + 1) state as
+		Right (True,state') -> tryRun' errnum state' as
+		Right (False,state') -> tryRun' (errnum + 1) state' as
+tryRun' errnum _ [] = when (errnum > 0) $ error $ show errnum ++ " failed"
 
 {- Actions to perform each time ran. -}
 startup :: Annex Bool
-startup = do
-	prepUUID
-	return True
+startup = return True
 
 {- Cleanup actions. -}
 shutdown :: Annex Bool
 shutdown = do
 	saveState
-	liftIO $ Git.reap
+	liftIO Git.reap
 	return True
diff --git a/Command.hs b/Command.hs
--- a/Command.hs
+++ b/Command.hs
@@ -102,7 +102,7 @@
 		stage a b = b >>= a
 		success = return True
 		failure = do
-			showProgress
+			showOutput -- avoid clutter around error message
 			showEndFail
 			return False
 
@@ -115,7 +115,7 @@
 notBareRepo :: Annex a -> Annex a
 notBareRepo a = do
 	g <- Annex.gitRepo
-	when (Git.repoIsLocalBare g) $ do
+	when (Git.repoIsLocalBare g) $
 		error "You cannot run this subcommand in a bare repository."
 	a
 
@@ -175,11 +175,9 @@
 	unlockedfiles' <- filterFiles unlockedfiles
 	backendPairs a unlockedfiles'
 withKeys :: CommandSeekKeys
-withKeys a params = return $ map a $ map parse params
+withKeys a params = return $ map (a . parse) params
 	where
-		parse p = maybe (error "bad key") id $ readKey p
-withTempFile :: CommandSeekStrings
-withTempFile a params = return $ map a params
+		parse p = fromMaybe (error "bad key") $ readKey p
 withNothing :: CommandSeekNothing
 withNothing a [] = return [a]
 withNothing _ _ = error "This command takes no parameters."
diff --git a/Command/Add.hs b/Command/Add.hs
--- a/Command/Add.hs
+++ b/Command/Add.hs
@@ -8,7 +8,12 @@
 module Command.Add where
 
 import Control.Monad.State (liftIO)
+import Control.Monad (when)
 import System.Posix.Files
+import System.Directory
+import Control.Exception.Control (handle)
+import Control.Exception.Base (throwIO)
+import Control.Exception.Extensible (IOException)
 
 import Command
 import qualified Annex
@@ -20,6 +25,7 @@
 import Messages
 import Utility
 import Touch
+import Locations
 
 command :: [Command]
 command = [repoCommand "add" paramPath seek "add files to annex"]
@@ -34,7 +40,7 @@
 start :: CommandStartBackendFile
 start pair@(file, _) = notAnnexed file $ do
 	s <- liftIO $ getSymbolicLinkStatus file
-	if (isSymbolicLink s) || (not $ isRegularFile s)
+	if isSymbolicLink s || not (isRegularFile s)
 		then stop
 		else do
 			showStart "add" file
@@ -46,23 +52,44 @@
 	case k of
 		Nothing -> stop
 		Just (key, _) -> do
-			moveAnnex key file
-			next $ cleanup file key
+			handle (undo file key) $ moveAnnex key file
+			next $ cleanup file key True
 
-cleanup :: FilePath -> Key -> CommandCleanup
-cleanup file key = do
-	link <- calcGitLink file key
-	liftIO $ createSymbolicLink link file
+{- On error, put the file back so it doesn't seem to have vanished.
+ - This can be called before or after the symlink is in place. -}
+undo :: FilePath -> Key -> IOException -> Annex a
+undo file key e = do
+	unlessM (inAnnex key) rethrow -- no cleanup to do
+	liftIO $ whenM (doesFileExist file) $ removeFile file
+	handle tryharder $ fromAnnex key file
+	logStatus key InfoMissing
+	rethrow
+	where
+		rethrow = liftIO $ throwIO e
 
-	logStatus key InfoPresent
+		-- fromAnnex could fail if the file ownership is weird
+		tryharder :: IOException -> Annex ()
+		tryharder _ = do
+			g <- Annex.gitRepo
+			liftIO $ renameFile (gitAnnexLocation g key) file
 
-	-- touch the symlink to have the same mtime as the file it points to
-	s <- liftIO $ getFileStatus file
-	let mtime = modificationTime s
-	liftIO $ touch file (TimeSpec mtime) False
+cleanup :: FilePath -> Key -> Bool -> CommandCleanup
+cleanup file key hascontent = do
+	handle (undo file key) $ do
+		link <- calcGitLink file key
+		liftIO $ createSymbolicLink link file
 
+		when hascontent $ do
+			logStatus key InfoPresent
+	
+			-- touch the symlink to have the same mtime as the
+			-- file it points to
+			s <- liftIO $ getFileStatus file
+			let mtime = modificationTime s
+			liftIO $ touch file (TimeSpec mtime) False
+
 	force <- Annex.getState Annex.force
 	if force
-		then AnnexQueue.add "add" [Param "-f", Param "--"] file
-		else AnnexQueue.add "add" [Param "--"] file
+		then AnnexQueue.add "add" [Param "-f", Param "--"] [file]
+		else AnnexQueue.add "add" [Param "--"] [file]
 	return True
diff --git a/Command/AddUrl.hs b/Command/AddUrl.hs
--- a/Command/AddUrl.hs
+++ b/Command/AddUrl.hs
@@ -14,13 +14,14 @@
 
 import Command
 import qualified Backend
+import qualified Remote.Helper.Url
 import qualified Remote.Web
 import qualified Command.Add
 import qualified Annex
+import qualified Backend.URL
 import Messages
 import Content
 import PresenceLog
-import Types.Key
 import Locations
 import Utility
 
@@ -42,12 +43,17 @@
 			
 perform :: String -> FilePath -> CommandPerform
 perform url file = do
+	fast <- Annex.getState Annex.fast
+	if fast then nodownload url file else download url file
+
+download :: String -> FilePath -> CommandPerform
+download url file = do
 	g <- Annex.gitRepo
-	showNote $ "downloading " ++ url
-	let dummykey = stubKey { keyName = url, keyBackendName = "URL" }
+	showAction $ "downloading " ++ url ++ " "
+	let dummykey = Backend.URL.fromUrl url
 	let tmp = gitAnnexTmpLocation g dummykey
 	liftIO $ createDirectoryIfMissing True (parentDir tmp)
-	ok <- Remote.Web.download [url] tmp
+	ok <- Remote.Helper.Url.download url tmp
 	if ok
 		then do
 			[(_, backend)] <- Backend.chooseBackends [file]
@@ -57,9 +63,16 @@
 				Just (key, _) -> do
 					moveAnnex key tmp
 					Remote.Web.setUrl key url InfoPresent
-					next $ Command.Add.cleanup file key
+					next $ Command.Add.cleanup file key True
 		else stop
 
+nodownload :: String -> FilePath -> CommandPerform
+nodownload url file = do
+	let key = Backend.URL.fromUrl url
+	Remote.Web.setUrl key url InfoPresent
+	
+	next $ Command.Add.cleanup file key False
+
 url2file :: URI -> IO FilePath
 url2file url = do
 	let parts = filter safe $ split "/" $ uriPath url
@@ -75,8 +88,7 @@
 			e <- doesFileExist file
 			when e $ error "already have this url"
 			return file
-		safe s
-			| null s = False
-			| s == "." = False
-			| s == ".." = False
-			| otherwise = True
+		safe "" = False
+		safe "." = False
+		safe ".." = False
+		safe _ = True
diff --git a/Command/ConfigList.hs b/Command/ConfigList.hs
--- a/Command/ConfigList.hs
+++ b/Command/ConfigList.hs
@@ -14,7 +14,7 @@
 import UUID
 
 command :: [Command]
-command = [standaloneCommand "configlist" paramNothing seek
+command = [repoCommand "configlist" paramNothing seek
 		"outputs relevant git configuration"]
 
 seek :: [CommandSeek]
diff --git a/Command/DropUnused.hs b/Command/DropUnused.hs
--- a/Command/DropUnused.hs
+++ b/Command/DropUnused.hs
@@ -49,7 +49,7 @@
 	]
 	where
 		search [] = stop
-		search ((m, a):rest) = do
+		search ((m, a):rest) =
 			case M.lookup s m of
 				Nothing -> search rest
 				Just key -> do
@@ -61,7 +61,7 @@
 	where
 		dropremote name = do
 			r <- Remote.byName name
-			showNote $ "from " ++ Remote.name r ++ "..."
+			showAction $ "from " ++ Remote.name r
 			next $ Command.Move.fromCleanup r True key
 		droplocal = Command.Drop.perform key (Just 0) -- force drop
 
@@ -78,10 +78,9 @@
 	let f = gitAnnexUnusedLog prefix g
 	e <- liftIO $ doesFileExist f
 	if e
-		then do
-			l <- liftIO $ readFile f
-			return $ M.fromList $ map parse $ lines l
-		else return $ M.empty
+		then return . M.fromList . map parse . lines
+			=<< liftIO (readFile f)
+		else return M.empty
 	where
 		parse line = (head ws, fromJust $ readKey $ unwords $ tail ws)
 			where
diff --git a/Command/Fix.hs b/Command/Fix.hs
--- a/Command/Fix.hs
+++ b/Command/Fix.hs
@@ -44,5 +44,5 @@
 
 cleanup :: FilePath -> CommandCleanup
 cleanup file = do
-	AnnexQueue.add "add" [Param "--"] file
+	AnnexQueue.add "add" [Param "--"] [file]
 	return True
diff --git a/Command/FromKey.hs b/Command/FromKey.hs
--- a/Command/FromKey.hs
+++ b/Command/FromKey.hs
@@ -45,5 +45,5 @@
 
 cleanup :: FilePath -> CommandCleanup
 cleanup file = do
-	AnnexQueue.add "add" [Param "--"] file
+	AnnexQueue.add "add" [Param "--"] [file]
 	return True
diff --git a/Command/Fsck.hs b/Command/Fsck.hs
--- a/Command/Fsck.hs
+++ b/Command/Fsck.hs
@@ -94,7 +94,7 @@
 fsckKey backend key file numcopies = do
 	size_ok <- checkKeySize key
 	copies_ok <- checkKeyNumCopies key file numcopies
-	backend_ok <-(Types.Backend.fsckKey backend) key
+	backend_ok <- (Types.Backend.fsckKey backend) key
 	return $ size_ok && copies_ok && backend_ok
 
 {- The size of the data for a key is checked against the size encoded in
diff --git a/Command/Get.hs b/Command/Get.hs
--- a/Command/Get.hs
+++ b/Command/Get.hs
@@ -75,7 +75,7 @@
 						Left _ -> return False
 				else return True
 		docopy r continue = do
-			showNote $ "from " ++ Remote.name r ++ "..."
+			showAction $ "from " ++ Remote.name r
 			copied <- Remote.retrieveKeyFile r key file
 			if copied
 				then return True
diff --git a/Command/InAnnex.hs b/Command/InAnnex.hs
--- a/Command/InAnnex.hs
+++ b/Command/InAnnex.hs
@@ -25,4 +25,4 @@
 	present <- inAnnex key
 	if present
 		then stop
-		else liftIO $ exitFailure
+		else liftIO exitFailure
diff --git a/Command/Init.hs b/Command/Init.hs
--- a/Command/Init.hs
+++ b/Command/Init.hs
@@ -7,19 +7,13 @@
 
 module Command.Init where
 
-import Control.Monad.State (liftIO)
-import Control.Monad (when, unless)
-import System.Directory
+import Control.Monad (when)
 
 import Command
 import qualified Annex
-import qualified Git
-import qualified Branch
 import UUID
-import Version
 import Messages
-import Types
-import Utility
+import Init
 	
 command :: [Command]
 command = [standaloneCommand "init" paramDesc seek
@@ -39,34 +33,8 @@
 
 perform :: String -> CommandPerform
 perform description = do
-	Branch.create
+	initialize
 	g <- Annex.gitRepo
 	u <- getUUID g
-	setVersion
 	describeUUID u description
-	unless (Git.repoIsLocalBare g) $
-		gitPreCommitHookWrite g
 	next $ return True
-
-{- set up a git pre-commit hook, if one is not already present -}
-gitPreCommitHookWrite :: Git.Repo -> Annex ()
-gitPreCommitHookWrite repo = do
-	exists <- liftIO $ doesFileExist hook
-	if exists
-		then warning $ "pre-commit hook (" ++ hook ++ ") already exists, not configuring"
-		else liftIO $ do
-			viaTmp writeFile hook preCommitScript
-			p <- getPermissions hook
-			setPermissions hook $ p {executable = True}
-	where
-		hook = preCommitHook repo
-
-preCommitHook :: Git.Repo -> FilePath
-preCommitHook repo = 
-	Git.workTree repo ++ "/" ++ Git.gitDir repo ++ "/hooks/pre-commit"
-
-preCommitScript :: String
-preCommitScript = 
-		"#!/bin/sh\n" ++
-		"# automatically configured by git-annex\n" ++ 
-		"git annex pre-commit .\n"
diff --git a/Command/InitRemote.hs b/Command/InitRemote.hs
--- a/Command/InitRemote.hs
+++ b/Command/InitRemote.hs
@@ -24,7 +24,7 @@
 command :: [Command]
 command = [repoCommand "initremote"
 	(paramPair paramName $
-		paramOptional $ paramRepeating $ paramKeyValue) seek
+		paramOptional $ paramRepeating paramKeyValue) seek
 	"sets up a special (non-git) remote"]
 
 seek :: [CommandSeek]
@@ -32,7 +32,7 @@
 
 start :: CommandStartWords
 start ws = do
-	when (null ws) $ needname
+	when (null ws) needname
 
 	(u, c) <- findByName name
 	let fullconfig = M.union config c	
@@ -69,7 +69,7 @@
 	maybe generate return $ findByName' name m
 	where
 		generate = do
-			uuid <- liftIO $ genUUID
+			uuid <- liftIO genUUID
 			return (uuid, M.insert nameKey name M.empty)
 
 findByName' :: String ->  M.Map UUID R.RemoteConfig -> Maybe (UUID, R.RemoteConfig)
@@ -85,7 +85,7 @@
 remoteNames :: Annex [String]
 remoteNames = do
 	m <- RemoteLog.readRemoteLog
-	return $ catMaybes $ map ((M.lookup nameKey) . snd) $ M.toList m
+	return $ mapMaybe (M.lookup nameKey . snd) $ M.toList m
 
 {- find the specified remote type -}
 findType :: R.RemoteConfig -> Annex (R.RemoteType Annex)
diff --git a/Command/Lock.hs b/Command/Lock.hs
--- a/Command/Lock.hs
+++ b/Command/Lock.hs
@@ -33,5 +33,5 @@
 	-- Checkout from HEAD to get rid of any changes that might be 
 	-- staged in the index, and get back to the previous symlink to
 	-- the content.
-	AnnexQueue.add "checkout" [Param "HEAD", Param "--"] file
+	AnnexQueue.add "checkout" [Param "HEAD", Param "--"] [file]
 	next $ return True -- no cleanup needed
diff --git a/Command/Map.hs b/Command/Map.hs
--- a/Command/Map.hs
+++ b/Command/Map.hs
@@ -12,6 +12,7 @@
 import System.Cmd.Utils
 import qualified Data.Map as M
 import Data.List.Utils
+import Data.Maybe
 
 import Command
 import qualified Annex
@@ -21,7 +22,7 @@
 import Utility
 import UUID
 import Trust
-import Remote.Ssh
+import Remote.Helper.Ssh
 import qualified Utility.Dot as Dot
 
 -- a link from the first repository to the second (its remote)
@@ -43,7 +44,7 @@
 
 	liftIO $ writeFile file (drawMap rs umap trusted)
 	showLongNote $ "running: dot -Tx11 " ++ file
-	showProgress
+	showOutput
 	r <- liftIO $ boolSystem "dot" [Param "-Tx11", File file]
 	next $ next $ return r
 	where
@@ -58,7 +59,7 @@
  - the repositories first, followed by uuids that were not matched
  - to a repository.
  -}
-drawMap :: [Git.Repo] -> (M.Map UUID String) -> [UUID] -> String
+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
@@ -78,23 +79,23 @@
 
 {- A name to display for a repo. Uses the name from uuid.log if available,
  - or the remote name if not. -}
-repoName :: (M.Map UUID String) -> Git.Repo -> String
+repoName :: M.Map UUID String -> Git.Repo -> String
 repoName umap r
 	| null repouuid = fallback
 	| otherwise = M.findWithDefault fallback repouuid umap
 	where
 		repouuid = getUncachedUUID r
-		fallback = maybe "unknown" id $ Git.repoRemoteName r
+		fallback = fromMaybe "unknown" $ Git.repoRemoteName r
 
 {- A unique id for the node for a repo. Uses the annex.uuid if available. -}
 nodeId :: Git.Repo -> String
 nodeId r =
-	case (getUncachedUUID r) of
+	case getUncachedUUID r of
 		"" -> Git.repoLocation r
 		u -> u
 
 {- A node representing a repo. -}
-node :: (M.Map UUID String) -> [Git.Repo] -> Git.Repo -> String
+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" $
@@ -105,14 +106,14 @@
 			| 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 :: 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
+			case filter (same n) fullinfo of
 				[] -> n
 				(n':_) -> n'
 		{- Only name an edge if the name is different than the name
@@ -120,7 +121,7 @@
 		 - different from its hostname. (This reduces visual clutter.) -}
 		edgename = maybe Nothing calcname $ Git.repoRemoteName to
 		calcname n
-			| n == repoName umap fullto || n == hostname fullto = Nothing
+			| n `elem` [repoName umap fullto, hostname fullto] = Nothing
 			| otherwise = Just n
 
 unreachable :: String -> String
@@ -175,7 +176,7 @@
 			showEndOk
 			return r'
 		Nothing -> do
-			showProgress
+			showOutput
 			showEndFail
 			return r
 
@@ -188,7 +189,7 @@
 	| otherwise = safely $ Git.configRead r
 	where
 		safely a = do
-			result <- liftIO (try (a)::IO (Either SomeException Git.Repo))
+			result <- liftIO (try a :: IO (Either SomeException Git.Repo))
 			case result of
 				Left _ -> return Nothing
 				Right r' -> return $ Just r'
@@ -223,5 +224,5 @@
 				ok -> return ok
 
 		sshnote = do
-			showNote "sshing..."
-			showProgress
+			showAction "sshing"
+			showOutput
diff --git a/Command/Migrate.hs b/Command/Migrate.hs
--- a/Command/Migrate.hs
+++ b/Command/Migrate.hs
@@ -72,7 +72,7 @@
 				then do
 					-- Update symlink to use the new key.
 					liftIO $ removeFile file
-					next $ Command.Add.cleanup file newkey
+					next $ Command.Add.cleanup file newkey True
 				else stop
 	where
 		cleantmp t = whenM (doesFileExist t) $ removeFile t
diff --git a/Command/Move.hs b/Command/Move.hs
--- a/Command/Move.hs
+++ b/Command/Move.hs
@@ -44,9 +44,9 @@
 			fromStart src move file
 		(_ ,  _) -> error "only one of --from or --to can be specified"
 
-showAction :: Bool -> FilePath -> Annex ()
-showAction True file = showStart "move" file
-showAction False file = showStart "copy" file
+showMoveAction :: Bool -> FilePath -> Annex ()
+showMoveAction True file = showStart "move" file
+showMoveAction False file = showStart "copy" file
 
 {- Used to log a change in a remote's having a key. The change is logged
  - in the local repo, not on the remote. The process of transferring the
@@ -77,7 +77,7 @@
 	if not ishere || u == Remote.uuid dest
 		then stop -- not here, so nothing to do
 		else do
-			showAction move file
+			showMoveAction move file
 			next $ toPerform dest move key
 toPerform :: Remote.Remote Annex -> Bool -> Key -> CommandPerform
 toPerform dest move key = do
@@ -97,7 +97,7 @@
 			showNote $ show err
 			stop
 		Right False -> do
-			showNote $ "to " ++ Remote.name dest ++ "..."
+			showAction $ "to " ++ Remote.name dest
 			ok <- Remote.storeKey dest key
 			if ok
 				then next $ toCleanup dest move key
@@ -124,10 +124,10 @@
 	g <- Annex.gitRepo
 	u <- getUUID g
 	remotes <- Remote.keyPossibilities key
-	if (u == Remote.uuid src) || (null $ filter (== src) remotes)
+	if u == Remote.uuid src || not (any (== src) remotes)
 		then stop
 		else do
-			showAction move file
+			showMoveAction move file
 			next $ fromPerform src move key
 fromPerform :: Remote.Remote Annex -> Bool -> Key -> CommandPerform
 fromPerform src move key = do
@@ -135,7 +135,7 @@
 	if ishere
 		then next $ fromCleanup src move key
 		else do
-			showNote $ "from " ++ Remote.name src ++ "..."
+			showAction $ "from " ++ Remote.name src
 			ok <- getViaTmp key $ Remote.retrieveKeyFile src key
 			if ok
 				then next $ fromCleanup src move key
diff --git a/Command/SetKey.hs b/Command/SetKey.hs
--- a/Command/SetKey.hs
+++ b/Command/SetKey.hs
@@ -16,11 +16,11 @@
 import Messages
 
 command :: [Command]
-command = [repoCommand "setkey" (paramPath) seek
+command = [repoCommand "setkey" paramPath seek
 	"sets annexed content for a key using a temp file"]
 
 seek :: [CommandSeek]
-seek = [withTempFile start]
+seek = [withStrings start]
 
 {- Sets cached content for a key. -}
 start :: CommandStartString
@@ -34,7 +34,7 @@
 	-- the file might be on a different filesystem, so mv is used
 	-- rather than simply calling moveToObjectDir; disk space is also
 	-- checked this way.
-	ok <- getViaTmp key $ \dest -> do
+	ok <- getViaTmp key $ \dest ->
 		if dest /= file
 			then liftIO $
 				boolSystem "mv" [File file, File dest]
diff --git a/Command/Status.hs b/Command/Status.hs
--- a/Command/Status.hs
+++ b/Command/Status.hs
@@ -32,8 +32,8 @@
 
 -- cached info that multiple Stats may need
 data StatInfo = StatInfo
-	{ keysPresentCache :: (Maybe (SizeList Key))
-	, keysReferencedCache :: (Maybe (SizeList Key))
+	{ keysPresentCache :: Maybe (SizeList Key)
+	, keysReferencedCache :: Maybe (SizeList Key)
 	}
 
 -- a state monad for running Stats in
@@ -84,7 +84,7 @@
 stat desc a = return $ Just (desc, a)
 
 nostat :: Stat
-nostat = return $ Nothing
+nostat = return Nothing
 
 showStat :: Stat -> StatState ()
 showStat s = calc =<< s
@@ -144,7 +144,7 @@
 	case keysPresentCache s of
 		Just v -> return v
 		Nothing -> do
-			keys <- lift $ getKeysPresent
+			keys <- lift getKeysPresent
 			let v = sizeList keys
 			put s { keysPresentCache = Just v }
 			return v
@@ -155,7 +155,7 @@
 	case keysReferencedCache s of
 		Just v -> return v
 		Nothing -> do
-			keys <- lift $ Command.Unused.getKeysReferenced
+			keys <- lift Command.Unused.getKeysReferenced
 			-- A given key may be referenced repeatedly.
 			-- nub does not seem too slow (yet)..
 			let v = sizeList $ nub keys
@@ -164,9 +164,9 @@
 
 keySizeSum :: SizeList Key -> StatState String
 keySizeSum (keys, len) = do
-	let knownsize = catMaybes $ map keySize keys
-	let total = roughSize storageUnits False $ foldl (+) 0 knownsize
-	let missing = len - genericLength knownsize
+	let knownsizes = mapMaybe keySize keys
+	let total = roughSize storageUnits False $ sum knownsizes
+	let missing = len - genericLength knownsizes
 	return $ total ++
 		if missing > 0
 			then aside $ "but " ++ show missing ++ " keys have unknown size"
diff --git a/Command/Unannex.hs b/Command/Unannex.hs
--- a/Command/Unannex.hs
+++ b/Command/Unannex.hs
@@ -78,6 +78,6 @@
 	-- Commit staged changes at end to avoid confusing the
 	-- pre-commit hook if this file is later added back to
 	-- git as a normal, non-annexed file.
-	AnnexQueue.add "commit" [Params "-a -m", Param "content removed from git annex"] "-a"
+	AnnexQueue.add "commit" [Param "-m", Param "content removed from git annex"] []
 	
 	return True
diff --git a/Command/Uninit.hs b/Command/Uninit.hs
--- a/Command/Uninit.hs
+++ b/Command/Uninit.hs
@@ -12,13 +12,11 @@
 import System.Exit
 
 import Command
-import Messages
-import Types
 import Utility
 import qualified Git
 import qualified Annex
 import qualified Command.Unannex
-import qualified Command.Init
+import Init
 import qualified Branch
 import Content
 import Locations
@@ -47,21 +45,11 @@
 cleanup :: CommandCleanup
 cleanup = do
 	g <- Annex.gitRepo
-	gitPreCommitHookUnWrite g
+	uninitialize
 	mapM_ removeAnnex =<< getKeysPresent
 	liftIO $ removeDirectoryRecursive (gitAnnexDir g)
 	-- avoid normal shutdown
 	saveState
-	liftIO $ Git.run g "branch" [Param "-D", Param Branch.name]
-	liftIO $ exitSuccess
-
-gitPreCommitHookUnWrite :: Git.Repo -> Annex ()
-gitPreCommitHookUnWrite repo = do
-	let hook = Command.Init.preCommitHook repo
-	whenM (liftIO $ doesFileExist hook) $ do
-		c <- liftIO $ readFile hook
-		if c == Command.Init.preCommitScript
-			then liftIO $ removeFile hook
-			else warning $ "pre-commit hook (" ++ hook ++ 
-				") contents modified; not deleting." ++
-				" Edit it to remove call to git annex."
+	liftIO $ do
+		Git.run g "branch" [Param "-D", Param Branch.name]
+		exitSuccess
diff --git a/Command/Unlock.hs b/Command/Unlock.hs
--- a/Command/Unlock.hs
+++ b/Command/Unlock.hs
@@ -45,7 +45,7 @@
 	let src = gitAnnexLocation g key
 	let tmpdest = gitAnnexTmpLocation g key
 	liftIO $ createDirectoryIfMissing True (parentDir tmpdest)
-	showNote "copying..."
+	showAction "copying"
 	ok <- liftIO $ copyFile src tmpdest
         if ok
                 then do
diff --git a/Command/Unused.hs b/Command/Unused.hs
--- a/Command/Unused.hs
+++ b/Command/Unused.hs
@@ -7,7 +7,7 @@
 
 module Command.Unused where
 
-import Control.Monad (filterM, unless, forM_, when)
+import Control.Monad (filterM, unless, forM_)
 import Control.Monad.State (liftIO)
 import qualified Data.Set as S
 import Data.Maybe
@@ -55,9 +55,9 @@
 	where
 		list file msg l c = do
 			let unusedlist = number c l
-			when (not $ null l) $ do
+			unless (null l) $ do
 				showLongNote $ msg unusedlist
-				showLongNote $ "\n"
+				showLongNote "\n"
 			writeUnusedFile file unusedlist
 			return $ c + length l
 
@@ -68,7 +68,7 @@
 
 checkRemoteUnused' :: Remote.Remote Annex -> Annex ()
 checkRemoteUnused' r = do
-	showNote $ "checking for unused data..."
+	showAction "checking for unused data"
 	referenced <- getKeysReferenced
 	remotehas <- filterM isthere =<< loggedKeys
 	let remoteunused = remotehas `exclude` referenced
@@ -76,7 +76,7 @@
 	writeUnusedFile "" list
 	unless (null remoteunused) $ do
 		showLongNote $ remoteUnusedMsg r list
-		showLongNote $ "\n"
+		showLongNote "\n"
 	where
 		isthere k = do
 			us <- keyLocations k
@@ -90,14 +90,14 @@
 		unlines $ map (\(n, k) -> show n ++ " " ++ show k) l
 
 table :: [(Int, Key)] -> [String]
-table l = ["  NUMBER  KEY"] ++ map cols l
+table l = "  NUMBER  KEY" : map cols l
 	where
 		cols (n,k) = "  " ++ pad 6 (show n) ++ "  " ++ show k
 		pad n s = s ++ replicate (n - length s) ' '
 
 number :: Int -> [a] -> [(Int, a)]
 number _ [] = []
-number n (x:xs) = (n+1, x):(number (n+1) xs)
+number n (x:xs) = (n+1, x) : number (n+1) xs
 
 staleTmpMsg :: [(Int, Key)] -> String
 staleTmpMsg t = unlines $ 
@@ -152,7 +152,7 @@
 			bad <- staleKeys gitAnnexBadDir
 			return ([], bad, tmp)
 		else do
-			showNote "checking for unused data..."
+			showAction "checking for unused data"
 			present <- getKeysPresent
 			referenced <- getKeysReferenced
 			let unused = present `exclude` referenced
@@ -210,4 +210,4 @@
 			contents <- liftIO $ getDirectoryContents dir
 			files <- liftIO $ filterM doesFileExist $
 				map (dir </>) contents
-			return $ catMaybes $ map (fileKey . takeFileName) files
+			return $ mapMaybe (fileKey . takeFileName) files
diff --git a/Command/Version.hs b/Command/Version.hs
--- a/Command/Version.hs
+++ b/Command/Version.hs
@@ -31,4 +31,4 @@
 	liftIO $ putStrLn $ "upgrade supported from repository versions: " ++ vs upgradableVersions
 	stop
 	where
-		vs l = join " " l
+		vs = join " "
diff --git a/Command/Whereis.hs b/Command/Whereis.hs
--- a/Command/Whereis.hs
+++ b/Command/Whereis.hs
@@ -30,12 +30,12 @@
 	uuids <- keyLocations key
 	let num = length uuids
 	showNote $ show num ++ " " ++ copiesplural num
-	if null $ uuids
+	if null uuids
 		then stop
 		else do
 			pp <- prettyPrintUUIDs uuids
-			showLongNote $ pp
-			showProgress	
+			showLongNote pp
+			showOutput
 			next $ return True
 	where
 		copiesplural 1 = "copy"
diff --git a/Config.hs b/Config.hs
--- a/Config.hs
+++ b/Config.hs
@@ -9,6 +9,8 @@
 
 import Data.Maybe
 import Control.Monad.State (liftIO)
+import Control.Monad (liftM)
+import System.Cmd.Utils
 
 import qualified Git
 import qualified Annex
@@ -37,17 +39,23 @@
 remoteConfig :: Git.Repo -> ConfigKey -> String
 remoteConfig r key = "remote." ++ fromMaybe "" (Git.repoRemoteName r) ++ ".annex-" ++ key
 
-{- Calculates cost for a remote.
- -
- - The default cost is 100 for local repositories, and 200 for remote
- - repositories; it can also be configured by remote.<name>.annex-cost
+{- Calculates cost for a remote. Either the default, or as configured 
+ - by remote.<name>.annex-cost, or if remote.<name>.annex-cost-command
+ - is set and prints a number, that is used.
  -}
 remoteCost :: Git.Repo -> Int -> Annex Int
 remoteCost r def = do
-	c <- getConfig r "cost" ""
-	if not $ null c
-		then return $ read c
-		else return def
+	cmd <- getConfig r "cost-command" ""
+	return . safeparse =<< if not $ null cmd
+			then liftM snd $ liftIO $ pipeFrom "sh" ["-c", cmd]
+			else getConfig r "cost" ""
+	where
+		safeparse v
+			| null ws || null ps = def
+			| otherwise = (fst . head) ps
+			where
+				ws = words v
+				ps = reads $ head ws
 
 cheapRemoteCost :: Int
 cheapRemoteCost = 100
diff --git a/Content.hs b/Content.hs
--- a/Content.hs
+++ b/Content.hs
@@ -57,8 +57,8 @@
 calcGitLink :: FilePath -> Key -> Annex FilePath
 calcGitLink file key = do
 	g <- Annex.gitRepo
-	cwd <- liftIO $ getCurrentDirectory
-	let absfile = maybe whoops id $ absNormPath cwd file
+	cwd <- liftIO getCurrentDirectory
+	let absfile = fromMaybe whoops $ absNormPath cwd file
 	return $ relPathDirToFile (parentDir absfile) 
 			(Git.workTree g) </> ".git" </> annexLocation key
 	where
@@ -94,15 +94,19 @@
 
 	getViaTmpUnchecked key action
 
+prepTmp :: Key -> Annex FilePath
+prepTmp key = do
+	g <- Annex.gitRepo
+	let tmp = gitAnnexTmpLocation g key
+	liftIO $ createDirectoryIfMissing True (parentDir tmp)
+	return tmp
+
 {- Like getViaTmp, but does not check that there is enough disk space
  - for the incoming key. For use when the key content is already on disk
  - and not being copied into place. -}
 getViaTmpUnchecked :: Key -> (FilePath -> Annex Bool) -> Annex Bool
 getViaTmpUnchecked key action = do
-	g <- Annex.gitRepo
-	let tmp = gitAnnexTmpLocation g key
-
-	liftIO $ createDirectoryIfMissing True (parentDir tmp)
+	tmp <- prepTmp key
 	success <- action tmp
 	if success
 		then do
@@ -117,9 +121,7 @@
 {- Creates a temp file, runs an action on it, and cleans up the temp file. -}
 withTmp :: Key -> (FilePath -> Annex a) -> Annex a
 withTmp key action = do
-	g <- Annex.gitRepo
-	let tmp = gitAnnexTmpLocation g key
-	liftIO $ createDirectoryIfMissing True (parentDir tmp)
+	tmp <- prepTmp key
 	res <- action tmp
 	liftIO $ whenM (doesFileExist tmp) $ liftIO $ removeFile tmp
 	return res
@@ -133,23 +135,21 @@
 checkDiskSpace' adjustment key = do
 	g <- Annex.gitRepo
 	r <- getConfig g "diskreserve" ""
-	let reserve = maybe megabyte id $ readSize dataUnits r
+	let reserve = fromMaybe megabyte $ readSize dataUnits r
 	stats <- liftIO $ getFileSystemStats (gitAnnexDir g)
 	case (stats, keySize key) of
 		(Nothing, _) -> return ()
 		(_, Nothing) -> return ()
 		(Just (FileSystemStats { fsStatBytesAvailable = have }), Just need) ->
-			if (need + reserve > have + adjustment)
-				then needmorespace (need + reserve - have - adjustment)
-				else return ()
+			when (need + reserve > have + adjustment) $
+				needmorespace (need + reserve - have - adjustment)
 	where
 		megabyte :: Integer
 		megabyte = 1000000
-		needmorespace n = do
-			unlessM (Annex.getState Annex.force) $
-				error $ "not enough free space, need " ++ 
-					roughSize storageUnits True n ++
-					" more (use --force to override this check or adjust annex.diskreserve)"
+		needmorespace n = unlessM (Annex.getState Annex.force) $
+			error $ "not enough free space, need " ++ 
+				roughSize storageUnits True n ++
+				" more (use --force to override this check or adjust annex.diskreserve)"
 
 {- Removes the write bits from a file. -}
 preventWrite :: FilePath -> IO ()
@@ -200,28 +200,27 @@
 			preventWrite dest
 			preventWrite dir
 
-{- Removes a key's file from .git/annex/objects/ -}
-removeAnnex :: Key -> Annex ()
-removeAnnex key = do
+withObjectLoc :: Key -> ((FilePath, FilePath) -> Annex a) -> Annex a
+withObjectLoc key a = do
 	g <- Annex.gitRepo
 	let file = gitAnnexLocation g key
 	let dir = parentDir file
-	liftIO $ do
-		allowWrite dir
-		removeFile file
-		removeDirectory dir
+	a (dir, file)
 
+{- Removes a key's file from .git/annex/objects/ -}
+removeAnnex :: Key -> Annex ()
+removeAnnex key = withObjectLoc key $ \(dir, file) -> liftIO $ do
+	allowWrite dir
+	removeFile file
+	removeDirectory dir
+
 {- Moves a key's file out of .git/annex/objects/ -}
 fromAnnex :: Key -> FilePath -> Annex ()
-fromAnnex key dest = do
-	g <- Annex.gitRepo
-	let file = gitAnnexLocation g key
-	let dir = parentDir file
-	liftIO $ do
-		allowWrite dir
-		allowWrite file
-		renameFile file dest
-		removeDirectory dir
+fromAnnex key dest = withObjectLoc key $ \(dir, file) -> liftIO $ do
+	allowWrite dir
+	allowWrite file
+	renameFile file dest
+	removeDirectory dir
 
 {- Moves a key out of .git/annex/objects/ into .git/annex/bad, and
  - returns the file it was moved to. -}
@@ -246,7 +245,7 @@
 getKeysPresent' :: FilePath -> Annex [Key]
 getKeysPresent' dir = do
 	exists <- liftIO $ doesDirectoryExist dir
-	if (not exists)
+	if not exists
 		then return []
 		else liftIO $ do
 			-- 2 levels of hashing
@@ -254,7 +253,7 @@
 			levelb <- mapM dirContents levela
 			contents <- mapM dirContents (concat levelb)
 			files <- filterM present (concat contents)
-			return $ catMaybes $ map (fileKey . takeFileName) files
+			return $ mapMaybe (fileKey . takeFileName) files
 	where
 		present d = do
 			result <- try $
diff --git a/Crypto.hs b/Crypto.hs
--- a/Crypto.hs
+++ b/Crypto.hs
@@ -33,6 +33,7 @@
 import System.Cmd.Utils
 import Data.String.Utils
 import Data.List
+import Data.Maybe
 import System.IO
 import System.Posix.IO
 import System.Posix.Types
@@ -125,11 +126,11 @@
 	return $ EncryptedCipher encipher (KeyIds ks')
 	where
 		encrypt = [ Params "--encrypt" ]
-		recipients l = 
-			-- Force gpg to only encrypt to the specified
-			-- recipients, not configured defaults.
-			[ Params "--no-encrypt-to --no-default-recipient"] ++
-			(concat $ map (\k -> [Param "--recipient", Param k]) l)
+		recipients l = force_recipients :
+			concatMap (\k -> [Param "--recipient", Param k]) l
+		-- Force gpg to only encrypt to the specified
+		-- recipients, not configured defaults.
+		force_recipients = Params "--no-encrypt-to --no-default-recipient"
 
 {- Decrypting an EncryptedCipher is expensive; the Cipher should be cached. -}
 decryptCipher :: RemoteConfig -> EncryptedCipher -> IO Cipher
@@ -152,24 +153,24 @@
 
 {- Runs an action, passing it a handle from which it can 
  - stream encrypted content. -}
-withEncryptedHandle :: Cipher -> (IO L.ByteString) -> (Handle -> IO a) -> IO a
+withEncryptedHandle :: Cipher -> IO L.ByteString -> (Handle -> IO a) -> IO a
 withEncryptedHandle = gpgCipherHandle [Params "--symmetric --force-mdc"]
 
 {- Runs an action, passing it a handle from which it can
  - stream decrypted content. -}
-withDecryptedHandle :: Cipher -> (IO L.ByteString) -> (Handle -> IO a) -> IO a
+withDecryptedHandle :: Cipher -> IO L.ByteString -> (Handle -> IO a) -> IO a
 withDecryptedHandle = gpgCipherHandle [Param "--decrypt"]
 
 {- Streams encrypted content to an action. -}
-withEncryptedContent :: Cipher -> (IO L.ByteString) -> (L.ByteString -> IO a) -> IO a
+withEncryptedContent :: Cipher -> IO L.ByteString -> (L.ByteString -> IO a) -> IO a
 withEncryptedContent = pass withEncryptedHandle
 
 {- Streams decrypted content to an action. -}
-withDecryptedContent :: Cipher -> (IO L.ByteString) -> (L.ByteString -> IO a) -> IO a
+withDecryptedContent :: Cipher -> IO L.ByteString -> (L.ByteString -> IO a) -> IO a
 withDecryptedContent = pass withDecryptedHandle
 
-pass :: (Cipher -> (IO L.ByteString) -> (Handle -> IO a) -> IO a) 
-      -> Cipher -> (IO L.ByteString) -> (L.ByteString -> IO a) -> IO a
+pass :: (Cipher -> IO L.ByteString -> (Handle -> IO a) -> IO a) 
+      -> Cipher -> IO L.ByteString -> (L.ByteString -> IO a) -> IO a
 pass to c i a = to c i $ \h -> a =<< L.hGetContents h
 
 gpgParams :: [CommandParam] -> IO [String]
@@ -202,7 +203,7 @@
  -
  - Note that to avoid deadlock with the cleanup stage,
  - the action must fully consume gpg's input before returning. -}
-gpgCipherHandle :: [CommandParam] -> Cipher -> (IO L.ByteString) -> (Handle -> IO a) -> IO a
+gpgCipherHandle :: [CommandParam] -> Cipher -> IO L.ByteString -> (Handle -> IO a) -> IO a
 gpgCipherHandle params c a b = do
 	-- pipe the passphrase into gpg on a fd
 	(frompipe, topipe) <- createPipe
@@ -235,10 +236,10 @@
 	where
 		parseWithColons s = map keyIdField $ filter pubKey $ lines s
 		pubKey = isPrefixOf "pub:"
-		keyIdField s = (split ":" s) !! 4
+		keyIdField s = split ":" s !! 4
 
 configGet :: RemoteConfig -> String -> String
-configGet c key = maybe missing id $ M.lookup key c
+configGet c key = fromMaybe missing $ M.lookup key c
 	where missing = error $ "missing " ++ key ++ " in remote config"
 
 hmacWithCipher :: Cipher -> String -> String
diff --git a/Git.hs b/Git.hs
--- a/Git.hs
+++ b/Git.hs
@@ -17,6 +17,7 @@
 	localToUrl,
 	repoIsUrl,
 	repoIsSsh,
+	repoIsHttp,
 	repoIsLocalBare,
 	repoDescribe,
 	repoLocation,
@@ -69,11 +70,10 @@
 import System.Posix.Process
 import System.Path
 import System.Cmd.Utils
-import IO (bracket_)
+import IO (bracket_, try)
 import Data.String.Utils
 import System.IO
-import IO (try)
-import qualified Data.Map as Map hiding (map, split)
+import qualified Data.Map as M hiding (map, split)
 import Network.URI
 import Data.Maybe
 import Data.Char
@@ -93,7 +93,7 @@
 
 data Repo = Repo {
 	location :: RepoLocation,
-	config :: Map.Map String String,
+	config :: M.Map String String,
 	remotes :: [Repo],
 	-- remoteName holds the name used for this repo in remotes
 	remoteName :: Maybe String 
@@ -103,7 +103,7 @@
 newFrom l = 
 	Repo {
 		location = l,
-		config = Map.empty,
+		config = M.empty,
 		remotes = [],
 		remoteName = Nothing
 	}
@@ -140,7 +140,7 @@
 	| startswith "file://" url = repoFromAbsPath $ uriPath u
 	| otherwise = return $ newFrom $ Url u
 		where
-			u = maybe bad id $ parseURI url
+			u = fromMaybe bad $ parseURI url
 			bad = error $ "bad url " ++ url
 
 {- Creates a repo that has an unknown location. -}
@@ -207,8 +207,15 @@
 	| otherwise = False
 repoIsSsh _ = False
 
+repoIsHttp :: Repo -> Bool
+repoIsHttp Repo { location = Url url } 
+	| uriScheme url == "http:" = True
+	| uriScheme url == "https:" = True
+	| otherwise = False
+repoIsHttp _ = False
+
 configAvail ::Repo -> Bool
-configAvail Repo { config = c } = c /= Map.empty
+configAvail Repo { config = c } = c /= M.empty
 
 repoIsLocalBare :: Repo -> Bool
 repoIsLocalBare r@(Repo { location = Dir _ }) = configAvail r && configBare r
@@ -228,7 +235,7 @@
 				" not supported"
 
 configBare :: Repo -> Bool
-configBare repo = maybe unknown configTrue $ Map.lookup "core.bare" $ config repo
+configBare repo = maybe unknown configTrue $ M.lookup "core.bare" $ config repo
 	where
 		unknown = error $ "it is not known if git repo " ++
 			repoDescribe repo ++
@@ -240,11 +247,11 @@
 	| configBare repo = workTree repo ++ "/info/.gitattributes"
 	| otherwise = workTree repo ++ "/.gitattributes"
 
-{- Path to a repository's .git directory, relative to its workTree. -}
+{- Path to a repository's .git directory. -}
 gitDir :: Repo -> String
 gitDir repo
-	| configBare repo = ""
-	| otherwise = ".git"
+	| configBare repo = workTree repo
+	| otherwise = workTree repo </> ".git"
 
 {- Path to a repository's --work-tree, that is, its top.
  -
@@ -272,14 +279,14 @@
 	let file' = absfile cwd
 	unless (inrepo file') $
 		error $ file ++ " is not located inside git repository " ++ absrepo
-	if (inrepo $ addTrailingPathSeparator cwd)
+	if inrepo $ addTrailingPathSeparator cwd
 		then return $ relPathDirToFile cwd file'
 		else return $ drop (length absrepo) file'
 	where
 		-- normalize both repo and file, so that repo
 		-- will be substring of file
 		absrepo = maybe bad addTrailingPathSeparator $ absNormPath "/" d
-		absfile c = maybe file id $ secureAbsNormPath c file
+		absfile c = fromMaybe file $ secureAbsNormPath c file
 		inrepo f = absrepo `isPrefixOf` f
 		bad = error $ "bad repo" ++ repoDescribe repo
 workTreeFile repo _ = assertLocal repo $ error "internal"
@@ -303,7 +310,7 @@
 			| rest !! len == ']' = take len rest
 			| otherwise = x
 			where
-				len  = (length rest) - 1
+				len  = length rest - 1
 		fixup x = x
 
 {- Hostname of an URL repo. -}
@@ -338,17 +345,17 @@
 
 {- Constructs a git command line operating on the specified repo. -}
 gitCommandLine :: Repo -> [CommandParam] -> [CommandParam]
-gitCommandLine repo@(Repo { location = Dir d} ) params =
+gitCommandLine repo@(Repo { location = Dir _ } ) params =
 	-- force use of specified repo via --git-dir and --work-tree
-	[ Param ("--git-dir=" ++ d ++ "/" ++ gitDir repo)
-	, Param ("--work-tree=" ++ d)
+	[ Param ("--git-dir=" ++ gitDir repo)
+	, Param ("--work-tree=" ++ workTree repo)
 	] ++ params
 gitCommandLine repo _ = assertLocal repo $ error "internal"
 
 {- Runs git in the specified repo. -}
 runBool :: Repo -> String -> [CommandParam] -> IO Bool
 runBool repo subcommand params = assertLocal repo $
-	boolSystem "git" (gitCommandLine repo ((Param subcommand):params))
+	boolSystem "git" $ gitCommandLine repo $ Param subcommand : params
 
 {- Runs git in the specified repo, throwing an error if it fails. -}
 run :: Repo -> String -> [CommandParam] -> IO ()
@@ -466,20 +473,31 @@
 	val <- hGetContentsStrict h
 	configStore repo val
 
-{- Parses a git config and returns a version of the repo using it. -}
+{- Stores a git config into a repo, returning the new version of the repo.
+ - The git config may be multiple lines, or a single line. Config settings
+ - can be updated inrementally. -}
 configStore :: Repo -> String -> IO Repo
 configStore repo s = do
-	rs <- configRemotes r
-	return $ r { remotes = rs }
+	let repo' = repo { config = configParse s `M.union` config repo }
+	rs <- configRemotes repo'
+	return $ repo' { remotes = rs }
+
+{- Parses git config --list output into a config map. -}
+configParse :: String -> M.Map String String
+configParse s = M.fromList $ map pair $ lines s
 	where
-		r = repo { config = configParse s }
+		pair l = (key l, val l)
+		key l = head $ keyval l
+		val l = join sep $ drop 1 $ keyval l
+		keyval l = split sep l :: [String]
+		sep = "="
 
 {- Calculates a list of a repo's configured remotes, by parsing its config. -}
 configRemotes :: Repo -> IO [Repo]
 configRemotes repo = mapM construct remotepairs
 	where
-		remotepairs = Map.toList $ filterremotes $ config repo
-		filterremotes = Map.filterWithKey (\k _ -> isremote k)
+		remotepairs = M.toList $ filterremotes $ config repo
+		filterremotes = M.filterWithKey (\k _ -> isremote k)
 		isremote k = startswith "remote." k && endswith ".url" k
 		construct (k,v) = do
 			r <- gen v
@@ -488,39 +506,29 @@
 			| isURI v = repoFromUrl v
 			| otherwise = repoFromRemotePath v repo
 		-- git remotes can be written scp style -- [user@]host:dir
-		scpstyle v = ":" `isInfixOf` v && (not $ "//" `isInfixOf` v)
+		scpstyle v = ":" `isInfixOf` v && not ("//" `isInfixOf` v)
 		scptourl v = "ssh://" ++ host ++ slash dir
 			where
 				bits = split ":" v
-				host = bits !! 0
+				host = head bits
 				dir = join ":" $ drop 1 bits
 				slash d	| d == "" = "/~/" ++ dir
-					| d !! 0 == '/' = dir
-					| d !! 0 == '~' = '/':dir
+					| head d == '/' = dir
+					| head d == '~' = '/':dir
 					| otherwise = "/~/" ++ dir
 
 {- Checks if a string from git config is a true value. -}
 configTrue :: String -> Bool
 configTrue s = map toLower s == "true"
 
-{- Parses git config --list output into a config map. -}
-configParse :: String -> Map.Map String String
-configParse s = Map.fromList $ map pair $ lines s
-	where
-		pair l = (key l, val l)
-		key l = head $ keyval l
-		val l = join sep $ drop 1 $ keyval l
-		keyval l = split sep l :: [String]
-		sep = "="
-
 {- Returns a single git config setting, or a default value if not set. -}
 configGet :: Repo -> String -> String -> String
 configGet repo key defaultValue = 
-	Map.findWithDefault defaultValue key (config repo)
+	M.findWithDefault defaultValue key (config repo)
 
 {- Access to raw config Map -}
-configMap :: Repo -> Map.Map String String
-configMap repo = config repo
+configMap :: Repo -> M.Map String String
+configMap = config
 
 {- Efficiently looks up a gitattributes value for each file in a list. -}
 checkAttr :: Repo -> String -> [FilePath] -> IO [(FilePath, String)]
@@ -530,6 +538,7 @@
 	-- directory. Convert to absolute, and then convert the filenames
 	-- in its output back to relative.
 	cwd <- getCurrentDirectory
+	let top = workTree repo
 	let absfiles = map (absPathFrom cwd) files
 	(_, fromh, toh) <- hPipeBoth "git" (toCommand params)
         _ <- forkProcess $ do
@@ -539,19 +548,21 @@
                 exitSuccess
         hClose toh
 	s <- hGetContents fromh
-	return $ map (topair $ cwd++"/") $ lines s
+	return $ map (topair cwd top) $ lines s
 	where
 		params = gitCommandLine repo [Param "check-attr", Param attr, Params "-z --stdin"]
-		topair cwd l = (relfile, value)
+		topair cwd top l = (relfile, value)
 			where 
-				relfile 
-					| startswith cwd file = drop (length cwd) file
-					| otherwise = file
+				relfile
+					| startswith cwd' file = drop (length cwd') file
+					| otherwise = relPathDirToFile top' file
 				file = decodeGitFile $ join sep $ take end bits
 				value = bits !! end
 				end = length bits - 1
 				bits = split sep l
 				sep = ": " ++ attr ++ ": "
+				cwd' = cwd ++ "/"
+				top' = top ++ "/"
 
 {- Some git commands output encoded filenames. Decode that (annoyingly
  - complex) encoding. -}
@@ -676,8 +687,8 @@
 seekUp want dir = do
 	ok <- want dir
 	if ok
-		then return (Just dir)
-		else case (parentDir dir) of
+		then return $ Just dir
+		else case parentDir dir of
 			"" -> return Nothing
 			d -> seekUp want d
 
diff --git a/Git/LsFiles.hs b/Git/LsFiles.hs
--- a/Git/LsFiles.hs
+++ b/Git/LsFiles.hs
@@ -21,7 +21,7 @@
 {- Scans for files that are checked into git at the specified locations. -}
 inRepo :: Repo -> [FilePath] -> IO [FilePath]
 inRepo repo l = pipeNullSplit repo $
-	[Params "ls-files --cached -z --"] ++ map File l
+	Params "ls-files --cached -z --" : map File l
 
 {- Scans for files at the specified locations that are not checked into
  - git. -}
@@ -44,12 +44,12 @@
 staged' repo l middle = pipeNullSplit repo $ start ++ middle ++ end
 	where
 		start = [Params "diff --cached --name-only -z"]
-		end = [Param "--"] ++ map File l
+		end = Param "--" : map File l
 
 {- Returns a list of files that have unstaged changes. -}
 changedUnstaged :: Repo -> [FilePath] -> IO [FilePath]
 changedUnstaged repo l = pipeNullSplit repo $
-	[Params "diff --name-only -z --"] ++ map File l
+	Params "diff --name-only -z --" : map File l
 
 {- Returns a list of the files in the specified locations that are staged
  - for commit, and whose type has changed. -}
@@ -65,4 +65,4 @@
 typeChanged' repo l middle = pipeNullSplit repo $ start ++ middle ++ end
 	where
 		start = [Params "diff --name-only --diff-filter=T -z"]
-		end = [Param "--"] ++ map File l
+		end = Param "--" : map File l
diff --git a/Git/Queue.hs b/Git/Queue.hs
--- a/Git/Queue.hs
+++ b/Git/Queue.hs
@@ -18,7 +18,7 @@
 import System.IO
 import System.Cmd.Utils
 import Data.String.Utils
-import Control.Monad (unless, forM_)
+import Control.Monad (forM_)
 import Utility
 
 import Git
@@ -53,15 +53,15 @@
 empty = Queue 0 M.empty
 
 {- Adds an action to a queue. -}
-add :: Queue -> String -> [CommandParam] -> FilePath -> Queue
-add (Queue n m) subcommand params file = Queue (n + 1) m'
+add :: Queue -> String -> [CommandParam] -> [FilePath] -> Queue
+add (Queue n m) subcommand params files = Queue (n + 1) m'
 	where
 		action = Action subcommand params
 		-- There are probably few items in the map, but there
 		-- can be a lot of files per item. So, optimise adding
 		-- files.
-		m' = M.insertWith' const action files m
-		files = file:(M.findWithDefault [] action m)
+		m' = M.insertWith' const action fs m
+		fs = files ++ M.findWithDefault [] action m
 
 {- Number of items in a queue. -}
 size :: Queue -> Int
@@ -79,11 +79,14 @@
 
 {- Runs an Action on a list of files in a git repository.
  -
- - Complicated by commandline length limits. -}
+ - Complicated by commandline length limits.
+ -
+ - Intentionally runs the command even if the list of files is empty;
+ - this allows queueing commands that do not need a list of files. -}
 runAction :: Repo -> Action -> [FilePath] -> IO ()
-runAction repo action files = unless (null files) runxargs
+runAction repo action files =
+	pOpen WriteToPipe "xargs" ("-0":"git":params) feedxargs
 	where
-		runxargs = pOpen WriteToPipe "xargs" ("-0":"git":params) feedxargs
 		params = toCommand $ gitCommandLine repo
 			(Param (getSubcommand action):getParams action)
 		feedxargs h = hPutStr h $ join "\0" files
diff --git a/Git/UnionMerge.hs b/Git/UnionMerge.hs
--- a/Git/UnionMerge.hs
+++ b/Git/UnionMerge.hs
@@ -91,5 +91,5 @@
 		return $ Just $ update_index_line sha file
 	where
 		[_colonamode, _bmode, asha, bsha, _status] = words info
-		nullsha = take shaSize $ repeat '0'
+		nullsha = replicate shaSize '0'
 		unionmerge = unlines . nub . lines
diff --git a/GitAnnex.hs b/GitAnnex.hs
--- a/GitAnnex.hs
+++ b/GitAnnex.hs
@@ -8,12 +8,14 @@
 module GitAnnex where
 
 import System.Console.GetOpt
+import Control.Monad.State (liftIO)
 
 import qualified Git
 import CmdLine
 import Command
 import Options
 import Utility
+import Types
 import Types.TrustLevel
 import qualified Annex
 import qualified Remote
@@ -102,9 +104,11 @@
 	, Option [] ["trust"] (ReqArg (Remote.forceTrust Trusted) paramRemote)
 		"override trust setting"
 	, Option [] ["semitrust"] (ReqArg (Remote.forceTrust SemiTrusted) paramRemote)
-		"override trust setting back to default value"
+		"override trust setting back to default"
 	, Option [] ["untrust"] (ReqArg (Remote.forceTrust UnTrusted) paramRemote)
 		"override trust setting to untrusted"
+	, Option ['c'] ["config"] (ReqArg setgitconfig "NAME=VALUE")
+		"override git configuration setting"
 	]
 	where
 		setto v = Annex.changeState $ \s -> s { Annex.toremote = Just v }
@@ -112,6 +116,11 @@
 		addexclude v = Annex.changeState $ \s -> s { Annex.exclude = v:Annex.exclude s }
 		setnumcopies v = Annex.changeState $ \s -> s {Annex.forcenumcopies = readMaybe v }
 		setkey v = Annex.changeState $ \s -> s { Annex.defaultkey = Just v }
+		setgitconfig :: String -> Annex ()
+		setgitconfig v = do
+			g <- Annex.gitRepo
+			g' <- liftIO $ Git.configStore g v
+			Annex.changeState $ \s -> s { Annex.repo = g' }
 
 header :: String
 header = "Usage: git-annex command [option ..]"
diff --git a/INSTALL b/INSTALL
--- a/INSTALL
+++ b/INSTALL
@@ -23,6 +23,7 @@
   * [utf8-string](http://hackage.haskell.org/package/utf8-string)
   * [SHA](http://hackage.haskell.org/package/SHA)
   * [dataenc](http://hackage.haskell.org/package/dataenc)
+  * [monad-control](http://hackage.haskell.org/package/monad-control)
   * [TestPack](http://hackage.haskell.org/cgi-bin/hackage-scripts/package/testpack)
   * [QuickCheck 2](http://hackage.haskell.org/package/QuickCheck)
   * [HTTP](http://hackage.haskell.org/package/HTTP)
diff --git a/Init.hs b/Init.hs
new file mode 100644
--- /dev/null
+++ b/Init.hs
@@ -0,0 +1,88 @@
+{- git-annex repository initialization
+ -
+ - Copyright 2011 Joey Hess <joey@kitenet.net>
+ -
+ - Licensed under the GNU GPL version 3 or higher.
+ -}
+
+module Init (
+	ensureInitialized,
+	initialize,
+	uninitialize
+) where
+
+import Control.Monad.State (liftIO)
+import Control.Monad (unless)
+import System.Directory
+
+import qualified Annex
+import qualified Git
+import qualified Branch
+import Version
+import Messages
+import Types
+import Utility
+import UUID
+
+initialize :: Annex ()
+initialize = do
+	prepUUID
+	Branch.create
+	setVersion
+	gitPreCommitHookWrite
+
+uninitialize :: Annex ()
+uninitialize = do
+	gitPreCommitHookUnWrite
+
+{- Will automatically initialize if there is already a git-annex
+   branch from somewhere. Otherwise, require a manual init
+   to avoid git-annex accidentially being run in git
+   repos that did not intend to use it. -}
+ensureInitialized :: Annex ()
+ensureInitialized = getVersion >>= maybe needsinit checkVersion
+	where
+		needsinit = do
+			annexed <- Branch.hasSomeBranch
+			if annexed
+				then initialize
+				else error "First run: git-annex init"
+
+{- set up a git pre-commit hook, if one is not already present -}
+gitPreCommitHookWrite :: Annex ()
+gitPreCommitHookWrite = unlessBare $ do
+	hook <- preCommitHook
+	exists <- liftIO $ doesFileExist hook
+	if exists
+		then warning $ "pre-commit hook (" ++ hook ++ ") already exists, not configuring"
+		else liftIO $ do
+			viaTmp writeFile hook preCommitScript
+			p <- getPermissions hook
+			setPermissions hook $ p {executable = True}
+
+gitPreCommitHookUnWrite :: Annex ()
+gitPreCommitHookUnWrite = unlessBare $ do
+	hook <- preCommitHook
+	whenM (liftIO $ doesFileExist hook) $ do
+		c <- liftIO $ readFile hook
+		if c == preCommitScript
+			then liftIO $ removeFile hook
+			else warning $ "pre-commit hook (" ++ hook ++ 
+				") contents modified; not deleting." ++
+				" Edit it to remove call to git annex."
+
+unlessBare :: Annex () -> Annex ()
+unlessBare a = do
+	g <- Annex.gitRepo
+	unless (Git.repoIsLocalBare g) a
+
+preCommitHook :: Annex FilePath
+preCommitHook = do
+	g <- Annex.gitRepo
+	return $ Git.gitDir g ++ "/hooks/pre-commit"
+
+preCommitScript :: String
+preCommitScript = 
+		"#!/bin/sh\n" ++
+		"# automatically configured by git-annex\n" ++ 
+		"git annex pre-commit .\n"
diff --git a/LocationLog.hs b/LocationLog.hs
--- a/LocationLog.hs
+++ b/LocationLog.hs
@@ -30,7 +30,6 @@
 import qualified Branch
 import UUID
 import Types
-import Types.Key
 import Locations
 import PresenceLog
 
@@ -50,8 +49,7 @@
 {- Finds all keys that have location log information.
  - (There may be duplicate keys in the list.) -}
 loggedKeys :: Annex [Key]
-loggedKeys =
-	return . catMaybes . map (logFileKey . takeFileName) =<< Branch.files
+loggedKeys = return . mapMaybe (logFileKey . takeFileName) =<< Branch.files
 
 {- The filename of the log file for a given key. -}
 logFile :: Key -> String
diff --git a/Locations.hs b/Locations.hs
--- a/Locations.hs
+++ b/Locations.hs
@@ -52,7 +52,7 @@
 {- The directory git annex uses for local state, relative to the .git
  - directory -}
 annexDir :: FilePath
-annexDir = addTrailingPathSeparator $ "annex"
+annexDir = addTrailingPathSeparator "annex"
 
 {- The directory git annex uses for locally available object content,
  - relative to the .git directory -}
@@ -167,8 +167,8 @@
 		-- a real word, use letters that appear less frequently.
 		chars = ['0'..'9'] ++ "zqjxkmvwgpfZQJXKMVWGPF"
 		cs = map (\x -> getc $ (shiftR w (6*x)) .&. 31) [0..7]
-		getc n = chars !! (fromIntegral n)
+		getc n = chars !! fromIntegral n
 		swap_pairs (x1:x2:xs) = x2:x1:swap_pairs xs
 		swap_pairs _ = []
 		-- Last 2 will always be 00, so omit.
-		trim s = take 6 s
+		trim = take 6
diff --git a/Messages.hs b/Messages.hs
--- a/Messages.hs
+++ b/Messages.hs
@@ -20,24 +20,32 @@
 	q <- Annex.getState Annex.quiet
 	unless q a
 
-showSideAction :: String -> Annex ()
-showSideAction s = verbose $ liftIO $ putStrLn $ "(" ++ s ++ ")"
-
 showStart :: String -> String -> Annex ()
-showStart command file = verbose $ do
-	liftIO $ putStr $ command ++ " " ++ file ++ " "
-	liftIO $ hFlush stdout
+showStart command file = verbose $ liftIO $ do
+	putStr $ command ++ " " ++ file ++ " "
+	hFlush stdout
 
 showNote :: String -> Annex ()
-showNote s = verbose $ do
-	liftIO $ putStr $ "(" ++ s ++ ") "
-	liftIO $ hFlush stdout
+showNote s = verbose $ liftIO $ do
+	putStr $ "(" ++ s ++ ") "
+	hFlush stdout
 
+showAction :: String -> Annex ()
+showAction s = showNote $ s ++ "..."
+
 showProgress :: Annex ()
-showProgress = verbose $ liftIO $ putStr "\n"
+showProgress = verbose $ liftIO $ do
+	putStr "."
+	hFlush stdout
 
+showSideAction :: String -> Annex ()
+showSideAction s = verbose $ liftIO $ putStrLn $ "(" ++ s ++ "...)"
+
+showOutput :: Annex ()
+showOutput = verbose $ liftIO $ putStr "\n"
+
 showLongNote :: String -> Annex ()
-showLongNote s = verbose $ liftIO $ putStr $ "\n" ++ indent s
+showLongNote s = verbose $ liftIO $ putStr $ '\n' : indent s
 
 showEndOk :: Annex ()
 showEndOk = verbose $ liftIO $ putStrLn "ok"
@@ -50,15 +58,16 @@
 showEndResult False = showEndFail
 
 showErr :: (Show a) => a -> Annex ()
-showErr e = do
-	liftIO $ hFlush stdout
-	liftIO $ hPutStrLn stderr $ "git-annex: " ++ show e
+showErr e = liftIO $ do
+	hFlush stdout
+	hPutStrLn stderr $ "git-annex: " ++ show e
 
 warning :: String -> Annex ()
 warning w = do
 	verbose $ liftIO $ putStr "\n"
-	liftIO $ hFlush stdout
-	liftIO $ hPutStrLn stderr $ indent w
+	liftIO $ do
+		hFlush stdout
+		hPutStrLn stderr $ indent w
 
 indent :: String -> String
 indent s = join "\n" $ map (\l -> "  " ++ l) $ lines s
diff --git a/PresenceLog.hs b/PresenceLog.hs
--- a/PresenceLog.hs
+++ b/PresenceLog.hs
@@ -15,10 +15,12 @@
 	LogStatus(..),
 	addLog,
 	readLog,
+	parseLog,
 	writeLog,
 	logNow,
 	compactLog,
-	currentLog
+	currentLog,
+	LogLine
 ) where
 
 import Data.Time.Clock.POSIX
@@ -94,7 +96,7 @@
 {- Generates a new LogLine with the current date. -}
 logNow :: LogStatus -> String -> Annex LogLine
 logNow s i = do
-	now <- liftIO $ getPOSIXTime
+	now <- liftIO getPOSIXTime
 	return $ LogLine now s i
 
 {- Reads a log and returns only the info that is still in effect. -}
@@ -112,7 +114,7 @@
 {- Compacts a set of logs, returning a subset that contains the current
  - status. -}
 compactLog :: [LogLine] -> [LogLine]
-compactLog ls = compactLog' Map.empty ls
+compactLog = compactLog' Map.empty
 compactLog' :: LogMap -> [LogLine] -> [LogLine]
 compactLog' m [] = Map.elems m
 compactLog' m (l:ls) = compactLog' (mapLog m l) ls
diff --git a/Remote.hs b/Remote.hs
--- a/Remote.hs
+++ b/Remote.hs
@@ -33,6 +33,7 @@
 import Data.List
 import qualified Data.Map as M
 import Data.String.Utils
+import Data.Maybe
 
 import Types
 import Types.Remote
@@ -97,7 +98,7 @@
 byName' n = do
 	allremotes <- genList
 	let match = filter matching allremotes
-	if (null match)
+	if null match
 		then return $ Left $ "there is no git remote named \"" ++ n ++ "\""
 		else return $ Right $ head match
 	where
@@ -110,7 +111,7 @@
 nameToUUID n = do
 	res <- byName' n
 	case res of
-		Left e -> return . (maybe (error e) id) =<< byDescription
+		Left e -> return . fromMaybe (error e) =<< byDescription
 		Right r -> return $ uuid r
 	where
 		byDescription = return . M.lookup n . invertMap =<< uuidMap
@@ -122,7 +123,7 @@
 prettyPrintUUIDs uuids = do
 	here <- getUUID =<< Annex.gitRepo
 	-- Show descriptions from the uuid log, falling back to remote names,
-	-- as some remotes may not be in the uuid log.
+	-- as some remotes may not be in the uuid log
 	m <- liftM2 M.union uuidMap $
 		return . M.fromList . map (\r -> (uuid r, name r)) =<< genList
 	return $ unwords $ map (\u -> "\t" ++ prettify m u here ++ "\n") uuids
diff --git a/Remote/Bup.hs b/Remote/Bup.hs
--- a/Remote/Bup.hs
+++ b/Remote/Bup.hs
@@ -8,7 +8,8 @@
 module Remote.Bup (remote) where
 
 import qualified Data.ByteString.Lazy.Char8 as L
-import IO
+import System.IO
+import System.IO.Error
 import Control.Exception.Extensible (IOException)
 import qualified Data.Map as M
 import Control.Monad (when)
@@ -16,6 +17,7 @@
 import System.Process
 import System.Exit
 import System.FilePath
+import Data.Maybe
 import Data.List.Utils
 import System.Cmd.Utils
 
@@ -28,9 +30,9 @@
 import Config
 import Utility
 import Messages
-import Remote.Ssh
-import Remote.Special
-import Remote.Encryptable
+import Remote.Helper.Ssh
+import Remote.Helper.Special
+import Remote.Helper.Encryptable
 import Crypto
 
 type BupRepo = String
@@ -68,13 +70,13 @@
 bupSetup :: UUID -> RemoteConfig -> Annex RemoteConfig
 bupSetup u c = do
 	-- verify configuration is sane
-	let buprepo = maybe (error "Specify buprepo=") id $
+	let buprepo = fromMaybe (error "Specify buprepo=") $
 		M.lookup "buprepo" c
 	c' <- encryptionSetup c
 
 	-- bup init will create the repository.
 	-- (If the repository already exists, bup init again appears safe.)
-	showNote "bup init"
+	showAction "bup init"
 	bup "init" buprepo [] >>! error "bup init failed"
 
 	storeBupUUID u buprepo
@@ -87,11 +89,11 @@
 
 bupParams :: String -> BupRepo -> [CommandParam] -> [CommandParam]
 bupParams command buprepo params = 
-	(Param command) : [Param "-r", Param buprepo] ++ params
+	Param command : [Param "-r", Param buprepo] ++ params
 
 bup :: String -> BupRepo -> [CommandParam] -> Annex Bool
 bup command buprepo params = do
-	showProgress -- make way for bup output
+	showOutput -- make way for bup output
 	liftIO $ boolSystem "bup" $ bupParams command buprepo params
 
 pipeBup :: [CommandParam] -> Maybe Handle -> Maybe Handle -> IO Bool
@@ -107,7 +109,7 @@
 bupSplitParams r buprepo k src = do
 	o <- getConfig r "bup-split-options" ""
 	let os = map Param $ words o
-	showProgress -- make way for bup output
+	showOutput -- make way for bup output
 	return $ bupParams "split" buprepo 
 		(os ++ [Param "-n", Param (show k), src])
 
@@ -123,8 +125,8 @@
 	g <- Annex.gitRepo
 	let src = gitAnnexLocation g k
 	params <- bupSplitParams r buprepo enck (Param "-")
-	liftIO $ catchBool $ do
-		withEncryptedHandle cipher (L.readFile src) $ \h -> do
+	liftIO $ catchBool $
+		withEncryptedHandle cipher (L.readFile src) $ \h ->
 			pipeBup params (Just h) Nothing
 
 retrieve :: BupRepo -> Key -> FilePath -> Annex Bool
@@ -155,7 +157,7 @@
 checkPresent :: Git.Repo -> Git.Repo -> Key -> Annex (Either IOException Bool)
 checkPresent r bupr k
 	| Git.repoIsUrl bupr = do
-		showNote ("checking " ++ Git.repoDescribe r ++ "...")
+		showAction $ "checking " ++ Git.repoDescribe r
 		ok <- onBupRemote bupr boolSystem "git" params
 		return $ Right ok
 	| otherwise = liftIO $ try $ boolSystem "git" $ Git.gitCommandLine bupr params
@@ -170,7 +172,7 @@
 	r <- liftIO $ bup2GitRemote buprepo
 	if Git.repoIsUrl r
 		then do
-			showNote "storing uuid"
+			showAction "storing uuid"
 			onBupRemote r boolSystem "git"
 				[Params $ "config annex.uuid " ++ u]
 					>>! error "ssh failed"
@@ -184,7 +186,7 @@
 onBupRemote r a command params = do
 	let dir = shellEscape (Git.workTree r)
 	sshparams <- sshToRepo r [Param $
-			"cd " ++ dir ++ " && " ++ (unwords $ command : toCommand params)]
+			"cd " ++ dir ++ " && " ++ unwords (command : toCommand params)]
 	liftIO $ a "ssh" sshparams
 
 {- Allow for bup repositories on removable media by checking
@@ -215,20 +217,20 @@
 	Git.repoFromAbsPath $ h </> ".bup"
 bup2GitRemote r
 	| bupLocal r = 
-		if r !! 0 == '/'
+		if head r == '/'
 			then Git.repoFromAbsPath r
 			else error "please specify an absolute path"
 	| otherwise = Git.repoFromUrl $ "ssh://" ++ host ++ slash dir
 		where
 			bits = split ":" r
-			host = bits !! 0
+			host = head bits
 			dir = join ":" $ drop 1 bits
 			-- "host:~user/dir" is not supported specially by bup;
 			-- "host:dir" is relative to the home directory;
 			-- "host:" goes in ~/.bup
 			slash d
 				| d == "" = "/~/.bup"
-				| d !! 0 == '/' = d
+				| head d == '/' = d
 				| otherwise = "/~/" ++ d
 
 bupLocal :: BupRepo -> Bool
diff --git a/Remote/Directory.hs b/Remote/Directory.hs
--- a/Remote/Directory.hs
+++ b/Remote/Directory.hs
@@ -8,13 +8,14 @@
 module Remote.Directory (remote) where
 
 import qualified Data.ByteString.Lazy.Char8 as L
-import IO
+import System.IO.Error
 import Control.Exception.Extensible (IOException)
 import qualified Data.Map as M
 import Control.Monad (when)
 import Control.Monad.State (liftIO)
 import System.Directory hiding (copyFile)
 import System.FilePath
+import Data.Maybe
 
 import Types
 import Types.Remote
@@ -26,8 +27,8 @@
 import Config
 import Content
 import Utility
-import Remote.Special
-import Remote.Encryptable
+import Remote.Helper.Special
+import Remote.Helper.Encryptable
 import Crypto
 
 remote :: RemoteType Annex
@@ -60,7 +61,7 @@
 directorySetup :: UUID -> RemoteConfig -> Annex RemoteConfig
 directorySetup u c = do
 	-- verify configuration is sane
-	let dir = maybe (error "Specify directory=") id $
+	let dir = fromMaybe (error "Specify directory=") $
 		M.lookup "directory" c
 	liftIO $ doesDirectoryExist dir
 		>>! error $ "Directory does not exist: " ++ dir
diff --git a/Remote/Encryptable.hs b/Remote/Encryptable.hs
deleted file mode 100644
--- a/Remote/Encryptable.hs
+++ /dev/null
@@ -1,87 +0,0 @@
-{- common functions for encryptable remotes
- -
- - Copyright 2011 Joey Hess <joey@kitenet.net>
- -
- - Licensed under the GNU GPL version 3 or higher.
- -}
-
-module Remote.Encryptable where
-
-import qualified Data.Map as M
-import Control.Monad.State (liftIO)
-
-import Types
-import Types.Remote
-import Crypto
-import qualified Annex
-import Messages
-import Config
-
-{- Encryption setup for a remote. The user must specify whether to use
- - an encryption key, or not encrypt. An encrypted cipher is created, or is
- - updated to be accessible to an additional encryption key. -}
-encryptionSetup :: RemoteConfig -> Annex RemoteConfig
-encryptionSetup c =
-	case (M.lookup "encryption" c, extractCipher c) of
-		(Nothing, Nothing) -> error "Specify encryption=key or encryption=none"
-		(Just "none", Nothing) -> return c
-		(Just "none", Just _) -> error "Cannot change encryption type of existing remote."
-		(Nothing, Just _) -> return c
-		(Just _, Nothing) -> use "encryption setup" $ genCipher c
-		(Just _, Just v) -> use "encryption updated" $ updateCipher c v
-	where
-		use m a = do
-			cipher <- liftIO a
-			showNote $ m ++ " " ++ describeCipher cipher
-			return $ M.delete "encryption" $ storeCipher c cipher
-
-{- Modifies a Remote to support encryption.
- -
- - Two additional functions must be provided by the remote,
- - to support storing and retrieving encrypted content. -}
-encryptableRemote
-	:: Maybe RemoteConfig
-	-> ((Cipher, Key) -> Key -> Annex Bool)
-	-> ((Cipher, Key) -> FilePath -> Annex Bool)
-	-> Remote Annex 
-	-> Remote Annex
-encryptableRemote c storeKeyEncrypted retrieveKeyFileEncrypted r = 
-	r {
-		storeKey = store,
-		retrieveKeyFile = retrieve,
-		removeKey = withkey $ removeKey r,
-		hasKey = withkey $ hasKey r,
-		cost = cost r + encryptedRemoteCostAdj
-	}
-	where
-		store k = cip k >>= maybe
-			(storeKey r k)
-			(\x -> storeKeyEncrypted x k)
-		retrieve k f = cip k >>= maybe
-			(retrieveKeyFile r k f)
-			(\x -> retrieveKeyFileEncrypted x f)
-		withkey a k = cip k >>= maybe (a k) (a . snd)
-		cip = cipherKey c
-
-{- Gets encryption Cipher. The decrypted Cipher is cached in the Annex
- - state. -}
-remoteCipher :: RemoteConfig -> Annex (Maybe Cipher)
-remoteCipher c = maybe expensive cached =<< Annex.getState Annex.cipher
-	where
-		cached cipher = return $ Just cipher
-		expensive = case extractCipher c of
-			Nothing -> return Nothing
-			Just encipher -> do
-				showNote "gpg"
-				cipher <- liftIO $ decryptCipher c encipher
-				Annex.changeState (\s -> s { Annex.cipher = Just cipher })
-				return $ Just cipher
-
-{- Gets encryption Cipher, and encrypted version of Key. -}
-cipherKey :: Maybe RemoteConfig -> Key -> Annex (Maybe (Cipher, Key))
-cipherKey Nothing _ = return Nothing
-cipherKey (Just c) k = remoteCipher c >>= maybe (return Nothing) encrypt
-	where
-		encrypt ciphertext = do
-			k' <- liftIO $ encryptKey ciphertext k
-			return $ Just (ciphertext, k')
diff --git a/Remote/Git.hs b/Remote/Git.hs
--- a/Remote/Git.hs
+++ b/Remote/Git.hs
@@ -12,6 +12,7 @@
 import qualified Data.Map as M
 import System.Cmd.Utils
 import System.Posix.Files
+import System.IO
 
 import Types
 import Types.Remote
@@ -24,8 +25,10 @@
 import Messages
 import Utility.CopyFile
 import Utility.RsyncFile
-import Remote.Ssh
+import Remote.Helper.Ssh
+import qualified Remote.Helper.Url as Url
 import Config
+import Init
 
 remote :: RemoteType Annex
 remote = RemoteType {
@@ -57,7 +60,7 @@
 	let defcst = if cheap then cheapRemoteCost else expensiveRemoteCost
 	cst <- remoteCost r' defcst
 
-	return $ Remote {
+	return Remote {
 		uuid = u',
 		cost = cst,
 		name = Git.repoDescribe r',
@@ -75,19 +78,32 @@
 tryGitConfigRead r 
 	| not $ M.null $ Git.configMap r = return r -- already read
 	| Git.repoIsSsh r = store $ onRemote r (pipedconfig, r) "configlist" []
+	| Git.repoIsHttp r = store $ safely $ geturlconfig
 	| Git.repoIsUrl r = return r
-	| otherwise = store $ safely $ Git.configRead r
+	| otherwise = store $ safely $ do
+		onLocal r ensureInitialized
+		Git.configRead r
 	where
 		-- Reading config can fail due to IO error or
 		-- for other reasons; catch all possible exceptions.
 		safely a = do
-			result <- liftIO (try (a)::IO (Either SomeException Git.Repo))
+			result <- liftIO (try a :: IO (Either SomeException Git.Repo))
 			case result of
 				Left _ -> return r
 				Right r' -> return r'
+
 		pipedconfig cmd params = safely $
 			pOpen ReadFromPipe cmd (toCommand params) $
 				Git.hConfigRead r
+
+		geturlconfig = do
+			s <- Url.get (Git.repoLocation r ++ "/config")
+			withTempFile "git-annex.tmp" $ \tmpfile -> \h -> do
+				hPutStr h s
+				hClose h
+				pOpen ReadFromPipe "git" ["config", "--list", "--file", tmpfile] $
+					Git.hConfigRead r
+
 		store a = do
 			r' <- a
 			g <- Annex.gitRepo
@@ -95,6 +111,7 @@
 			let g' = Git.remotesAdd g $ exchange l r'
 			Annex.changeState $ \s -> s { Annex.repo = g' }
 			return r'
+
 		exchange [] _ = []
 		exchange (old:ls) new =
 			if Git.repoRemoteName old == Git.repoRemoteName new
@@ -105,24 +122,34 @@
  - If the remote cannot be accessed, returns a Left error.
  -}
 inAnnex :: Git.Repo -> Key -> Annex (Either IOException Bool)
-inAnnex r key = if Git.repoIsUrl r
-		then checkremote
-		else liftIO (try checklocal ::IO (Either IOException Bool))
+inAnnex r key
+	| Git.repoIsHttp r = safely checkhttp
+	| Git.repoIsUrl r = checkremote
+	| otherwise = safely checklocal
 	where
-		checklocal = do
-			-- run a local check inexpensively,
-			-- by making an Annex monad using the remote
-			a <- Annex.new r
-			Annex.eval a (Content.inAnnex key)
+		checklocal = onLocal r (Content.inAnnex key)
 		checkremote = do
-			showNote ("checking " ++ Git.repoDescribe r ++ "...")
+			showAction $ "checking " ++ Git.repoDescribe r
 			inannex <- onRemote r (boolSystem, False) "inannex" 
 				[Param (show key)]
 			return $ Right inannex
-	
+		checkhttp = Url.exists $ keyUrl r key
+		safely a = liftIO (try a ::IO (Either IOException Bool))
+
+{- Runs an action on a local repository inexpensively, by making an annex
+ - monad using that repository. -}
+onLocal :: Git.Repo -> Annex a -> IO a
+onLocal r a = do
+	annex <- Annex.new r
+	Annex.eval annex a
+
+keyUrl :: Git.Repo -> Key -> String
+keyUrl r key = Git.repoLocation r ++ "/" ++ annexLocation key
+
 dropKey :: Git.Repo -> Key -> Annex Bool
-dropKey r key = 
-	onRemote r (boolSystem, False) "dropkey"
+dropKey r key
+	| Git.repoIsHttp r = error "dropping from http repo not supported"
+	| otherwise = onRemote r (boolSystem, False) "dropkey"
 		[ Params "--quiet --force"
 		, Param $ show key
 		]
@@ -132,8 +159,9 @@
 copyFromRemote r key file
 	| not $ Git.repoIsUrl r = rsyncOrCopyFile r (gitAnnexLocation r key) file
 	| Git.repoIsSsh r = rsyncHelper =<< rsyncParamsRemote r True key file
-	| otherwise = error "copying from non-ssh repo not supported"
-		
+	| Git.repoIsHttp r = Url.download (keyUrl r key) file
+	| otherwise = error "copying from non-ssh, non-http repo not supported"
+
 {- Tries to copy a key's content to a remote's annex. -}
 copyToRemote :: Git.Repo -> Key -> Annex Bool
 copyToRemote r key
@@ -141,22 +169,20 @@
 		g <- Annex.gitRepo
 		let keysrc = gitAnnexLocation g key
 		-- run copy from perspective of remote
-		liftIO $ do
-			a <- Annex.new r
-			Annex.eval a $ do
-				ok <- Content.getViaTmp key $
-					rsyncOrCopyFile r keysrc
-				Content.saveState
-				return ok
+		liftIO $ onLocal r $ do
+			ok <- Content.getViaTmp key $
+				rsyncOrCopyFile r keysrc
+			Content.saveState
+			return ok
 	| Git.repoIsSsh r = do
 		g <- Annex.gitRepo
 		let keysrc = gitAnnexLocation g key
 		rsyncHelper =<< rsyncParamsRemote r False key keysrc
 	| otherwise = error "copying to non-ssh repo not supported"
 
-rsyncHelper :: [CommandParam] -> Annex (Bool)
+rsyncHelper :: [CommandParam] -> Annex Bool
 rsyncHelper p = do
-	showProgress -- make way for progress bar
+	showOutput -- make way for progress bar
 	res <- liftIO $ rsync p
 	if res
 		then return res
diff --git a/Remote/Helper/Encryptable.hs b/Remote/Helper/Encryptable.hs
new file mode 100644
--- /dev/null
+++ b/Remote/Helper/Encryptable.hs
@@ -0,0 +1,87 @@
+{- common functions for encryptable remotes
+ -
+ - Copyright 2011 Joey Hess <joey@kitenet.net>
+ -
+ - Licensed under the GNU GPL version 3 or higher.
+ -}
+
+module Remote.Helper.Encryptable where
+
+import qualified Data.Map as M
+import Control.Monad.State (liftIO)
+
+import Types
+import Types.Remote
+import Crypto
+import qualified Annex
+import Messages
+import Config
+
+{- Encryption setup for a remote. The user must specify whether to use
+ - an encryption key, or not encrypt. An encrypted cipher is created, or is
+ - updated to be accessible to an additional encryption key. -}
+encryptionSetup :: RemoteConfig -> Annex RemoteConfig
+encryptionSetup c =
+	case (M.lookup "encryption" c, extractCipher c) of
+		(Nothing, Nothing) -> error "Specify encryption=key or encryption=none"
+		(Just "none", Nothing) -> return c
+		(Just "none", Just _) -> error "Cannot change encryption type of existing remote."
+		(Nothing, Just _) -> return c
+		(Just _, Nothing) -> use "encryption setup" $ genCipher c
+		(Just _, Just v) -> use "encryption updated" $ updateCipher c v
+	where
+		use m a = do
+			cipher <- liftIO a
+			showNote $ m ++ " " ++ describeCipher cipher
+			return $ M.delete "encryption" $ storeCipher c cipher
+
+{- Modifies a Remote to support encryption.
+ -
+ - Two additional functions must be provided by the remote,
+ - to support storing and retrieving encrypted content. -}
+encryptableRemote
+	:: Maybe RemoteConfig
+	-> ((Cipher, Key) -> Key -> Annex Bool)
+	-> ((Cipher, Key) -> FilePath -> Annex Bool)
+	-> Remote Annex 
+	-> Remote Annex
+encryptableRemote c storeKeyEncrypted retrieveKeyFileEncrypted r = 
+	r {
+		storeKey = store,
+		retrieveKeyFile = retrieve,
+		removeKey = withkey $ removeKey r,
+		hasKey = withkey $ hasKey r,
+		cost = cost r + encryptedRemoteCostAdj
+	}
+	where
+		store k = cip k >>= maybe
+			(storeKey r k)
+			(`storeKeyEncrypted` k)
+		retrieve k f = cip k >>= maybe
+			(retrieveKeyFile r k f)
+			(`retrieveKeyFileEncrypted` f)
+		withkey a k = cip k >>= maybe (a k) (a . snd)
+		cip = cipherKey c
+
+{- Gets encryption Cipher. The decrypted Cipher is cached in the Annex
+ - state. -}
+remoteCipher :: RemoteConfig -> Annex (Maybe Cipher)
+remoteCipher c = maybe expensive cached =<< Annex.getState Annex.cipher
+	where
+		cached cipher = return $ Just cipher
+		expensive = case extractCipher c of
+			Nothing -> return Nothing
+			Just encipher -> do
+				showNote "gpg"
+				cipher <- liftIO $ decryptCipher c encipher
+				Annex.changeState (\s -> s { Annex.cipher = Just cipher })
+				return $ Just cipher
+
+{- Gets encryption Cipher, and encrypted version of Key. -}
+cipherKey :: Maybe RemoteConfig -> Key -> Annex (Maybe (Cipher, Key))
+cipherKey Nothing _ = return Nothing
+cipherKey (Just c) k = remoteCipher c >>= maybe (return Nothing) encrypt
+	where
+		encrypt ciphertext = do
+			k' <- liftIO $ encryptKey ciphertext k
+			return $ Just (ciphertext, k')
diff --git a/Remote/Helper/Special.hs b/Remote/Helper/Special.hs
new file mode 100644
--- /dev/null
+++ b/Remote/Helper/Special.hs
@@ -0,0 +1,44 @@
+{- common functions for special remotes
+ -
+ - Copyright 2011 Joey Hess <joey@kitenet.net>
+ -
+ - Licensed under the GNU GPL version 3 or higher.
+ -}
+
+module Remote.Helper.Special where
+
+import qualified Data.Map as M
+import Data.Maybe
+import Data.String.Utils
+import Control.Monad.State (liftIO)
+
+import Types
+import Types.Remote
+import qualified Git
+import qualified Annex
+import UUID
+import Utility
+
+{- Special remotes don't have a configured url, so Git.Repo does not
+ - automatically generate remotes for them. This looks for a different
+ - configuration key instead.
+ -}
+findSpecialRemotes :: String -> Annex [Git.Repo]
+findSpecialRemotes s = do
+	g <- Annex.gitRepo
+	return $ map construct $ remotepairs g
+	where
+		remotepairs r = M.toList $ M.filterWithKey match $ Git.configMap r
+		construct (k,_) = Git.repoRemoteNameSet Git.repoFromUnknown k
+		match k _ = startswith "remote." k && endswith (".annex-"++s) k
+
+{- Sets up configuration for a special remote in .git/config. -}
+gitConfigSpecialRemote :: UUID -> RemoteConfig -> String -> String -> Annex ()
+gitConfigSpecialRemote u c k v = do
+	g <- Annex.gitRepo
+	liftIO $ do
+		Git.run g "config" [Param (configsetting $ "annex-"++k), Param v]
+		Git.run g "config" [Param (configsetting "annex-uuid"), Param u]
+	where
+		remotename = fromJust (M.lookup "name" c)
+		configsetting s = "remote." ++ remotename ++ "." ++ s
diff --git a/Remote/Helper/Ssh.hs b/Remote/Helper/Ssh.hs
new file mode 100644
--- /dev/null
+++ b/Remote/Helper/Ssh.hs
@@ -0,0 +1,61 @@
+{- git-annex remote access with ssh
+ -
+ - Copyright 2011 Joey Hess <joey@kitenet.net>
+ -
+ - Licensed under the GNU GPL version 3 or higher.
+ -}
+
+module Remote.Helper.Ssh where
+
+import Control.Monad.State (liftIO)
+
+import qualified Git
+import Utility
+import Types
+import Config
+
+{- Generates parameters to ssh to a repository's host and run a command.
+ - Caller is responsible for doing any neccessary shellEscaping of the
+ - passed command. -}
+sshToRepo :: Git.Repo -> [CommandParam] -> Annex [CommandParam]
+sshToRepo repo sshcmd = do
+	s <- getConfig repo "ssh-options" ""
+	let sshoptions = map Param (words s)
+	let sshport = case Git.urlPort repo of
+		Nothing -> []
+		Just p -> [Param "-p", Param (show p)]
+	let sshhost = Param $ Git.urlHostUser repo
+	return $ sshoptions ++ sshport ++ [sshhost] ++ sshcmd
+
+{- Generates parameters to run a git-annex-shell command on a remote
+ - repository. -}
+git_annex_shell :: Git.Repo -> String -> [CommandParam] -> Annex (Maybe (FilePath, [CommandParam]))
+git_annex_shell r command params
+	| not $ Git.repoIsUrl r = return $ Just (shellcmd, shellopts)
+	| Git.repoIsSsh r = do
+		sshparams <- sshToRepo r [Param sshcmd]
+		return $ Just ("ssh", sshparams)
+	| otherwise = return Nothing
+	where
+		dir = Git.workTree r
+		shellcmd = "git-annex-shell"
+		shellopts = Param command : File dir : params
+		sshcmd = shellcmd ++ " " ++ 
+			unwords (map shellEscape $ toCommand shellopts)
+
+{- Uses a supplied function (such as boolSystem) to run a git-annex-shell
+ - command on a remote.
+ -
+ - Or, if the remote does not support running remote commands, returns
+ - a specified error value. -}
+onRemote 
+	:: Git.Repo
+	-> (FilePath -> [CommandParam] -> IO a, a)
+	-> String
+	-> [CommandParam]
+	-> Annex a
+onRemote r (with, errorval) command params = do
+	s <- git_annex_shell r command params
+	case s of
+		Just (c, ps) -> liftIO $ with c ps
+		Nothing -> return errorval
diff --git a/Remote/Helper/Url.hs b/Remote/Helper/Url.hs
new file mode 100644
--- /dev/null
+++ b/Remote/Helper/Url.hs
@@ -0,0 +1,66 @@
+{- Url downloading for remotes.
+ -
+ - Copyright 2011 Joey Hess <joey@kitenet.net>
+ -
+ - Licensed under the GNU GPL version 3 or higher.
+ -}
+
+module Remote.Helper.Url (
+	exists,
+	download,
+	get
+) where
+
+import Control.Monad (liftM)
+import Control.Monad.State (liftIO)
+import qualified Network.Browser as Browser
+import Network.HTTP
+import Network.URI
+
+import Types
+import Messages
+import Utility
+
+type URLString = String
+
+{- Checks that an url exists and could be successfully downloaded. -}
+exists :: URLString -> IO Bool
+exists url =
+	case parseURI url of
+		Nothing -> return False
+		Just u -> do
+			r <- request u HEAD
+			case rspCode r of
+				(2,_,_) -> return True
+				_ -> return False
+
+{- Used to download large files, such as the contents of keys.
+ - Uses curl program for its progress bar. -}
+download :: URLString -> FilePath -> Annex Bool
+download url file = do
+	showOutput -- make way for curl progress bar
+	liftIO $ boolSystem "curl" [Params "-L -C - -# -o", File file, File url]
+
+{- Downloads a small file. -}
+get :: URLString -> IO String
+get url =
+	case parseURI url of
+		Nothing -> error "url parse error"
+		Just u -> do
+			r <- request u GET
+			case rspCode r of
+				(2,_,_) -> return $ rspBody r
+				_ -> error $ rspReason r
+
+{- Makes a http request of an url. For example, HEAD can be used to
+ - check if the url exists, or GET used to get the url content (best for
+ - small urls). -}
+request :: URI -> RequestMethod -> IO (Response String)
+request url requesttype = Browser.browse $ do
+	Browser.setErrHandler ignore
+	Browser.setOutHandler ignore
+	Browser.setAllowRedirects True
+	liftM snd $ Browser.request
+		(mkRequest requesttype url :: Request_String)
+	where
+		ignore = const $ return ()
diff --git a/Remote/Hook.hs b/Remote/Hook.hs
--- a/Remote/Hook.hs
+++ b/Remote/Hook.hs
@@ -17,6 +17,7 @@
 import System.IO
 import System.IO.Error (try)
 import System.Exit
+import Data.Maybe
 
 import Types
 import Types.Remote
@@ -27,8 +28,8 @@
 import Config
 import Content
 import Utility
-import Remote.Special
-import Remote.Encryptable
+import Remote.Helper.Special
+import Remote.Helper.Encryptable
 import Crypto
 import Messages
 
@@ -61,7 +62,7 @@
 
 hookSetup :: UUID -> RemoteConfig -> Annex RemoteConfig
 hookSetup u c = do
-	let hooktype = maybe (error "Specify hooktype=") id $
+	let hooktype = fromMaybe (error "Specify hooktype=") $
 		M.lookup "hooktype" c
 	c' <- encryptionSetup c
 	gitConfigSpecialRemote u c' "hooktype" hooktype
@@ -73,12 +74,13 @@
 		env s v = ("ANNEX_" ++ s, v)
 		keyenv =
 			[ env "KEY" (show k)
-			, env "HASH_1" (hashbits !! 0)
-			, env "HASH_2" (hashbits !! 1)
+			, env "HASH_1" hash_1
+			, env "HASH_2" hash_2
 			]
 		fileenv Nothing = []
 		fileenv (Just file) =  [env "FILE" file]
-		hashbits = map takeDirectory $ splitPath $ hashDirMixed k
+		[hash_1, hash_2, _rest] =
+			map takeDirectory $ splitPath $ hashDirMixed k
 
 lookupHook :: String -> String -> Annex (Maybe String)
 lookupHook hooktype hook =do
@@ -96,7 +98,7 @@
 runHook hooktype hook k f a = maybe (return False) run =<< lookupHook hooktype hook
 	where
 		run command = do
-			showProgress -- make way for hook output
+			showOutput -- make way for hook output
 			res <- liftIO $ boolSystemEnv
 				"sh" [Param "-c", Param command] $ hookEnv k f
 			if res
@@ -127,15 +129,15 @@
 		return True
 
 remove :: String -> Key -> Annex Bool
-remove h k = runHook h "remove" k Nothing $ do return True
+remove h k = runHook h "remove" k Nothing $ return True
 
 checkPresent :: Git.Repo -> String -> Key -> Annex (Either IOException Bool)
 checkPresent r h k = do
-	showNote ("checking " ++ Git.repoDescribe r ++ "...")
+	showAction $ "checking " ++ Git.repoDescribe r
 	v <- lookupHook h "checkpresent"
 	liftIO (try (check v) ::IO (Either IOException Bool))
 	where
-		findkey s = (show k) `elem` (lines s)
+		findkey s = show k `elem` lines s
 		env = hookEnv k Nothing
 		check Nothing = error "checkpresent hook misconfigured"
 		check (Just hook) = do
@@ -150,5 +152,5 @@
 			hClose fromh
 			s <- getProcessStatus True False pid
 			case s of
-				Just (Exited (ExitSuccess)) -> return $ findkey reply
+				Just (Exited ExitSuccess) -> return $ findkey reply
 				_ -> error "checkpresent hook failed"
diff --git a/Remote/Rsync.hs b/Remote/Rsync.hs
--- a/Remote/Rsync.hs
+++ b/Remote/Rsync.hs
@@ -15,6 +15,7 @@
 import System.Directory
 import System.Posix.Files
 import System.Posix.Process
+import Data.Maybe
 
 import Types
 import Types.Remote
@@ -25,8 +26,8 @@
 import Config
 import Content
 import Utility
-import Remote.Special
-import Remote.Encryptable
+import Remote.Helper.Special
+import Remote.Helper.Encryptable
 import Crypto
 import Messages
 import Utility.RsyncFile
@@ -82,7 +83,7 @@
 rsyncSetup :: UUID -> RemoteConfig -> Annex RemoteConfig
 rsyncSetup u c = do
 	-- verify configuration is sane
-	let url = maybe (error "Specify rsyncurl=") id $
+	let url = fromMaybe (error "Specify rsyncurl=") $
 		M.lookup "rsyncurl" c
 	c' <- encryptionSetup c
 
@@ -92,10 +93,13 @@
 	return c'
 
 rsyncKey :: RsyncOpts -> Key -> String
-rsyncKey o k = rsyncUrl o </> hashDirMixed k </> f </> f
+rsyncKey o k = rsyncUrl o </> hashDirMixed k </> shellEscape (f </> f)
         where
                 f = keyFile k
 
+rsyncKeyDir :: RsyncOpts -> Key -> String
+rsyncKeyDir o k = rsyncUrl o </> hashDirMixed k </> shellEscape (keyFile k)
+
 store :: RsyncOpts -> Key -> Annex Bool
 store o k = do
 	g <- Annex.gitRepo
@@ -135,19 +139,18 @@
 		[ Params "--delete --recursive"
 		, partialParams
 		, Param $ addTrailingPathSeparator dummy
-		, Param $ parentDir $ rsyncKey o k
+		, Param $ rsyncKeyDir o k
 		]
 
 checkPresent :: Git.Repo -> RsyncOpts -> Key -> Annex (Either IOException Bool)
 checkPresent r o k = do
-	showNote ("checking " ++ Git.repoDescribe r ++ "...")
+	showAction $ "checking " ++ Git.repoDescribe r
 	-- note: Does not currently differnetiate between rsync failing
 	-- to connect, and the file not being present.
 	res <- liftIO $ boolSystem "sh" [Param "-c", Param cmd]
 	return $ Right res
 	where
-		cmd = "rsync --quiet " ++ testfile ++ " 2>/dev/null"
-		testfile = shellEscape $ rsyncKey o k
+		cmd = "rsync --quiet " ++ shellEscape (rsyncKey o k) ++ " 2>/dev/null"
 
 {- Rsync params to enable resumes of sending files safely,
  - ensure that files are only moved into place once complete
@@ -160,10 +163,10 @@
 withRsyncScratchDir :: (FilePath -> Annex Bool) -> Annex Bool
 withRsyncScratchDir a = do
 	g <- Annex.gitRepo
-	pid <- liftIO $ getProcessID
+	pid <- liftIO getProcessID
 	let tmp = gitAnnexTmpDir g </> "rsynctmp" </> show pid
 	nuke tmp
-	liftIO $ createDirectoryIfMissing True $ tmp
+	liftIO $ createDirectoryIfMissing True tmp
 	res <- a tmp
 	nuke tmp
 	return res
@@ -173,7 +176,7 @@
 
 rsyncRemote :: RsyncOpts -> [CommandParam] -> Annex Bool
 rsyncRemote o params = do
-	showProgress -- make way for progress bar
+	showOutput -- make way for progress bar
 	res <- liftIO $ rsync $ rsyncOptions o ++ defaultParams ++ params
 	if res
 		then return res
@@ -189,15 +192,14 @@
 rsyncSend :: RsyncOpts -> Key -> FilePath -> Annex Bool
 rsyncSend o k src = withRsyncScratchDir $ \tmp -> do
 	let dest = tmp </> hashDirMixed k </> f </> f
-	liftIO $ createDirectoryIfMissing True $ parentDir $ dest
+	liftIO $ createDirectoryIfMissing True $ parentDir dest
 	liftIO $ createLink src dest
-	res <- rsyncRemote o
+	rsyncRemote o
 		[ Param "--recursive"
 		, partialParams
  		  -- tmp/ to send contents of tmp dir
 		, Param $ addTrailingPathSeparator tmp
 		, Param $ rsyncUrl o
 		]
-	return res
 	where
 		f = keyFile k
diff --git a/Remote/S3real.hs b/Remote/S3real.hs
--- a/Remote/S3real.hs
+++ b/Remote/S3real.hs
@@ -33,8 +33,8 @@
 import Messages
 import Locations
 import Config
-import Remote.Special
-import Remote.Encryptable
+import Remote.Helper.Special
+import Remote.Helper.Encryptable
 import Crypto
 import Content
 import Utility.Base64
@@ -52,7 +52,7 @@
 	cst <- remoteCost r expensiveRemoteCost
 	return $ gen' r u c cst
 gen' :: Git.Repo -> UUID -> Maybe RemoteConfig -> Int -> Remote Annex
-gen' r u c cst = do
+gen' r u c cst =
 	encryptableRemote c
 		(storeEncrypted this)
 		(retrieveEncrypted this)
@@ -85,7 +85,7 @@
 		
 		handlehost Nothing = defaulthost
 		handlehost (Just h)
-			| ".archive.org" `isSuffixOf` (map toLower h) = archiveorg
+			| ".archive.org" `isSuffixOf` map toLower h = archiveorg
 			| otherwise = defaulthost
 
 		use fullconfig = do
@@ -99,7 +99,7 @@
 			use fullconfig
 
 		archiveorg = do
-			showNote $ "Internet Archive mode"
+			showNote "Internet Archive mode"
 			maybe (error "specify bucket=") (const $ return ()) $
 				M.lookup "bucket" archiveconfig
 			use archiveconfig
@@ -185,7 +185,7 @@
 
 checkPresent :: Remote Annex -> Key -> Annex (Either IOException Bool)
 checkPresent r k = s3Action r noconn $ \(conn, bucket) -> do
-	showNote ("checking " ++ name r ++ "...")
+	showAction $ "checking " ++ name r
 	res <- liftIO $ getObjectInfo conn $ bucketKey r bucket k
 	case res of
 		Right _ -> return $ Right True
@@ -203,10 +203,8 @@
 s3Error e = error $ prettyReqError e
 
 s3Bool :: AWSResult () -> Annex Bool
-s3Bool res = do
-	case res of
-		Right _ -> return True
-		Left e -> s3Warning e
+s3Bool (Right _) = return True
+s3Bool (Left e) = s3Warning e
 
 s3Action :: Remote Annex -> a -> ((AWSConnection, String) -> Annex a) -> Annex a
 s3Action r noconn action = do
@@ -219,7 +217,7 @@
 		_ -> return noconn
 
 bucketFile :: Remote Annex -> Key -> FilePath
-bucketFile r k = (munge $ show k)
+bucketFile r = munge . show
 	where
 		munge s = case M.lookup "mungekeys" $ fromJust $ config r of
 			Just "ia" -> iaMunge s
@@ -243,13 +241,13 @@
 genBucket :: RemoteConfig -> Annex ()
 genBucket c = do
 	conn <- s3ConnectionRequired c
-	showNote "checking bucket"
+	showAction "checking bucket"
 	loc <- liftIO $ getBucketLocation conn bucket 
 	case loc of
 		Right _ -> return ()
 		Left err@(NetworkError _) -> s3Error err
 		Left (AWSError _ _) -> do
-			showNote $ "creating bucket in " ++ datacenter
+			showAction $ "creating bucket in " ++ datacenter
 			res <- liftIO $ createBucketIn conn bucket datacenter
 			case res of
 				Right _ -> return ()
@@ -271,8 +269,8 @@
 			warning $ "Set both " ++ s3AccessKey ++ " and " ++ s3SecretKey  ++ " to use S3"
 			return Nothing
 	where
-		host = fromJust $ (M.lookup "host" c)
-		port = let s = fromJust $ (M.lookup "port" c) in
+		host = fromJust $ M.lookup "host" c
+		port = let s = fromJust $ M.lookup "port" c in
 			case reads s of
 			[(p, _)] -> p
 			_ -> error $ "bad S3 port value: " ++ s
@@ -283,7 +281,7 @@
 s3GetCreds c = do
 	ak <- getEnvKey s3AccessKey
 	sk <- getEnvKey s3SecretKey
-	if (null ak || null sk)
+	if null ak || null sk
 		then do
 			mcipher <- remoteCipher c
 			case (M.lookup "s3creds" c, mcipher) of
@@ -291,9 +289,7 @@
 					s <- liftIO $ withDecryptedContent cipher
 						(return $ L.pack $ fromB64 encrypted)
 						(return . L.unpack)
-					let line = lines s
-					let ak' = line !! 0
-					let sk' = line !! 1
+					let [ak', sk', _rest] = lines s
 					liftIO $ do
 						setEnv s3AccessKey ak True
 						setEnv s3SecretKey sk True
diff --git a/Remote/Special.hs b/Remote/Special.hs
deleted file mode 100644
--- a/Remote/Special.hs
+++ /dev/null
@@ -1,44 +0,0 @@
-{- common functions for special remotes
- -
- - Copyright 2011 Joey Hess <joey@kitenet.net>
- -
- - Licensed under the GNU GPL version 3 or higher.
- -}
-
-module Remote.Special where
-
-import qualified Data.Map as M
-import Data.Maybe
-import Data.String.Utils
-import Control.Monad.State (liftIO)
-
-import Types
-import Types.Remote
-import qualified Git
-import qualified Annex
-import UUID
-import Utility
-
-{- Special remotes don't have a configured url, so Git.Repo does not
- - automatically generate remotes for them. This looks for a different
- - configuration key instead.
- -}
-findSpecialRemotes :: String -> Annex [Git.Repo]
-findSpecialRemotes s = do
-	g <- Annex.gitRepo
-	return $ map construct $ remotepairs g
-	where
-		remotepairs r = M.toList $ M.filterWithKey match $ Git.configMap r
-		construct (k,_) = Git.repoRemoteNameSet Git.repoFromUnknown k
-		match k _ = startswith "remote." k && endswith (".annex-"++s) k
-
-{- Sets up configuration for a special remote in .git/config. -}
-gitConfigSpecialRemote :: UUID -> RemoteConfig -> String -> String -> Annex ()
-gitConfigSpecialRemote u c k v = do
-	g <- Annex.gitRepo
-	liftIO $ do
-		Git.run g "config" [Param (configsetting $ "annex-"++k), Param v]
-		Git.run g "config" [Param (configsetting $ "annex-uuid"), Param u]
-	where
-		remotename = fromJust (M.lookup "name" c)
-		configsetting s = "remote." ++ remotename ++ "." ++ s
diff --git a/Remote/Ssh.hs b/Remote/Ssh.hs
deleted file mode 100644
--- a/Remote/Ssh.hs
+++ /dev/null
@@ -1,61 +0,0 @@
-{- git-annex remote access with ssh
- -
- - Copyright 2011 Joey Hess <joey@kitenet.net>
- -
- - Licensed under the GNU GPL version 3 or higher.
- -}
-
-module Remote.Ssh where
-
-import Control.Monad.State (liftIO)
-
-import qualified Git
-import Utility
-import Types
-import Config
-
-{- Generates parameters to ssh to a repository's host and run a command.
- - Caller is responsible for doing any neccessary shellEscaping of the
- - passed command. -}
-sshToRepo :: Git.Repo -> [CommandParam] -> Annex [CommandParam]
-sshToRepo repo sshcmd = do
-	s <- getConfig repo "ssh-options" ""
-	let sshoptions = map Param (words s)
-	let sshport = case Git.urlPort repo of
-		Nothing -> []
-		Just p -> [Param "-p", Param (show p)]
-	let sshhost = Param $ Git.urlHostUser repo
-	return $ sshoptions ++ sshport ++ [sshhost] ++ sshcmd
-
-{- Generates parameters to run a git-annex-shell command on a remote
- - repository. -}
-git_annex_shell :: Git.Repo -> String -> [CommandParam] -> Annex (Maybe (FilePath, [CommandParam]))
-git_annex_shell r command params
-	| not $ Git.repoIsUrl r = return $ Just (shellcmd, shellopts)
-	| Git.repoIsSsh r = do
-		sshparams <- sshToRepo r [Param sshcmd]
-		return $ Just ("ssh", sshparams)
-	| otherwise = return Nothing
-	where
-		dir = Git.workTree r
-		shellcmd = "git-annex-shell"
-		shellopts = (Param command):(File dir):params
-		sshcmd = shellcmd ++ " " ++ 
-			unwords (map shellEscape $ toCommand shellopts)
-
-{- Uses a supplied function (such as boolSystem) to run a git-annex-shell
- - command on a remote.
- -
- - Or, if the remote does not support running remote commands, returns
- - a specified error value. -}
-onRemote 
-	:: Git.Repo
-	-> (FilePath -> [CommandParam] -> IO a, a)
-	-> String
-	-> [CommandParam]
-	-> Annex a
-onRemote r (with, errorval) command params = do
-	s <- git_annex_shell r command params
-	case s of
-		Just (c, ps) -> liftIO $ with c ps
-		Nothing -> return errorval
diff --git a/Remote/Web.hs b/Remote/Web.hs
--- a/Remote/Web.hs
+++ b/Remote/Web.hs
@@ -7,28 +7,24 @@
 
 module Remote.Web (
 	remote,
-	setUrl,
-	download
+	setUrl
 ) where
 
 import Control.Monad.State (liftIO)
 import Control.Exception
 import System.FilePath
-import Network.Browser
-import Network.HTTP
-import Network.URI
 
 import Types
 import Types.Remote
 import qualified Git
 import qualified Annex
 import Messages
-import Utility
 import UUID
 import Config
 import PresenceLog
 import LocationLog
 import Locations
+import qualified Remote.Helper.Url as Url
 
 type URLString = String
 
@@ -52,7 +48,7 @@
 
 gen :: Git.Repo -> UUID -> Maybe RemoteConfig -> Annex (Remote Annex)
 gen r _ _ = 
-	return $ Remote {
+	return Remote {
 		uuid = webUUID,
 		cost = expensiveRemoteCost,
 		name = Git.repoDescribe r,
@@ -67,10 +63,17 @@
 {- The urls for a key are stored in remote/web/hash/key.log 
  - in the git-annex branch. -}
 urlLog :: Key -> FilePath
-urlLog key = "remote/web" </> hashDirLower key </> show key ++ ".log"
+urlLog key = "remote/web" </> hashDirLower key </> keyFile key ++ ".log"
+oldurlLog :: Key -> FilePath
+{- A bug used to store the urls elsewhere. -}
+oldurlLog key = "remote/web" </> hashDirLower key </> show key ++ ".log"
 
 getUrls :: Key -> Annex [URLString]
-getUrls key = currentLog (urlLog key)
+getUrls key = do
+	us <- currentLog (urlLog key)
+	if null us
+		then currentLog (oldurlLog key)
+		else return us
 
 {- Records a change in an url for a key. -}
 setUrl :: Key -> URLString -> LogStatus -> Annex ()
@@ -83,9 +86,12 @@
 	logChange g key webUUID (if null us then InfoMissing else InfoPresent)
 
 downloadKey :: Key -> FilePath -> Annex Bool
-downloadKey key file = do
-	us <- getUrls key
-	download us file
+downloadKey key file = iter =<< getUrls key
+	where
+		iter [] = return False
+		iter (url:urls) = do
+			ok <- Url.download url file
+			if ok then return ok else iter urls
 
 uploadKey :: Key -> Annex Bool
 uploadKey _ = do
@@ -106,29 +112,6 @@
 checkKey' :: [URLString] -> Annex Bool
 checkKey' [] = return False
 checkKey' (u:us) = do
-	showNote ("checking " ++ u)
-	e <- liftIO $ urlexists u
+	showAction $ "checking " ++ u
+	e <- liftIO $ Url.exists u
 	if e then return e else checkKey' us
-
-urlexists :: URLString -> IO Bool
-urlexists url = do
-	case parseURI url of
-		Nothing -> return False
-		Just u -> do
-			(_, r) <- Network.Browser.browse $ do
-				setErrHandler ignore
-				setOutHandler ignore
-				setAllowRedirects True
-				request (mkRequest HEAD u :: Request_String)
-			case rspCode r of
-				(2,_,_) -> return True
-				_ -> return False
-	where
-		ignore = const $ return ()
-
-download :: [URLString] -> FilePath -> Annex Bool
-download [] _ = return False
-download (url:us) file = do
-	showProgress -- make way for curl progress bar
-	ok <- liftIO $ boolSystem "curl" [Params "-L -C - -# -o", File file, File url]
-	if ok then return ok else download us file
diff --git a/RemoteLog.hs b/RemoteLog.hs
--- a/RemoteLog.hs
+++ b/RemoteLog.hs
@@ -36,7 +36,7 @@
 	Branch.change remoteLog $ unlines $ sort $
 		map toline $ M.toList $ M.insert u c m
 	where
-		toline (u', c') = u' ++ " " ++ (unwords $ configToKeyVal c')
+		toline (u', c') = u' ++ " " ++ unwords (configToKeyVal c')
 
 {- Map of remotes by uuid containing key/value config maps. -}
 readRemoteLog :: Annex (M.Map UUID RemoteConfig)
@@ -44,14 +44,14 @@
 
 remoteLogParse :: String -> M.Map UUID RemoteConfig
 remoteLogParse s =
-	M.fromList $ catMaybes $ map parseline $ filter (not . null) $ lines s
+	M.fromList $ mapMaybe parseline $ filter (not . null) $ lines s
 	where
 		parseline l
 			| length w > 2 = Just (u, c)
 			| otherwise = Nothing
 			where
 				w = words l
-				u = w !! 0
+				u = head w
 				c = keyValToConfig $ tail w
 
 {- Given Strings like "key=value", generates a RemoteConfig. -}
@@ -90,8 +90,8 @@
 				r = drop (length num) s
 				rest = drop 1 r
 				ok = not (null num) && 
-					not (null r) && r !! 0 == ';'
+					not (null r) && head r == ';'
 
 {- for quickcheck -}
 prop_idempotent_configEscape :: String -> Bool
-prop_idempotent_configEscape s = s == (configUnEscape $ configEscape s)
+prop_idempotent_configEscape s = s == (configUnEscape . configEscape) s
diff --git a/TestConfig.hs b/TestConfig.hs
--- a/TestConfig.hs
+++ b/TestConfig.hs
@@ -45,7 +45,7 @@
 
 runTests :: [TestCase] -> IO [Config]
 runTests [] = return []
-runTests ((TestCase tname t):ts) = do
+runTests (TestCase tname t : ts) = do
 	testStart tname
 	c <- t
 	testEnd c
@@ -62,7 +62,7 @@
 		handle r = do
 			testEnd r
 			error $ "** the " ++ c ++ " command is required"
-		c = (words cmdline) !! 0
+		c = head $ words cmdline
 
 {- Checks if a command is available by running a command line. -}
 testCmd :: ConfigKey -> String -> Test
@@ -74,7 +74,7 @@
  - turn. The Config is set to the first one found. -}
 selectCmd :: ConfigKey -> [String] -> String -> Test
 selectCmd k = searchCmd
-		(\match -> return $ Config k $ StringConfig match)
+		(return . Config k . StringConfig)
 		(\cmds -> do
 			testEnd $ Config k $ BoolConfig False
 			error $ "* need one of these commands, but none are available: " ++ show cmds
@@ -82,7 +82,7 @@
 
 maybeSelectCmd :: ConfigKey -> [String] -> String -> Test
 maybeSelectCmd k = searchCmd
-		(\match -> return $ Config k $ MaybeStringConfig $ Just match)
+		(return . Config k . MaybeStringConfig . Just)
 		(\_ -> return $ Config k $ MaybeStringConfig Nothing)
 
 searchCmd :: (String -> Test) -> ([String] -> Test) -> [String] -> String -> Test
@@ -91,7 +91,7 @@
 		search [] = failure cmds
 		search (c:cs) = do
 			ret <- system $ quiet c ++ " " ++ param
-			if (ret == ExitSuccess)
+			if ret == ExitSuccess
 				then success c
 				else search cs
 
@@ -104,8 +104,11 @@
 	hFlush stdout
 
 testEnd :: Config -> IO ()
-testEnd (Config _ (BoolConfig True)) = putStrLn $ " yes"
-testEnd (Config _ (BoolConfig False)) = putStrLn $ " no"
-testEnd (Config _ (StringConfig s)) = putStrLn $ " " ++ s
-testEnd (Config _ (MaybeStringConfig (Just s))) = putStrLn $ " " ++ s
-testEnd (Config _ (MaybeStringConfig Nothing)) = putStrLn $ " not available"
+testEnd (Config _ (BoolConfig True)) = status "yes"
+testEnd (Config _ (BoolConfig False)) = status "no"
+testEnd (Config _ (StringConfig s)) = status s
+testEnd (Config _ (MaybeStringConfig (Just s))) = status s
+testEnd (Config _ (MaybeStringConfig Nothing)) = status "not available"
+
+status :: String -> IO ()
+status s = putStrLn $ ' ':s
diff --git a/Touch.hsc b/Touch.hsc
--- a/Touch.hsc
+++ b/Touch.hsc
@@ -15,6 +15,7 @@
 
 import Foreign
 import Foreign.C
+import Control.Monad (when)
 
 newtype TimeSpec = TimeSpec CTime
 
@@ -66,9 +67,7 @@
 	withCString file $ \f -> do
 		pokeArray ptr [atime, mtime]
 		r <- c_utimensat at_fdcwd f ptr flags
-		if (r /= 0)
-			then throwErrno "touchBoth"
-			else return ()
+		when (r /= 0) $ throwErrno "touchBoth"
 	where
 		flags = if follow
 			then 0
diff --git a/Types/Key.hs b/Types/Key.hs
--- a/Types/Key.hs
+++ b/Types/Key.hs
@@ -48,7 +48,7 @@
 			"" +++ y = y
 			x +++ "" = x
 			x +++ y = x ++ fieldSep:y
-			c ?: (Just v) = c:(show v)
+			c ?: (Just v) = c : show v
 			_ ?: _ = ""
 
 readKey :: String -> Maybe Key
@@ -73,4 +73,4 @@
 		addfield _ _ _ = Nothing
 
 prop_idempotent_key_read_show :: Key -> Bool
-prop_idempotent_key_read_show k = Just k == (readKey $ show k)
+prop_idempotent_key_read_show k = Just k == (readKey . show) k
diff --git a/Types/Remote.hs b/Types/Remote.hs
--- a/Types/Remote.hs
+++ b/Types/Remote.hs
@@ -11,6 +11,7 @@
 
 import Control.Exception
 import Data.Map as M
+import Data.Ord
 
 import qualified Git
 import Types.Key
@@ -62,4 +63,4 @@
 
 -- order remotes by cost
 instance Ord (Remote a) where
-	compare x y = compare (cost x) (cost y)
+	compare = comparing cost
diff --git a/UUID.hs b/UUID.hs
--- a/UUID.hs
+++ b/UUID.hs
@@ -49,7 +49,7 @@
 genUUID = liftIO $ pOpen ReadFromPipe command params $ \h -> hGetLine h
 	where
 		command = SysConfig.uuid
-		params = if (command == "uuid")
+		params = if command == "uuid"
 			-- request a random uuid be generated
 			then ["-m"]
 			-- uuidgen generates random uuid by default
@@ -82,7 +82,7 @@
 prepUUID = do
 	u <- getUUID =<< Annex.gitRepo
 	when ("" == u) $ do
-		uuid <- liftIO $ genUUID
+		uuid <- liftIO genUUID
 		setConfig configkey uuid
 
 {- Records a description for a uuid in the uuidLog. -}
diff --git a/Upgrade/V0.hs b/Upgrade/V0.hs
--- a/Upgrade/V0.hs
+++ b/Upgrade/V0.hs
@@ -23,7 +23,7 @@
 
 upgrade :: Annex Bool
 upgrade = do
-	showNote "v0 to v1..."
+	showAction "v0 to v1"
 	g <- Annex.gitRepo
 
 	-- do the reorganisation of the key files
@@ -48,7 +48,7 @@
 getKeysPresent0 :: FilePath -> Annex [Key]
 getKeysPresent0 dir = do
 	exists <- liftIO $ doesDirectoryExist dir
-	if (not exists)
+	if not exists
 		then return []
 		else do
 			contents <- liftIO $ getDirectoryContents dir
diff --git a/Upgrade/V1.hs b/Upgrade/V1.hs
--- a/Upgrade/V1.hs
+++ b/Upgrade/V1.hs
@@ -22,7 +22,7 @@
 import Content
 import Types
 import Locations
-import LocationLog
+import PresenceLog
 import qualified Annex
 import qualified AnnexQueue
 import qualified Git
@@ -58,7 +58,7 @@
 
 upgrade :: Annex Bool
 upgrade = do
-	showNote "v1 to v2"
+	showAction "v1 to v2"
 
 	g <- Annex.gitRepo
 	if Git.repoIsLocalBare g
@@ -77,7 +77,7 @@
 
 moveContent :: Annex ()
 moveContent = do
-	showNote "moving content..."
+	showAction "moving content"
 	files <- getKeyFilesPresent1
 	forM_ files move
 	where
@@ -91,10 +91,10 @@
 
 updateSymlinks :: Annex ()
 updateSymlinks = do
-	showNote "updating symlinks..."
+	showAction "updating symlinks"
 	g <- Annex.gitRepo
 	files <- liftIO $ LsFiles.inRepo g [Git.workTree g]
-	forM_ files $ fixlink
+	forM_ files fixlink
 	where
 		fixlink f = do
 			r <- lookupFile1 f
@@ -104,11 +104,11 @@
 					link <- calcGitLink f k
 					liftIO $ removeFile f
 					liftIO $ createSymbolicLink link f
-					AnnexQueue.add "add" [Param "--"] f
+					AnnexQueue.add "add" [Param "--"] [f]
 
 moveLocationLogs :: Annex ()
 moveLocationLogs = do
-	showNote "moving location logs..."
+	showAction "moving location logs"
 	logkeys <- oldlocationlogs
 	forM_ logkeys move
 		where
@@ -119,11 +119,11 @@
 				if exists
 					then do
 						contents <- liftIO $ getDirectoryContents dir
-						return $ catMaybes $ map oldlog2key contents
+						return $ mapMaybe oldlog2key contents
 					else return []
 			move (l, k) = do
 				g <- Annex.gitRepo
-				let dest = logFile k
+				let dest = logFile2 g k
 				let dir = Upgrade.V2.gitStateDir g
 				let f = dir </> l
 				liftIO $ createDirectoryIfMissing True (parentDir dest)
@@ -131,12 +131,12 @@
 				-- log files that are not checked into git,
 				-- as well as merging with already upgraded
 				-- logs that have been pulled from elsewhere
-				old <- readLog f
-				new <- readLog dest
-				writeLog dest (old++new)
-				AnnexQueue.add "add" [Param "--"] dest
-				AnnexQueue.add "add" [Param "--"] f
-				AnnexQueue.add "rm" [Param "--quiet", Param "-f", Param "--"] f
+				old <- liftIO $ readLog1 f
+				new <- liftIO $ readLog1 dest
+				liftIO $ writeLog1 dest (old++new)
+				AnnexQueue.add "add" [Param "--"] [dest]
+				AnnexQueue.add "add" [Param "--"] [f]
+				AnnexQueue.add "rm" [Param "--quiet", Param "-f", Param "--"] [f]
 		
 oldlog2key :: FilePath -> Maybe (FilePath, Key)
 oldlog2key l = 
@@ -186,9 +186,12 @@
 fileKey1 file = readKey1 $
 	replace "&a" "&" $ replace "&s" "%" $ replace "%" "/" file
 
-logFile1 :: Git.Repo -> Key -> String
-logFile1 repo key = Upgrade.V2.gitStateDir repo ++ keyFile1 key ++ ".log"
+writeLog1 :: FilePath -> [LogLine] -> IO ()
+writeLog1 file ls = viaTmp writeFile file (unlines $ map show ls)
 
+readLog1 :: FilePath -> IO [LogLine]
+readLog1 file = catch (return . parseLog =<< readFileStrict file) (const $ return [])
+
 lookupFile1 :: FilePath -> Annex (Maybe (Key, Backend Annex))
 lookupFile1 file = do
 	tl <- liftIO $ try getsymlink
@@ -196,17 +199,14 @@
 		Left _ -> return Nothing
 		Right l -> makekey l
 	where
-		getsymlink = do
-			l <- readSymbolicLink file
-			return $ takeFileName l
-		makekey l = do
-			case maybeLookupBackendName bname of
-				Nothing -> do
-					unless (null kname || null bname ||
-					        not (isLinkToAnnex l)) $
-						warning skip
-					return Nothing
-				Just backend -> return $ Just (k, backend)
+		getsymlink = return . takeFileName =<< readSymbolicLink file
+		makekey l = case maybeLookupBackendName bname of
+			Nothing -> do
+				unless (null kname || null bname ||
+				        not (isLinkToAnnex l)) $
+					warning skip
+				return Nothing
+			Just backend -> return $ Just (k, backend)
 			where
 				k = fileKey1 l
 				bname = keyBackendName k
@@ -221,7 +221,7 @@
 getKeyFilesPresent1' :: FilePath -> Annex [FilePath]
 getKeyFilesPresent1' dir = do
 	exists <- liftIO $ doesDirectoryExist dir
-	if (not exists)
+	if not exists
 		then return []
 		else do
 			dirs <- liftIO $ getDirectoryContents dir
@@ -233,3 +233,19 @@
 			case result of
 				Right s -> return $ isRegularFile s
 				Left _ -> return False
+
+logFile1 :: Git.Repo -> Key -> String
+logFile1 repo key = Upgrade.V2.gitStateDir repo ++ keyFile1 key ++ ".log"
+
+logFile2 :: Git.Repo -> Key -> String
+logFile2 = logFile' hashDirLower
+
+logFile' :: (Key -> FilePath) -> Git.Repo -> Key -> String
+logFile' hasher repo key =
+	gitStateDir repo ++ hasher key ++ keyFile key ++ ".log"
+
+stateDir :: FilePath
+stateDir = addTrailingPathSeparator $ ".git-annex"
+
+gitStateDir :: Git.Repo -> FilePath
+gitStateDir repo = addTrailingPathSeparator $ Git.workTree repo </> stateDir
diff --git a/Upgrade/V2.hs b/Upgrade/V2.hs
--- a/Upgrade/V2.hs
+++ b/Upgrade/V2.hs
@@ -10,7 +10,7 @@
 import System.Directory
 import System.FilePath
 import Control.Monad.State (unless, when, liftIO)
-import List
+import Data.List
 import Data.Maybe
 
 import Types.Key
@@ -45,23 +45,27 @@
  -}
 upgrade :: Annex Bool
 upgrade = do
-	showNote "v2 to v3"
+	showAction "v2 to v3"
 	g <- Annex.gitRepo
 	let bare = Git.repoIsLocalBare g
 
 	Branch.create
+	showProgress
+
 	e <- liftIO $ doesDirectoryExist (olddir g)
 	when e $ do
 		mapM_ (\(k, f) -> inject f $ logFile k) =<< locationLogs g
 		mapM_ (\f -> inject f f) =<< logFiles (olddir g)
 
 	saveState
+	showProgress
 
 	when e $ liftIO $ do
 		Git.run g "rm" [Param "-r", Param "-f", Param "-q", File (olddir g)]
 		unless bare $ gitAttributesUnWrite g
+	showProgress
 
-	unless bare $ push
+	unless bare push
 
 	return True
 
@@ -70,11 +74,11 @@
 	levela <- dirContents dir
 	levelb <- mapM tryDirContents levela
 	files <- mapM tryDirContents (concat levelb)
-	return $ catMaybes $ map islogfile (concat files)
+	return $ mapMaybe islogfile (concat files)
 	where
 		tryDirContents d = catch (dirContents d) (return . const [])
 		dir = gitStateDir repo
-		islogfile f = maybe Nothing (\k -> Just $ (k, f)) $
+		islogfile f = maybe Nothing (\k -> Just (k, f)) $
 				logFileKey $ takeFileName f
 
 inject :: FilePath -> FilePath -> Annex ()
@@ -83,6 +87,7 @@
 	new <- liftIO (readFile $ olddir g </> source)
 	prev <- Branch.get dest
 	Branch.change dest $ unlines $ nub $ lines prev ++ lines new
+	showProgress
 
 logFiles :: FilePath -> Annex [FilePath]
 logFiles dir = return . filter (".log" `isSuffixOf`)
@@ -105,8 +110,8 @@
 			-- "git push" will from then on
 			-- automatically push it
 			Branch.update -- just in case
-			showNote "pushing new git-annex branch to origin"
-			showProgress
+			showAction "pushing new git-annex branch to origin"
+			showOutput
 			g <- Annex.gitRepo
 			liftIO $ Git.run g "push" [Param "origin", Param Branch.name]
 		_ -> do
@@ -116,7 +121,7 @@
 			showLongNote $
 				"git-annex branch created\n" ++
 				"Be sure to push this branch when pushing to remotes.\n"
-			showProgress
+			showOutput
 
 {- Old .gitattributes contents, not needed anymore. -}
 attrLines :: [String]
@@ -131,10 +136,10 @@
 	whenM (doesFileExist attributes) $ do
 		c <- readFileStrict attributes
 		liftIO $ viaTmp writeFile attributes $ unlines $
-			filter (\l -> not $ l `elem` attrLines) $ lines c
+			filter (`notElem` attrLines) $ lines c
 		Git.run repo "add" [File attributes]
 
 stateDir :: FilePath
-stateDir = addTrailingPathSeparator $ ".git-annex"
+stateDir = addTrailingPathSeparator ".git-annex"
 gitStateDir :: Git.Repo -> FilePath
 gitStateDir repo = addTrailingPathSeparator $ Git.workTree repo </> stateDir
diff --git a/Utility.hs b/Utility.hs
--- a/Utility.hs
+++ b/Utility.hs
@@ -23,6 +23,7 @@
 	unsetFileMode,
 	readMaybe,
 	viaTmp,
+	withTempFile,
 	dirContains,
 	dirContents,
 	myHomeDir,
@@ -38,6 +39,7 @@
 	prop_relPathDirToFile_basics
 ) where
 
+import IO (bracket)
 import System.IO
 import System.Exit
 import qualified System.Posix.Process
@@ -141,9 +143,9 @@
 
 {- For quickcheck. -}
 prop_idempotent_shellEscape :: String -> Bool
-prop_idempotent_shellEscape s = [s] == (shellUnEscape $ shellEscape s)
+prop_idempotent_shellEscape s = [s] == (shellUnEscape . shellEscape) s
 prop_idempotent_shellEscape_multiword :: [String] -> Bool
-prop_idempotent_shellEscape_multiword s = s == (shellUnEscape $ unwords $ map shellEscape s)
+prop_idempotent_shellEscape_multiword s = s == (shellUnEscape . unwords . map shellEscape) s
 
 {- A version of hgetContents that is not lazy. Ensures file is 
  - all read before it gets closed. -}
@@ -253,6 +255,18 @@
 	a tmpfile content
 	renameFile tmpfile file
 
+{- Runs an action with a temp file, then removes the file. -}
+withTempFile :: String -> (FilePath -> Handle -> IO a) -> IO a
+withTempFile template action = bracket create remove use
+	where
+		create = do
+			tmpdir <- catch getTemporaryDirectory (const $ return ".")
+			openTempFile tmpdir template
+		remove (name, handle) = do
+			hClose handle
+			catchBool (removeFile name >> return True)
+		use (name, handle) = action name handle
+
 {- Lists the contents of a directory.
  - Unlike getDirectoryContents, paths are not relative to the directory. -}
 dirContents :: FilePath -> IO [FilePath]
@@ -288,6 +302,6 @@
 (>>!) :: Monad m => m Bool -> m () -> m ()
 (>>!) = unlessM
 
--- low fixity allows eg, foo bar <|> error $ "failed " ++ meep
+-- low fixity allows eg, foo bar >>! error $ "failed " ++ meep
 infixr 0 >>?
 infixr 0 >>!
diff --git a/Utility/CopyFile.hs b/Utility/CopyFile.hs
--- a/Utility/CopyFile.hs
+++ b/Utility/CopyFile.hs
@@ -20,10 +20,8 @@
 		removeFile dest
 	boolSystem "cp" [params, File src, File dest]
 	where
-		params = if SysConfig.cp_reflink_auto
-			then Params "--reflink=auto"
-			else if SysConfig.cp_a
-				then Params "-a"
-				else if SysConfig.cp_p
-					then Params "-p"
-					else Params ""
+		params
+			| SysConfig.cp_reflink_auto = Params "--reflink=auto"
+			| SysConfig.cp_a = Params "-a"
+			| SysConfig.cp_p = Params "-p"
+			| otherwise = Params ""
diff --git a/Utility/DataUnits.hs b/Utility/DataUnits.hs
--- a/Utility/DataUnits.hs
+++ b/Utility/DataUnits.hs
@@ -106,7 +106,7 @@
 {- approximate display of a particular number of bytes -}
 roughSize :: [Unit] -> Bool -> ByteSize -> String
 roughSize units abbrev i
-	| i < 0 = "-" ++ findUnit units' (negate i)
+	| i < 0 = '-' : findUnit units' (negate i)
 	| otherwise = findUnit units' i
 	where
 		units' = reverse $ sort units -- largest first
@@ -139,10 +139,10 @@
 readSize units input
 	| null parsednum = Nothing
 	| null parsedunit = Nothing
-	| otherwise = Just $ round $ number * (fromIntegral multiplier)
+	| otherwise = Just $ round $ number * fromIntegral multiplier
 	where
 		(number, rest) = head parsednum
-		multiplier = head $ parsedunit
+		multiplier = head parsedunit
 		unitname = takeWhile isAlpha $ dropWhile isSpace rest
 
 		parsednum = reads input :: [(Double, String)]
diff --git a/Utility/Dot.hs b/Utility/Dot.hs
--- a/Utility/Dot.hs
+++ b/Utility/Dot.hs
@@ -20,13 +20,13 @@
 
 {- an edge between two nodes -}
 graphEdge :: String -> String -> Maybe String -> String
-graphEdge fromid toid desc = indent $ maybe edge (\d -> label d edge) desc
+graphEdge fromid toid desc = indent $ maybe edge (`label` edge) desc
 	where
 		edge = quote fromid ++ " -> " ++ quote toid
 
 {- adds a label to a node or edge -}
 label :: String -> String -> String
-label l s = attr "label" l s
+label = attr "label"
 
 {- adds an attribute to a node or edge
  - (can be called multiple times for multiple attributes) -}
@@ -35,7 +35,7 @@
 
 {- fills a node with a color -}
 fillColor :: String -> String -> String
-fillColor color s = attr "fillcolor" color $ attr "style" "filled" $ s
+fillColor color s = attr "fillcolor" color $ attr "style" "filled" s
 
 {- apply to graphNode to put the node in a labeled box -}
 subGraph :: String -> String -> String -> String -> String
@@ -52,10 +52,10 @@
 		setlabel = "label=" ++ quote l
 		setfilled = "style=" ++ quote "filled"
 		setcolor = "fillcolor=" ++ quote color
-		ii x = (indent $ indent x) ++ "\n"
+		ii x = indent (indent x) ++ "\n"
 
 indent ::String -> String
-indent s = "\t" ++ s
+indent s = '\t' : s
 
 quote :: String -> String
 quote s = "\"" ++ s' ++ "\""
diff --git a/Utility/RsyncFile.hs b/Utility/RsyncFile.hs
--- a/Utility/RsyncFile.hs
+++ b/Utility/RsyncFile.hs
@@ -19,7 +19,7 @@
 		{- rsync requires some weird, non-shell like quoting in
                  - here. A doubled single quote inside the single quoted
                  - string is a single quote. -}
-		escape s = "'" ++  (join "''" $ split "'" s) ++ "'"
+		escape s = "'" ++  join "''" (split "'" s) ++ "'"
 
 {- Runs rsync in server mode to send a file, and exits. -}
 rsyncServerSend :: FilePath -> IO ()
diff --git a/Version.hs b/Version.hs
--- a/Version.hs
+++ b/Version.hs
@@ -7,8 +7,6 @@
 
 module Version where
 
-import Control.Monad (unless)
-
 import Types
 import qualified Annex
 import qualified Git
@@ -39,15 +37,11 @@
 setVersion :: Annex ()
 setVersion = setConfig versionField defaultVersion
 
-checkVersion :: Annex ()
-checkVersion = getVersion >>= handle
+checkVersion :: Version -> Annex ()
+checkVersion v
+	| v `elem` supportedVersions = return ()
+	| v `elem` upgradableVersions = err "Upgrade this repository: git-annex upgrade"
+	| otherwise = err "Upgrade git-annex."
 	where
-		handle Nothing = error "First run: git-annex init"
-		handle (Just v) = do
-			unless (v `elem` supportedVersions) $ do
-			error $ "Repository version " ++ v ++ 
-				" is not supported. " ++
-				msg v
-		msg v
-			| v `elem` upgradableVersions = "Upgrade this repository: git-annex upgrade"
-			| otherwise = "Upgrade git-annex."
+		err msg = error $ "Repository version " ++ v ++
+			" is not supported. " ++ msg
diff --git a/configure.hs b/configure.hs
--- a/configure.hs
+++ b/configure.hs
@@ -7,7 +7,7 @@
 
 tests :: [TestCase]
 tests =
-	[ TestCase "version" $ getVersion
+	[ TestCase "version" getVersion
 	, testCp "cp_a" "-a"
 	, testCp "cp_p" "-p"
 	, testCp "cp_reflink_auto" "--reflink=auto"
@@ -77,8 +77,7 @@
 	writeFile testFile "test file contents"
 
 cleanup :: IO ()
-cleanup = do
-	removeDirectoryRecursive tmpDir
+cleanup = removeDirectoryRecursive tmpDir
 
 main :: IO ()
 main = do
diff --git a/debian/changelog b/debian/changelog
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,34 @@
+git-annex (3.20110819) unstable; urgency=low
+
+  * Now "git annex init" only has to be run once, when a git repository
+    is first being created. Clones will automatically notice that git-annex
+    is in use and automatically perform a basic initalization. It's
+    still recommended to run "git annex init" in any clones, to describe them.
+  * Added annex-cost-command configuration, which can be used to vary the
+    cost of a remote based on the output of a shell command.
+  * Fix broken upgrade from V1 repository. Closes: #638584
+
+ -- Joey Hess <joeyh@debian.org>  Fri, 19 Aug 2011 20:34:09 -0400
+
+git-annex (3.20110817) unstable; urgency=low
+
+  * Fix shell escaping in rsync special remote.
+  * addurl: --fast can be used to avoid immediately downloading the url.
+  * Added support for getting content from git remotes using http (and https).
+  * Added curl to Debian package dependencies.
+
+ -- Joey Hess <joeyh@debian.org>  Wed, 17 Aug 2011 01:29:02 -0400
+
+git-annex (3.20110719) unstable; urgency=low
+
+  * add: Be even more robust to avoid ever leaving the file seemingly deleted.
+    Closes: #634233
+  * Bugfix: Make add ../ work.
+  * Support the standard git -c name=value
+  * unannex: Clean up use of git commit -a.
+
+ -- Joey Hess <joeyh@debian.org>  Tue, 19 Jul 2011 23:39:53 -0400
+
 git-annex (3.20110707) unstable; urgency=low
 
   * Fix sign bug in disk free space checking.
diff --git a/debian/control b/debian/control
--- a/debian/control
+++ b/debian/control
@@ -13,6 +13,7 @@
 	libghc-utf8-string-dev,
 	libghc-hs3-dev (>= 0.5.6),
 	libghc-testpack-dev [any-i386 any-amd64],
+	libghc-monad-control-dev,
 	ikiwiki,
 	perlmagick,
 	git | git-core,
@@ -30,6 +31,7 @@
 	git | git-core,
 	uuid,
 	rsync,
+	curl,
 	openssh-client
 Suggests: graphviz, bup, gnupg
 Description: manage files with git, without checking their contents into git
diff --git a/doc/bugs/--git-dir_and_--work-tree_options.mdwn b/doc/bugs/--git-dir_and_--work-tree_options.mdwn
new file mode 100644
--- /dev/null
+++ b/doc/bugs/--git-dir_and_--work-tree_options.mdwn
@@ -0,0 +1,29 @@
+git-annex does not take into account the --git-dir and --work-tree command line options (while they can be useful when scripting).
+
+    > mkdir /tmp/test
+    > cd /tmp/test
+    > git init
+    Initialized empty Git repository in /tmp/test/.git/
+    > git annex init test
+    init test ok
+    > touch foo
+    > cd
+    > git --git-dir=/tmp/test/.git --work-tree=/tmp/test annex add foo
+    git-annex: Not in a git repository.
+
+regular git add works:
+
+    > git --git-dir=/tmp/test/.git --work-tree=/tmp/test add foo
+    > git --git-dir=/tmp/test/.git --work-tree=/tmp/test status 
+    # On branch master
+    #
+    # Initial commit
+    #
+    # Changes to be committed:
+    #   (use "git rm --cached <file>..." to unstage)
+    #
+    #       new file:   foo
+    #
+
+git-annex version: 3.20110702
+
diff --git a/doc/bugs/Cabal_dependency_monadIO_missing.mdwn b/doc/bugs/Cabal_dependency_monadIO_missing.mdwn
new file mode 100644
--- /dev/null
+++ b/doc/bugs/Cabal_dependency_monadIO_missing.mdwn
@@ -0,0 +1,14 @@
+Just issuing the command `cabal install` results in the following error message.
+
+    Command/Add.hs:54:3:
+        No instance for (Control.Monad.IO.Control.MonadControlIO
+                           (Control.Monad.State.Lazy.StateT Annex.AnnexState IO))
+          arising from a use of `handle' at Command/Add.hs:54:3-24
+
+Adding the dependency for `monadIO` to `git-annex.cabal` should fix this?  
+-- Thomas
+
+> No, it's already satisfied by `monad-control` being listed as a
+> dependency in the cabal file. Your system might be old/new/or broken,
+> perhaps it's time to provide some details about the version of haskell
+> and of `monad-control` you have installed? --[[Joey]] 
diff --git a/doc/bugs/Cabal_dependency_monadIO_missing/comment_1_14be660aa57fadec0d81b32a8b52c66f._comment b/doc/bugs/Cabal_dependency_monadIO_missing/comment_1_14be660aa57fadec0d81b32a8b52c66f._comment
new file mode 100644
--- /dev/null
+++ b/doc/bugs/Cabal_dependency_monadIO_missing/comment_1_14be660aa57fadec0d81b32a8b52c66f._comment
@@ -0,0 +1,75 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawmFgsNxmnGznb5bbmcoWhoQOoxZZ-io61s"
+ nickname="Thomas"
+ subject="comment 1"
+ date="2011-08-08T09:04:20Z"
+ content="""
+I use Debian Squeeze, I have the Debian package cabal-install 0.8.0-1 installed.
+
+    $ git clone git://git-annex.branchable.com/
+    $ cd git-annex.branchable.com
+    $ cabal update
+    $ cabal install cabal-install
+
+This installed: Cabal-1.10.2.0, zlib-0.5.3.1, cabal-install 0.10.2.
+No version of monad-control or monadIO installed.
+
+    $ ~/.cabal/bin/cabal install
+    Registering QuickCheck-2.4.1.1...
+    Registering Crypto-4.2.3...
+    Registering base-unicode-symbols-0.2.2.1...
+    Registering deepseq-1.1.0.2...
+    Registering hxt-charproperties-9.1.0...
+    Registering hxt-regex-xmlschema-9.0.0...
+    Registering hxt-unicode-9.0.1...
+    Registering hxt-9.1.2...
+    Registering stm-2.2.0.1...
+    Registering hS3-0.5.6...
+    Registering transformers-0.2.2.0...
+    Registering monad-control-0.2.0.1...
+    [1 of 1] Compiling Main             ( Setup.hs, dist/setup/Main.o )
+    Linking ./dist/setup/setup ...
+    ghc -O2 -Wall -ignore-package monads-fd -fspec-constr-count=5 --make configure
+    [1 of 2] Compiling TestConfig       ( TestConfig.hs, TestConfig.o )
+    [2 of 2] Compiling Main             ( configure.hs, configure.o )
+    Linking configure ...
+    ./configure
+      checking version... 3.20110720
+      checking cp -a... yes
+      checking cp -p... yes
+      checking cp --reflink=auto... yes
+      checking uuid generator... uuid
+      checking xargs -0... yes
+      checking rsync... yes
+      checking curl... yes
+      checking bup... yes
+      checking gpg... yes
+      checking sha1... sha1sum
+      checking sha256... sha256sum
+      checking sha512... sha512sum
+      checking sha224... sha224sum
+      checking sha384... sha384sum
+
+    ...
+
+    Command/Add.hs:54:3:
+        No instance for (Control.Monad.IO.Control.MonadControlIO
+                           (Control.Monad.State.Lazy.StateT Annex.AnnexState IO))
+          arising from a use of `handle' at Command/Add.hs:54:3-24
+        Possible fix:
+          add an instance declaration for
+          (Control.Monad.IO.Control.MonadControlIO
+             (Control.Monad.State.Lazy.StateT Annex.AnnexState IO))
+        In the first argument of `($)', namely `handle (undo file key)'
+        In a stmt of a 'do' expression:
+              handle (undo file key) $ moveAnnex key file
+        In the expression:
+            do { handle (undo file key) $ moveAnnex key file;
+                 next $ cleanup file key }
+    cabal: Error: some packages failed to install:
+    git-annex-3.20110719 failed during the building phase. The exception was:
+    ExitFailure 1
+
+After I added a depencency for monadIO to the git-annex.cabal file, it installed correctly.  
+-- Thomas
+"""]]
diff --git a/doc/bugs/Cabal_dependency_monadIO_missing/comment_2_4f4d8e1e00a2a4f7e8a8ab082e16adac._comment b/doc/bugs/Cabal_dependency_monadIO_missing/comment_2_4f4d8e1e00a2a4f7e8a8ab082e16adac._comment
new file mode 100644
--- /dev/null
+++ b/doc/bugs/Cabal_dependency_monadIO_missing/comment_2_4f4d8e1e00a2a4f7e8a8ab082e16adac._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="http://joey.kitenet.net/"
+ nickname="joey"
+ subject="comment 2"
+ date="2011-08-17T04:56:30Z"
+ content="""
+Finally got a chance to try to reproduce this. I followed your recipe exactly in a clean squeeze chroot. monadIO was not installed, but git-annex built ok, using monad-control.
+"""]]
diff --git a/doc/bugs/Prevent_accidental_merges.mdwn b/doc/bugs/Prevent_accidental_merges.mdwn
new file mode 100644
--- /dev/null
+++ b/doc/bugs/Prevent_accidental_merges.mdwn
@@ -0,0 +1,14 @@
+With the storage layout v3, pulling the git-annex branch into the master branch is... less than ideal.
+
+The fact that the two branches contain totally different data make an accidental merge worse, arguably.
+
+Adding a tiny binary file called .gitnomerge to both branches would solve that without any noticeable overhead.
+
+Yes, there is an argument to be made that this is too much hand-holding, but I still think it's worth it.
+
+-- Richard
+
+> It should be as easy to undo such an accidential merge
+> as it is to undo any other git commit, right? I quite like that git-annex 
+> no longer adds any clutter to the master branch, and would be reluctant
+> to change that. --[[Joey]]
diff --git a/doc/bugs/WORM:_Handle_long_filenames_correctly.mdwn b/doc/bugs/WORM:_Handle_long_filenames_correctly.mdwn
--- a/doc/bugs/WORM:_Handle_long_filenames_correctly.mdwn
+++ b/doc/bugs/WORM:_Handle_long_filenames_correctly.mdwn
@@ -1,1 +1,4 @@
 I have files with very long filenames on an xfs at home. On my laptop the annex should have been checked out on an encfs, but there filenames can't be as long as on the xfs. So perhaps it would be good to limit the keysize to a sane substring of the filename e.g. use only the first 120 characters.
+
+> Since there seems no strong argument for a WORM100, and better options
+> exist, closing. [[done]] --[[Joey]] 
diff --git a/doc/bugs/__39__annex_add__39___fails_to___39__git_add__39___for_parent_relative_path.mdwn b/doc/bugs/__39__annex_add__39___fails_to___39__git_add__39___for_parent_relative_path.mdwn
new file mode 100644
--- /dev/null
+++ b/doc/bugs/__39__annex_add__39___fails_to___39__git_add__39___for_parent_relative_path.mdwn
@@ -0,0 +1,15 @@
+The following commands show the failure:
+
+$ mkdir d && touch d/f
+
+$ mkdir g && cd g && git annex add ../d/f 
+
+add ... ok
+
+error: Invalid path '.git/annex/objects/Jx/...
+
+...
+
+Then it seems it is enough to 'git add ../d/f' to complete the operation.
+
+> Thanks for reporting, [[fixed|done]] --[[Joey]] 
diff --git a/doc/bugs/git_annex_fsck_is_a_no-op_in_bare_repos.mdwn b/doc/bugs/git_annex_fsck_is_a_no-op_in_bare_repos.mdwn
--- a/doc/bugs/git_annex_fsck_is_a_no-op_in_bare_repos.mdwn
+++ b/doc/bugs/git_annex_fsck_is_a_no-op_in_bare_repos.mdwn
@@ -13,3 +13,7 @@
 
 >> Even if there is nothing it can _do_, knowing that the data is intact,
 >> or not, is valuable in and as of itself. -- RichiH
+
+>>> While storing the data is no longer an issue in bare repos, fsck would
+>>> need a special mode that examines all the location logs, since it
+>>> cannot run thru the checked out files. --[[Joey]] 
diff --git a/doc/bugs/git_command_line_constructed_by_unannex_command_has_tons_of_redundant_-a_paramters.mdwn b/doc/bugs/git_command_line_constructed_by_unannex_command_has_tons_of_redundant_-a_paramters.mdwn
new file mode 100644
--- /dev/null
+++ b/doc/bugs/git_command_line_constructed_by_unannex_command_has_tons_of_redundant_-a_paramters.mdwn
@@ -0,0 +1,15 @@
+This doesn't look right:
+
+    simons   11148  0.0  0.0  15572  1268 pts/1    SN+  04:00   0:00              |               \_ git annex unannex stuff
+    simons   11150  0.5  0.0 130504 11212 pts/1    SN+  04:00   3:40              |               |   \_ git-annex unannex stuff
+    simons   11152  0.0  0.1  39536 23932 pts/1    SN+  04:00   0:00              |               |       \_ git --git-dir=/home/simons/annex/.git --work-tree=/home/simons/annex ls-files --cached -z -- stuff
+    simons   11288  0.0  0.0      0     0 pts/1    ZN+  04:01   0:00              |               |       \_ [git] <defunct>
+    simons   11339  0.0  0.0      0     0 pts/1    ZN+  04:02   0:00              |               |       \_ [git-annex] <defunct>
+    simons   11442  0.0  0.0      0     0 pts/1    ZN+  04:06   0:00              |               |       \_ [git] <defunct>
+    simons   11443  0.0  0.0      0     0 pts/1    ZN+  04:06   0:05              |               |       \_ [git] <defunct>
+    simons   16541  0.0  0.0      0     0 pts/1    ZN+  04:14   0:00              |               |       \_ [git] <defunct>
+    simons   16543  0.3  0.0  15644  1744 pts/1    SN+  04:14   2:13              |               |       \_ git --git-dir=/home/simons/annex/.git --work-tree=/home/simons/annex cat-file --batch
+    simons   14224  0.0  0.0 100744   796 pts/1    SN+  14:10   0:00              |               |       \_ xargs -0 git --git-dir=/home/simons/annex/.git --work-tree=/home/simons/annex commit -a -m content removed from git annex
+    simons   14225  0.4  0.1  32684 18652 pts/1    DN+  14:10   0:00              |               |           \_ git --git-dir=/home/simons/annex/.git --work-tree=/home/simons/annex commit -a -m content removed from git annex -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a -a
+
+> [[Fixed|done]] --[[Joey]] 
diff --git a/doc/bugs/making_annex-merge_try_a_fast-forward.mdwn b/doc/bugs/making_annex-merge_try_a_fast-forward.mdwn
--- a/doc/bugs/making_annex-merge_try_a_fast-forward.mdwn
+++ b/doc/bugs/making_annex-merge_try_a_fast-forward.mdwn
@@ -1,3 +1,29 @@
 While merging the git-annex branch, annex-merge does not end up in a fast-forward even when it would be possible.
 But as sometimes annex-merge takes time, it would probably be worth it
 (but maybe I miss something with my workflow...).
+
+> I don't think a fast-forward will make things much faster.
+> 
+> git-annex needs its index file to be updated to reflect the merge.
+> With the union merge it does now, this can be accomplished by using
+> `git-diff-index` to efficiently get a list of files that have changed,
+> and only merge those changes into the index with `git-update-index`.
+> Then the index gets committed, generating the merge.
+> 
+> To fast-forward, it would just reset the git-annex branch to the new
+> head of the remote it's merging to. But then the index needs to be
+> updated to reflect this new head too. To do that needs the same method
+> described above, essentially (with the difference that it can replace
+> files in the index with the version from the git-annex branch, rather
+> than merging in the changes... but only if the index is known to be
+> already committed and have no other changes, which would require both
+> an attempt to commit it first, and
+> locking). 
+> 
+> So will take basically the same amount of time, except
+> it would not need to commit the index at the end of the merge. The
+> most expensive work is the `git-diff-index` and `git-update-index`,
+> which are not avoided.
+> 
+> Although, perhaps fast-forward merge would use slightly
+> less space. --[[Joey]]
diff --git a/doc/bugs/support_bare_git_repo__44___with_the_annex_directory_exposed_to_http.mdwn b/doc/bugs/support_bare_git_repo__44___with_the_annex_directory_exposed_to_http.mdwn
new file mode 100644
--- /dev/null
+++ b/doc/bugs/support_bare_git_repo__44___with_the_annex_directory_exposed_to_http.mdwn
@@ -0,0 +1,20 @@
+Let's say that http://people.collabora.com/~alsuren/git/fate-suite.git/ is a bare git repo. It has been 'git update-server-info'd so that it can be served on a dumb http server.
+
+The repo is also a git annex remote, created using the following commands:
+
+* git remote add alsuren git+ssh://people.collabora.co.uk/user/alsuren/public_html/fate-suite.git
+* git push alsuren --all
+* git annex copy --to=alsuren
+
+so http://people.collabora.com/~alsuren/git/fate-suite.git/annex is a valid git annex (though listing dirs is forbidden, so you need to know the filenames ahead of time).
+
+I would like to be able to use the following commands to get a clone of the repo:
+
+* git clone http://people.collabora.com/~alsuren/git/fate-suite.git/
+* cd fate-suite
+* git annex get
+
+This would allow contributors to quickly get a copy of our upstream repo and start contributing with minimal bandwidth/effort.
+
+> This is now supported.. I look forward to seeing your project using it!
+> --[[Joey]] [[!tag done]]
diff --git a/doc/bugs/unannex_command_doesn__39__t_all_files.mdwn b/doc/bugs/unannex_command_doesn__39__t_all_files.mdwn
new file mode 100644
--- /dev/null
+++ b/doc/bugs/unannex_command_doesn__39__t_all_files.mdwn
@@ -0,0 +1,26 @@
+    $ git init ; git annex init test ; dd if=/dev/urandom of=file1 count=128 ; cp file1 file2 ; git annex add --backend=SHA1 file? ; git commit -m init ; git annex unannex ; ls -l
+    Initialized empty Git repository in /tmp/annex/.git/
+    init test ok
+    128+0 records in
+    128+0 records out
+    65536 bytes (66 kB) copied, 0.007173 s, 9.1 MB/s
+    add file1 (checksum...) ok
+    add file2 (checksum...) ok
+    (Recording state in git...)
+    [master (root-commit) 2177b10] init
+     2 files changed, 2 insertions(+), 0 deletions(-)
+     create mode 120000 file1
+     create mode 120000 file2
+    unannex file1 ok
+    (Recording state in git...)
+    [master bef78b1] content removed from git annex
+     1 files changed, 0 insertions(+), 1 deletions(-)
+     delete mode 120000 file1
+    total 72
+    -rw-r--r-- 1 simons users 65536 Jul 15 17:29 file1
+    lrwxrwxrwx 1 simons users   132 Jul 15 17:29 file2 -> .git/annex/objects/jp/Fk/SHA1-s65536--795b58cc4e5190b02e7026fd9e94a10c98c6475f/SHA1-s65536--795b58cc4e5190b02e7026fd9e94a10c98c6475f
+
+> This was recently discussed in
+> [[annex_unannex__47__uninit_should_handle_copies]] and `unannex --fast`
+> added to leave contents behind in the annex, which allows handling
+> copies. But needs manual cleanup later with dropunused. --[[Joey]] 
diff --git a/doc/bugs/wishlist:_more_descriptive_commit_messages_in_git-annex_branch.mdwn b/doc/bugs/wishlist:_more_descriptive_commit_messages_in_git-annex_branch.mdwn
new file mode 100644
--- /dev/null
+++ b/doc/bugs/wishlist:_more_descriptive_commit_messages_in_git-annex_branch.mdwn
@@ -0,0 +1,36 @@
+as of git-annex version 3.20110719, all git-annex commits only contain the word "update" as a commit message. given that the contents of the commit are pretty non-descriptive (SHA1 hashes for file names, uuids for repository names), i suggest to have more descriptive commit messages, as shown here:
+
+    /mnt/usb_disk/photos/2011$ git annex get
+    /mnt/usb_disk/photos/2011$ git show git-annex
+    [...]
+    usb-disk-photos: get 2011
+    
+    * 10 files retrieved from 2 sources (9 from local-harddisk, 1 from my-server)
+    * 120 files were already present
+    * 2 files could not be retrieved
+    /mnt/usb_disk/photos/2011$ cd ~/photos/2011/07
+    ~/photos/2011/07$ git copy --to my-server
+    ~/photos/2011/07$ git show git-annex
+    [...]
+    local-harddisk: copy 2011/07 to my-server
+    
+    * 20 files pushed
+    ~/photos/2011/07$
+
+in my opinion, the messages should at least contain
+
+* what command was used
+* in which repository they were executed
+* which files or directories they affected (not necessarily all files, but what was given on command line or implicitly from the working directory)
+
+--[[chrysn]]
+
+> The implementation of the git-annex branch precludes more descriptive
+> commit messages, since a single commit can include changes that were
+> previously staged to the branch's index file, or spooled to its journal
+> by other git-annex commands (either concurrently running or
+> interrupted commands, or even changes needed to automatically merge
+> other git-annex branches).
+> 
+> It would be possible to make it *less* verbose, with an empty commit
+> message. :) --[[Joey]] 
diff --git a/doc/cheatsheet.mdwn b/doc/cheatsheet.mdwn
--- a/doc/cheatsheet.mdwn
+++ b/doc/cheatsheet.mdwn
@@ -1,4 +1,4 @@
-A suppliment to the [[walkthrough]].
+A supplement to the [[walkthrough]].
 
 [[!toc]]
 
diff --git a/doc/forum/Can_I_store_normal_files_in_the_git-annex_git_repository__63__.mdwn b/doc/forum/Can_I_store_normal_files_in_the_git-annex_git_repository__63__.mdwn
new file mode 100644
--- /dev/null
+++ b/doc/forum/Can_I_store_normal_files_in_the_git-annex_git_repository__63__.mdwn
@@ -0,0 +1,6 @@
+Is it possible to story ordinary files in the git repository, or is this going to confuse git-annex? In other words, can I safely run
+
+    git add .gitattributes
+    git commit -m 'remember attributes' .gitattributes
+
+..., or do I have to use `git-annex add` all time?
diff --git a/doc/forum/example_of_massively_disconnected_operation.mdwn b/doc/forum/example_of_massively_disconnected_operation.mdwn
new file mode 100644
--- /dev/null
+++ b/doc/forum/example_of_massively_disconnected_operation.mdwn
@@ -0,0 +1,33 @@
+I found this archival drive that had been offline since October 26th 2010. Since I released git-annex 0.02 on October 27th, this must have been made using the very first release of git-annex, ever.
+
+So, I synced it back up! :) --[[Joey]]
+
+<pre>
+commit 4151f4595fe6205d4aed653617ab23eb3335130a
+Author: Joey Hess <joey@kitenet.net>
+Date:   Tue Oct 26 02:18:03 2010 -0400
+
+joey> git pull
+remote: Counting objects: 428782, done.
+remote: Compressing objects: 100% (280714/280714), done.
+remote: Total 416692 (delta 150923), reused 389593 (delta 125143)
+Receiving objects: 100% (416692/416692), 44.71 MiB | 495 KiB/s, done.
+Resolving deltas: 100% (150923/150923), completed with 818 local objects.
+ * [new branch]      git-annex  -> origin/git-annex
+   1893f9c..9ebcc0e  master     -> origin/master
+Updating 1893f9c..9ebcc0e
+Checking out files: 100% (76884/76884), done.
+joey> git annex version
+git-annex version: 3.20110611
+local repository version: unknown
+default repository version: 3
+supported repository versions: 3
+upgrade supported from repository versions: 0 1 2
+joey> git config annex.version 0
+joey> git annex upgrade
+upgrade . (v0 to v1...) (v1 to v2) (moving content...) (updating symlinks...)  (moving location logs...) (v2 to v3) (merging origin/git-annex into git-annex...)
+
+  git-annex branch created
+  Be sure to push this branch when pushing to remotes.
+ok
+</pre>
diff --git a/doc/forum/version_3_upgrade.mdwn b/doc/forum/version_3_upgrade.mdwn
new file mode 100644
--- /dev/null
+++ b/doc/forum/version_3_upgrade.mdwn
@@ -0,0 +1,9 @@
+after upgrading to git-annex 3, i'm stuck with diverging git-annex branches -- i didn't manage to follow this line in the directions:
+
+> After this upgrade, you should make sure you include the git-annex branch when git pushing and pulling.
+
+could you explain how to do that in a littel more detail? git pull seems to only merge master, although i have these ``.git/config`` settings:
+
+    [branch "git-annex"]
+    	remote = origin
+    	merge = git-annex
diff --git a/doc/forum/version_3_upgrade/comment_1_05fc9c9cad26c520bebb98c852c71e35._comment b/doc/forum/version_3_upgrade/comment_1_05fc9c9cad26c520bebb98c852c71e35._comment
new file mode 100644
--- /dev/null
+++ b/doc/forum/version_3_upgrade/comment_1_05fc9c9cad26c520bebb98c852c71e35._comment
@@ -0,0 +1,13 @@
+[[!comment format=mdwn
+ username="http://joey.kitenet.net/"
+ nickname="joey"
+ subject="comment 1"
+ date="2011-08-17T01:33:08Z"
+ content="""
+It's ok that `git pull` does not merge the git-annex branch. You can merge it with `git annex merge`, or it will be done
+automatically when you use other git-annex commands.
+
+If you use `git pull` and `git push` without any options, the defaults will make git pull and push the git-annex branch automatically.
+
+But if you're in the habit of doing `git push origin master`, that won't cause the git-annex branch to be pushed (use `git push origin git-annex` to manually push it then). Similarly, `git pull origin master` won't pull it. And also, the `remote.origin.fetch` setting in `.git/config` can be modified in ways that make `git pull` not automatically pull the git-annex branch. So those are the things to avoid after upgrade to v3, basically.
+"""]]
diff --git a/doc/git-annex.mdwn b/doc/git-annex.mdwn
--- a/doc/git-annex.mdwn
+++ b/doc/git-annex.mdwn
@@ -121,9 +121,15 @@
 
 * init description
 
-  Initializes git-annex with a description of the git repository,
-  and sets up `.gitattributes` and the pre-commit hook.
+  Initializes git-annex with a description of the git repository.
 
+  Until a repository (or one of its remotes) has been initialized,
+  git-annex will refuse to operate on it, to avoid accidentially
+  using it in a repository that was not intended to have an annex.
+
+  It's useful, but not mandatory, to initialize each new clone
+  of a repository with its own description.
+
 * describe repository description
 
   Changes the description of a repository.
@@ -282,6 +288,8 @@
 
   Downloads each url to a file, which is added to the annex.
 
+  To avoid immediately downloading the url, specify --fast
+
 * fromkey file
 
   This plumbing-level command can be used to manually set up a file
@@ -387,6 +395,10 @@
 
   Specifies a key to operate on.
 
+* -c name=value
+
+  Used to override git configuration settings. May be specified multiple times.
+
 # CONFIGURATION
 
 Like other git commands, git-annex is configured via `.git/config`.
@@ -411,6 +423,12 @@
   transfer annexed files from or to, ones with lower costs are preferred.
   The default cost is 100 for local repositories, and 200 for remote
   repositories.
+
+* `remote.<name>.annex-cost-command`
+
+  If set, the command is run, and the number it outputs is used as the cost.
+  This allows varying the cost based on eg, the current network. The
+  cost-command can be any shell command line.
 
 * `remote.<name>.annex-ignore`
 
diff --git a/doc/index.mdwn b/doc/index.mdwn
--- a/doc/index.mdwn
+++ b/doc/index.mdwn
@@ -12,7 +12,7 @@
 * [[forum]]
 * [[comments]]
 * [[contact]]
-* <a href="http://flattr.com/thing/84843/git-annex"><img src="http://api.flattr.com/button/button-compact-static-100x17.png" alt="Flattr this" title="Flattr this" /></a>
+* <a href="http://flattr.com/thing/84843/git-annex"><img src="https://api.flattr.com/button/flattr-badge-large.png" alt="Flattr this" title="Flattr this" /></a>
 
 [[News]]:
 
diff --git a/doc/install.mdwn b/doc/install.mdwn
--- a/doc/install.mdwn
+++ b/doc/install.mdwn
@@ -23,6 +23,7 @@
   * [utf8-string](http://hackage.haskell.org/package/utf8-string)
   * [SHA](http://hackage.haskell.org/package/SHA)
   * [dataenc](http://hackage.haskell.org/package/dataenc)
+  * [monad-control](http://hackage.haskell.org/package/monad-control)
   * [TestPack](http://hackage.haskell.org/cgi-bin/hackage-scripts/package/testpack)
   * [QuickCheck 2](http://hackage.haskell.org/package/QuickCheck)
   * [HTTP](http://hackage.haskell.org/package/HTTP)
diff --git a/doc/install/Debian/comment_1_029486088d098c2d4f1099f2f0e701a9._comment b/doc/install/Debian/comment_1_029486088d098c2d4f1099f2f0e701a9._comment
new file mode 100644
--- /dev/null
+++ b/doc/install/Debian/comment_1_029486088d098c2d4f1099f2f0e701a9._comment
@@ -0,0 +1,9 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawla7u6eLKNYZ09Z7xwBffqLaXquMQC07fU"
+ nickname="Matthias"
+ subject="squeeze-backports update?"
+ date="2011-08-17T12:34:46Z"
+ content="""
+Is there going to be an update of git-annex in debian squeeze-backports to a version that supports repository version 3?
+Thx
+"""]]
diff --git a/doc/install/Debian/comment_2_648e3467e260cdf233acdb0b53313ce0._comment b/doc/install/Debian/comment_2_648e3467e260cdf233acdb0b53313ce0._comment
new file mode 100644
--- /dev/null
+++ b/doc/install/Debian/comment_2_648e3467e260cdf233acdb0b53313ce0._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="http://joey.kitenet.net/"
+ nickname="joey"
+ subject="Re: squeeze-backports update?"
+ date="2011-08-17T15:34:29Z"
+ content="""
+Yes, I uploaded it last night.
+"""]]
diff --git a/doc/install/Fedora.mdwn b/doc/install/Fedora.mdwn
--- a/doc/install/Fedora.mdwn
+++ b/doc/install/Fedora.mdwn
@@ -9,6 +9,7 @@
 sudo cabal install quickcheck
 sudo cabal install SHA
 sudo cabal install dataenc
+sudo cabal install monad-control
 sudo cabal install HTTP
 sudo cabal install hS3
 
diff --git a/doc/install/OSX.mdwn b/doc/install/OSX.mdwn
--- a/doc/install/OSX.mdwn
+++ b/doc/install/OSX.mdwn
@@ -1,5 +1,9 @@
+Install Haskel Platform from [[http://hackage.haskell.org/platform/mac.html]]. The version provided by Macports is too old to work with current versions of git-annex. Then execute
+
 <pre>
-sudo port install haskell-platform git-core ossp-uuid md5sha1sum coreutils pcre
+sudo port install git-core ossp-uuid md5sha1sum coreutils pcre
+
+sudo ln -s /opt/local/include/pcre.h  /usr/include/pcre.h # This is hack that allows pcre-light to find pcre
 sudo cabal update
 sudo cabal install missingh
 sudo cabal install utf8-string
@@ -7,6 +11,7 @@
 sudo cabal install quickcheck  
 sudo cabal install SHA
 sudo cabal install dataenc
+sudo cabal install monad-control
 sudo cabal install HTTP
 sudo cabal install hS3 # optional
 
@@ -20,7 +25,7 @@
 sudo make install
 </pre>
 
-Originally posted by Jon at <https://gist.github.com/671785> --[[Joey]]
+Originally posted by Jon at <https://gist.github.com/671785> --[[Joey]], modified by [[kristianrumberg]]
 
 See also:
 
diff --git a/doc/internals.mdwn b/doc/internals.mdwn
--- a/doc/internals.mdwn
+++ b/doc/internals.mdwn
@@ -22,7 +22,7 @@
 This branch is managed by git-annex, with the contents listed below.
 
 The file `.git/annex/index` is a separate git index file it uses
-to accumlate changes for the git-annex. Also, `.git/annex/journal/` is used
+to accumulate changes for the git-annex. Also, `.git/annex/journal/` is used
 to record changes before they are added to git.
 
 Note that for speed reasons, git-annex assumes only it will modify this
diff --git a/doc/news/version_0.20110610.mdwn b/doc/news/version_0.20110610.mdwn
deleted file mode 100644
--- a/doc/news/version_0.20110610.mdwn
+++ /dev/null
@@ -1,6 +0,0 @@
-git-annex 0.20110610 released with [[!toggle text="these changes"]]
-[[!toggleable text="""
-   * Add --numcopies option.
-   * Add --trust, --untrust, and --semitrust options.
-   * get --from is the same as copy --from
-   * Bugfix: Fix fsck to not think all SHAnE keys are bad."""]]
diff --git a/doc/news/version_3.20110624.mdwn b/doc/news/version_3.20110624.mdwn
deleted file mode 100644
--- a/doc/news/version_3.20110624.mdwn
+++ /dev/null
@@ -1,33 +0,0 @@
-News for git-annex 3.20110624:
-
-There has been another change to the git-annex data store.
-Use `git annex upgrade` to migrate your repositories to the new
-layout. See [[upgrades]].
-
-The significant change this time is that the .git-annex/ directory
-is gone; instead there is a git-annex branch that is automatically
-maintained by git-annex, and encapsulates all its state nicely out
-of your way.
-
-You should make sure you include the git-annex branch when
-git pushing and pulling.
-
-git-annex 3.20110624 released with [[!toggle text="these changes"]]
-[[!toggleable text="""
-   * New repository format, annex.version=3. Use `git annex upgrade` to migrate.
-   * git-annex now stores its logs in a git-annex branch.
-   * merge: New subcommand. Auto-merges the new git-annex branch.
-   * Improved handling of bare git repos with annexes. Many more commands will
-     work in them.
-   * git-annex is now more robust; it will never leave state files
-     uncommitted when some other git process comes along and locks the index
-     at an inconvenient time.
-   * rsync is now used when copying files from repos on other filesystems.
-     cp is still used when copying file from repos on the same filesystem,
-     since --reflink=auto can make it significantly faster on filesystems
-     such as btrfs.
-   * Allow --trust etc to specify a repository by name, for temporarily
-     trusting repositories that are not configured remotes.
-   * unlock: Made atomic.
-   * git-union-merge: New git subcommand, that does a generic union merge
-     operation, and operates efficiently without touching the working tree."""]]
diff --git a/doc/news/version_3.20110702.mdwn b/doc/news/version_3.20110702.mdwn
deleted file mode 100644
--- a/doc/news/version_3.20110702.mdwn
+++ /dev/null
@@ -1,22 +0,0 @@
-News for git-annex 3.20110702:
-
-The URL backend has been removed. Instead the new web remote can be used.
-
-git-annex 3.20110702 released with [[!toggle text="these changes"]]
-[[!toggleable text="""
-   * Now the web can be used as a special remote.
-     This feature replaces the old URL backend.
-   * addurl: New command to download an url and store it in the annex.
-   * Sped back up fsck, copy --from, and other commands that often
-     have to read a lot of information from the git-annex branch. Such
-     commands are now faster than they were before introduction of the
-     git-annex branch.
-   * Always ensure git-annex branch exists.
-   * Modify location log parser to allow future expansion.
-   * --force will cause add, etc, to operate on ignored files.
-   * Avoid mangling encoding when storing the description of repository
-     and other content.
-   * cabal can now be used to build git-annex. This is substantially
-     slower than using make, does not build or install documentation,
-     does not run the test suite, and is not particularly recommended,
-     but could be useful to some."""]]
diff --git a/doc/news/version_3.20110719.mdwn b/doc/news/version_3.20110719.mdwn
new file mode 100644
--- /dev/null
+++ b/doc/news/version_3.20110719.mdwn
@@ -0,0 +1,7 @@
+git-annex 3.20110719 released with [[!toggle text="these changes"]]
+[[!toggleable text="""
+   * add: Be even more robust to avoid ever leaving the file seemingly deleted.
+     Closes: #[634233](http://bugs.debian.org/634233)
+   * Bugfix: Make add ../ work.
+   * Support the standard git -c name=value
+   * unannex: Clean up use of git commit -a."""]]
diff --git a/doc/news/version_3.20110817.mdwn b/doc/news/version_3.20110817.mdwn
new file mode 100644
--- /dev/null
+++ b/doc/news/version_3.20110817.mdwn
@@ -0,0 +1,6 @@
+git-annex 3.20110817 released with [[!toggle text="these changes"]]
+[[!toggleable text="""
+   * Fix shell escaping in rsync special remote.
+   * addurl: --fast can be used to avoid immediately downloading the url.
+   * Added support for getting content from git remotes using http (and https).
+   * Added curl to Debian package dependencies."""]]
diff --git a/doc/news/version_3.20110819.mdwn b/doc/news/version_3.20110819.mdwn
new file mode 100644
--- /dev/null
+++ b/doc/news/version_3.20110819.mdwn
@@ -0,0 +1,9 @@
+git-annex 3.20110819 released with [[!toggle text="these changes"]]
+[[!toggleable text="""
+   * Now "git annex init" only has to be run once, when a git repository
+     is first being created. Clones will automatically notice that git-annex
+     is in use and automatically perform a basic initalization. It's
+     still recommended to run "git annex init" in any clones, to describe them.
+   * Added annex-cost-command configuration, which can be used to vary the
+     cost of a remote based on the output of a shell command.
+   * Fix broken upgrade from V1 repository. Closes: #[638584](http://bugs.debian.org/638584)"""]]
diff --git a/doc/special_remotes.mdwn b/doc/special_remotes.mdwn
--- a/doc/special_remotes.mdwn
+++ b/doc/special_remotes.mdwn
@@ -1,6 +1,7 @@
 Most [[backends]] can transfer data to and from configured git remotes.
-Normally those remotes are normal git repositories (bare and non-bare),
-that store the file contents in their own git annex directory.
+Normally those remotes are normal git repositories (bare and non-bare;
+local and remote), that store the file contents in their own git annex
+directory.
 
 But, git-annex also extends git's concept of remotes, with these special
 types of remotes. These can be used just like any normal remote by git-annex.
diff --git a/doc/special_remotes/web.mdwn b/doc/special_remotes/web.mdwn
--- a/doc/special_remotes/web.mdwn
+++ b/doc/special_remotes/web.mdwn
@@ -1,7 +1,11 @@
 git-annex can use the WWW as a special remote, downloading urls to files.
-See [[walkthrough/using_web_web]] for usage examples.
+See [[walkthrough/using_the_web]] for usage examples.
 
 ## notes
 
 Currently git-annex only supports downloading content from the web; 
 it cannot upload to it or remove content.
+
+This special remote uses arbitrary urls on the web as the source for content.
+git-annex can also download content from a normal git remote, accessible by
+http.
diff --git a/doc/transferring_data.mdwn b/doc/transferring_data.mdwn
--- a/doc/transferring_data.mdwn
+++ b/doc/transferring_data.mdwn
@@ -1,8 +1,12 @@
 git-annex can transfer data to or from any of a repository's git remotes.
 Depending on where the remote is, the data transfer is done using rsync
-(over ssh, with automatic resume), or plain cp (with copy-on-write
-optimisations on supported filesystems). Some [[special_remotes]]
-are also supported that are not traditional git remotes.
+(over ssh or locally), or plain cp (with copy-on-write
+optimisations on supported filesystems), or using curl (for repositories
+on the web). Some [[special_remotes]] are also supported that are not
+traditional git remotes.
+
+If a data transfer is interrupted, git-annex retains the partial transfer
+to allow it to be automatically resumed later.
 
 It's equally easy to transfer a single file to or from a repository,
 or to launch a retrievel of a massive pile of files from whatever
diff --git a/doc/upgrades.mdwn b/doc/upgrades.mdwn
--- a/doc/upgrades.mdwn
+++ b/doc/upgrades.mdwn
@@ -88,5 +88,6 @@
 Handled more or less transparently, although git-annex was just 2 weeks
 old at the time, and had few users other than Joey.
 
-This upgrade is believed to still be supported, but has not been tested
-lately.
+Before doing this upgrade, set annex.version:
+
+	git config annex.version 0
diff --git a/git-annex-shell.hs b/git-annex-shell.hs
--- a/git-annex-shell.hs
+++ b/git-annex-shell.hs
@@ -58,10 +58,10 @@
 builtin :: String -> String -> [String] -> IO ()
 builtin cmd dir params =
 	Git.repoAbsPath dir >>= Git.repoFromAbsPath >>=
-		dispatch (cmd:(filterparams params)) cmds commonOptions header
+		dispatch (cmd : filterparams params) cmds commonOptions header
 
 external :: [String] -> IO ()
-external params = do
+external params =
 	unlessM (boolSystem "git-shell" $ map Param $ "-c":filterparams params) $
 		error "git-shell failed"
 
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: 3.20110707
+Version: 3.20110819
 Cabal-Version: >= 1.6
 License: GPL
 Maintainer: Joey Hess <joey@kitenet.net>
@@ -7,7 +7,7 @@
 Stability: Stable
 Copyright: 2010-2011 Joey Hess
 License-File: GPL
-Extra-Source-Files: ./debian/NEWS ./debian/control ./debian/rules ./debian/manpages ./debian/changelog ./debian/doc-base ./debian/copyright ./debian/compat ./AnnexQueue.hs ./configure.hs ./Annex.hs ./PresenceLog.hs ./Version.hs ./Crypto.hs ./RemoteLog.hs ./README ./Command/Merge.hs ./Command/AddUrl.hs ./Command/Whereis.hs ./Command/Unlock.hs ./Command/Version.hs ./Command/FromKey.hs ./Command/PreCommit.hs ./Command/Map.hs ./Command/Unused.hs ./Command/Uninit.hs ./Command/Migrate.hs ./Command/Init.hs ./Command/ConfigList.hs ./Command/Trust.hs ./Command/Lock.hs ./Command/SendKey.hs ./Command/RecvKey.hs ./Command/Add.hs ./Command/Fix.hs ./Command/Untrust.hs ./Command/InitRemote.hs ./Command/Semitrust.hs ./Command/Fsck.hs ./Command/Move.hs ./Command/DropUnused.hs ./Command/Get.hs ./Command/Upgrade.hs ./Command/Describe.hs ./Command/Drop.hs ./Command/DropKey.hs ./Command/InAnnex.hs ./Command/Find.hs ./Command/Unannex.hs ./Command/Status.hs ./Command/Copy.hs ./Command/SetKey.hs ./Types.hs 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./Backend/SHA.hs ./Options.hs ./git-annex-shell.hs ./test.hs ./INSTALL ./Remote/Web.hs ./Remote/S3stub.hs ./Remote/Helper/Encryptable.hs ./Remote/Helper/Url.hs ./Remote/Helper/Ssh.hs ./Remote/Helper/Special.hs ./Remote/Directory.hs ./Remote/S3real.hs ./Remote/Bup.hs ./Remote/Hook.hs ./Remote/Rsync.hs ./Remote/Git.hs ./Utility.hs ./Upgrade.hs ./git-union-merge.hs ./Utility/DataUnits.hs ./Utility/RsyncFile.hs ./Utility/CopyFile.hs ./Utility/Dot.hs ./Utility/Base64.hs ./Types/Crypto.hs ./Types/UUID.hs ./Types/TrustLevel.hs ./Types/Remote.hs ./Types/BranchState.hs ./Types/Backend.hs ./Types/Key.hs ./Config.hs ./Command.hs ./.gitignore ./Backend.hs ./Touch.hsc ./Content.hs ./.gitattributes ./Git.hs ./GitAnnex.hs
 Homepage: http://git-annex.branchable.com/
 Build-type: Custom
 Category: Utility
@@ -31,7 +31,7 @@
   Build-Depends: haskell98, MissingH, hslogger, directory, filepath,
    unix, containers, utf8-string, network, mtl, bytestring, old-locale, time,
    pcre-light, extensible-exceptions, dataenc, SHA, process, hS3, HTTP,
-   base < 5
+   base < 5, monad-control
 
 Executable git-annex-shell
   Main-Is: git-annex-shell.hs
diff --git a/git-union-merge.hs b/git-union-merge.hs
--- a/git-union-merge.hs
+++ b/git-union-merge.hs
@@ -20,11 +20,10 @@
 usage = error $ "bad parameters\n\n" ++ header
 
 tmpIndex :: Git.Repo -> FilePath
-tmpIndex g = Git.workTree g </> Git.gitDir g </> "index.git-union-merge"
+tmpIndex g = Git.gitDir g </> "index.git-union-merge"
 
 setup :: Git.Repo -> IO ()
-setup g = do
-	cleanup g -- idempotency
+setup g = cleanup g -- idempotency
 
 cleanup :: Git.Repo -> IO ()
 cleanup g = do
@@ -34,7 +33,7 @@
 parseArgs :: IO [String]
 parseArgs = do
 	args <- getArgs
-	if (length args /= 3)
+	if length args /= 3
 		then usage
 		else return args
 
diff --git a/test.hs b/test.hs
--- a/test.hs
+++ b/test.hs
@@ -19,7 +19,7 @@
 import System.Posix.Env
 import qualified Control.Exception.Extensible as E
 import Control.Exception (throw)
-import Maybe
+import Data.Maybe
 import qualified Data.Map as M
 import System.Path (recurseDir)
 import System.IO.HVFS (SystemFS(..))
@@ -48,7 +48,7 @@
 	arbitrary = do
 		n <- arbitrary
 		b <- elements ['A'..'Z']
-		return $ Types.Key.Key {
+		return Types.Key.Key {
 			Types.Key.keyName = n,
 			Types.Key.keyBackendName = [b],
 			Types.Key.keySize = Nothing,
@@ -108,7 +108,7 @@
 		reponame = "test repo"
 
 test_add :: Test
-test_add = "git-annex add" ~: TestList [basic, sha1dup]
+test_add = "git-annex add" ~: TestList [basic, sha1dup, subdirs]
 	where
 		-- this test case runs in the main repo, to set up a basic
 		-- annexed file that later tests will use
@@ -129,6 +129,14 @@
 			git_annex "add" ["-q", sha1annexedfiledup, "--backend=SHA1"] @? "add of second file with same SHA1 failed"
 			annexed_present sha1annexedfiledup
 			annexed_present sha1annexedfile
+		subdirs = TestCase $ intmpclonerepo $ do
+			createDirectory "dir"
+			writeFile "dir/foo" $ content annexedfile
+			git_annex "add" ["-q", "dir"] @? "add of subdir failed"
+			createDirectory "dir2"
+			writeFile "dir2/foo" $ content annexedfile
+			changeWorkingDirectory "dir"
+			git_annex "add" ["-q", "../dir2"] @? "add of ../subdir failed"
 
 test_setkey :: Test
 test_setkey = "git-annex setkey/fromkey" ~: TestCase $ inmainrepo $ do
@@ -270,7 +278,7 @@
 	-- write different content, to verify that lock
 	-- throws it away
 	changecontent annexedfile
-	writeFile annexedfile $ (content annexedfile) ++ "foo"
+	writeFile annexedfile $ content annexedfile ++ "foo"
 	git_annex "lock" ["-q", annexedfile] @? "lock failed"
 	annexed_present annexedfile
 	git_annex "unlock" ["-q", annexedfile] @? "unlock failed"		
@@ -279,7 +287,7 @@
 	git_annex "add" ["-q", annexedfile] @? "add of modified file failed"
 	runchecks [checklink, checkunwritable] annexedfile
 	c <- readFile annexedfile
-	assertEqual ("content of modified file") c (changedcontent annexedfile)
+	assertEqual "content of modified file" c (changedcontent annexedfile)
 	r' <- git_annex "drop" ["-q", annexedfile]
 	not r' @? "drop wrongly succeeded with no known copy of modified file"
 
@@ -304,9 +312,9 @@
 					@? "git commit of edited file failed"
 		runchecks [checklink, checkunwritable] annexedfile
 		c <- readFile annexedfile
-		assertEqual ("content of modified file") c (changedcontent annexedfile)
+		assertEqual "content of modified file" c (changedcontent annexedfile)
 		r <- git_annex "drop" ["-q", annexedfile]
-		(not r) @? "drop wrongly succeeded with no known copy of modified file"
+		not r @? "drop wrongly succeeded with no known copy of modified file"
 
 test_fix :: Test
 test_fix = "git-annex fix" ~: intmpclonerepo $ do
@@ -323,7 +331,7 @@
 	git_annex "fix" ["-q", newfile] @? "fix of moved file failed"
 	runchecks [checklink, checkunwritable] newfile
 	c <- readFile newfile
-	assertEqual ("content of moved file") c (content annexedfile)
+	assertEqual "content of moved file" c (content annexedfile)
 	where
 		subdir = "s"
 		newfile = subdir ++ "/" ++ annexedfile